jimnoneill/paper-to-field-training huggingface dataset:
MzrA-EnvZ Interactions in the Periplasm Influence the EnvZ/OmpR Two-Component Regulon

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

ABSTRACT MzrA was identified as a modulator of the EnvZ/OmpR two-component signal transduction system. Previous evidence indicated that MzrA interacts with EnvZ and modulates its enzymatic activities to influence OmpR phosphate (OmpR∼P) levels. Moreover, MzrA was shown to connect the bacterial envelope stress response systems CpxA/CpxR and σ E to EnvZ/OmpR to widen the defensive response regulatory network. In this study, experiments were carried out to establish whether the membrane or periplasmic domain of MzrA is critical for MzrA-EnvZ interactions and to reveal MzrA residues that play an important role in these interactions. Data obtained from chimeric constructs, in which the transmembrane domain of MzrA was replaced with the unrelated transmembrane domain of NarX or signal sequence of PhoA, showed that the transmembrane domain residues of MzrA do not play a critical role in MzrA-EnvZ interactions. The importance of the periplasmic domain of MzrA in MzrA-EnvZ interactions was revealed by characterizing bifunctional, fully soluble, and periplasmically localized MalE::MzrA chimeras. This was further corroborated through the isolation of loss-of-function, single-amino-acid substitutions in the conserved periplasmic domain of MzrA that interfered with MzrA-EnvZ binding in a bacterial two-hybrid system. Together, the data suggest that the binding of MzrA to EnvZ influences the ability of EnvZ to receive and/or respond to environmental signals in the periplasm and modulate its biochemical output to OmpR.
TET3 regulates hematopoietic stem cell homeostasis during embryonic and adult hematopoiesis

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

ABSTRACT The ten‐eleven translocation family of enzymes (TET1/2/3) promotes DNA demethylation and is essential for hematopoiesis. While the roles of TET1 and TET2 are well‐studied in hematopoiesis, the requirement of TET3 in embryonic and adult hematopoiesis is less investigated. In this study, by characterizing embryonic and adult hematopoiesis in Tie2 +/cre ; Tet3 f/f mice, we have established a requirement for TET3 in regulating hematopoietic stem cells (HSCs; CD150 + CD48 – ). We found that loss of TET3 in the fetal liver and adult bone marrow causes a reduction in the percent of long‐term HSCs (LT‐HSCs; CD150 + CD48 – CD34 – ). This was accompanied by reduced colony forming capacity of TET3‐deficient HSCs in vitro and reduced contribution of HSCs after a competitive bone marrow transplantation in vivo. TET3 deficiency increased DNA methylation at several cell cycle regulator genes leading to their down regulation. This is consistent with, and likely underpins, the reduced number of quiescent HSCs in TET3‐deficient bone marrow. These findings uncover a new role for TET3 in HSC homeostasis during embryonic and adult hematopoiesis.
Measurements of rheumatoid arthritis disease activity and damage using magnetic resonance imaging. Truth and discrimination: does MRI make the grade?

Field: Medicine (Health Sciences)

Magnetic resonance imaging (MRI) is a tool with unprecedented capabilities. Rheumatoid arthritis (RA) abnormalities that can be measured with MRI include erosions, articular cartilage thickness, synovial membrane volume, and pannus. However, as access to MRI increases, there is a risk that its use will not be evaluated using rigorous scientific measurement principles. We reviewed published MRI measurement methods for RA and investigated whether the methods were systematically evaluated for reliability, validity, and responsiveness to change--components of the OMERACT filter. Medline and Embase databases were searched from 1966 to 1999. Titles and abstracts were scanned to identify publications on MRI methods used to assess either disease activity or damage in RA. A data extraction template was developed and 68 peer reviewed publications from 40 research groups were appraised; 40 addressed RA disease activity, 4 RA damage, and 24 both activity and damage. Joints most frequently assessed were knee (32 publications) and wrist (31 publications). Ninety-one percent of publications evaluated either reliability or validity or responsiveness to change. Thirteen percent evaluated all 3 and only 9% evaluated none of these measurement properties. Validity was evaluated in 85%, responsiveness to change in 37%, and reliability in 35% of publications. Only 12% of publications evaluated both intra and inter-reliability. Few publications of MRI measures of disease activity or damage in RA met the OMERACT filter for all measurement properties. It would be regrettable if MRI measures are developed ad hoc, with little regard to considerations of scaling, reliability, validity, and responsiveness to change, because this will severely limit their ability to confidently assess treatment efficacy and prognostic indicators.
Light-Regulated Transcription of Genes Encoding Peridinin Chlorophyll a Proteins and the Major Intrinsic Light-Harvesting Complex Proteins in the DinoflagellateAmphidinium carterae Hulburt (Dinophycae)1

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

Abstract In the dinoflagellateAmphidinium carterae, photoadaptation involves changes in the transcription of genes encoding both of the major classes of light-harvesting proteins, the peridinin chlorophyll aproteins (PCPs) and the majora/c-containing intrinsic light-harvesting proteins (LHCs). PCP and LHC transcript levels were increased up to 86- and 6-fold higher, respectively, under low-light conditions relative to cells grown at high illumination. These increases in transcript abundance were accompanied by decreases in the extent of methylation of CpG and CpNpG motifs within or near PCP- and LHC-coding regions. Cytosine methylation levels in A. carterae are therefore nonstatic and may vary with environmental conditions in a manner suggestive of involvement in the regulation of gene expression. However, chemically induced undermethylation was insufficient in activating transcription, because treatment with two methylation inhibitors had no effect on PCP mRNA or protein levels. Regulation of gene activity through changes in DNA methylation has traditionally been assumed to be restricted to higher eukaryotes (deuterostomes and green plants); however, the atypically large genomes of dinoflagellates may have generated the requirement for systems of this type in a relatively “primitive” organism. Dinoflagellates may therefore provide a unique perspective on the evolution of eukaryotic DNA-methylation systems.
Comparison of error properties of techniques used for measuring second-order nonlinear optical coefficients with least-squares fitting

Field: Physics and Astronomy (Physical Sciences)

The technique of second-harmonic generation with an evanescent wave (SHEW) and the Maker fringe technique were examined by simulation of least-squares fitting. The calculations were made for correlation among parameters in a fit and error-propagation coefficients between parameters. Correlation among parameters for the SHEW technique is lower and the parameter value for the second-order nonlinear optical coefficient d is less sensitive to errors of refractive indices than for the Maker fringe technique. As a result, use of the SHEW technique can provide more-accurate values for the d coefficient than use of the Maker fringe technique.
Thermodynamic potential and drag force of the impurity-polariton many-body interaction

Field: Physics and Astronomy (Physical Sciences)

Abstract Investigating the many-body interaction among polaritons is a fundamental goal in comprehending nonlinear behaviors in microcavity semiconductor systems. Hence, the present study focuses on exploring the many-body interaction between excitons and impurities. It was observed that the energy eigenequation governing this system is of sixth-order, rendering it unsolvable. Consequently, a strategy involving the utilization of impurity weight was employed to partition the initial energy eigenequation into two fourth-order equations, a method deemed suitable for lower order approximations. Subsequently, Green’s function was applied to these two fourth-order equations. The analysis of the computed results, encompassing the energy spectrum, polariton density, and thermodynamic potential of the system, reveals that the many-body interaction between excitons and impurities induces the emergence of novel bound states of quasiparticles. Moreover, the inclusion of impurities leads to a decrease in both energy and density of polaritons. Furthermore, the investigation delves into the drag force exerted by impurities on excitons, demonstrating that the drag force escalates in a second-order fashion with impurity velocity and persists even as impurity velocity increases, surpassing the Landau’s equilibrium theory.
Electoral responses to economic crises

Field: Economics, Econometrics and Finance (Social Sciences)

Abstract How do voters respond to economic crises: Do they turn against the incumbent, reward a certain political camp, polarize to the extremes, or perhaps continue to vote much like before? Analyzing extensive data on electorates, parties, and individuals in 24 countries for over half a century, we document a systematic pattern whereby economic crises tend to disproportionately favor the right. Three main forces underlie this pattern. First, voters tend to decrease support for the party heading the government when the crisis erupts. Second, after crises, voters tend to assign greater importance to issues typically owned by the right. Third, when center‐right parties preside over a crisis, voters often drift further rightward to nationalist parties rather than defect to the left. The far‐right thus serves as an effective vehicle for keeping the center‐right in power even when facing postcrisis disaffection by its voters.
Hodge genera of algebraic varieties, II

Field: Mathematics (Physical Sciences)

We study the behavior of Hodge-theoretic genera under morphisms of complex algebraic varieties. We prove that the additive $χ_y$-genus which arises in the motivic context satisfies the so-called ``stratified multiplicative property", which shows how to compute the invariant of the source of a proper surjective morphism from its values on various varieties that arise from the singularities of the map. By considering morphisms to a curve, we obtain a Hodge-theoretic analogue of the Riemann-Hurwitz formula. We also study the contribution of monodromy to the $χ_y$-genus of a smooth projective family, and prove an Atiyah-Meyer type formula for twisted $χ_y$-genera. This formula measures the deviation from multiplicativity of the $χ_y$-genus, and expresses the correction terms as higher-genera associated to cohomology classes of the quotient of the total period domain by the action of the monodromy group. By making use of Saito's theory of mixed Hodge modules, we also obtain formulae of Atiyah-Meyer type for the corresponding Hirzebruch characteristic classes.
Stalinist Collectivization In Chechnya: Stages And Methods Of Implementation

Field: Social Sciences (Social Sciences)

The policy of collectivization in the history of Russia occupies a special place. Despite the fact that the "perestroika" leaders officially condemned violence against the peasantry, ongoing discussions indicate an increased interest in the problems of collectivization of agriculture and dispossession in the 1920–1930s. The results of a scientific analysis formed the basis for a conceptual rethinking of the history of collectivization. However, the results confirmed only the official assessment: collectivization is a forced measure, and dispossession is a crime. In Chechnya, the diversity of natural and climatic zones played a decisive role in the development of agriculture: transhumant cattle breeding prevailed in the mountainous areas, and agriculture – in the flat areas. Private land ownership was registered under the dominance of patriarchal-clan relations. The agrarian reform of the tsarist administration at the beginning of the 20th century aimed at developing capitalist relations caused the impoverishment of mountain peasants. The Land Decree determined the choice of the Chechen people in favor of the Bolsheviks during the years of revolutionary events and civil war (1918–1920). The liberal policy of the Bolsheviks towards the mountain peasantry and the entire Russian peasantry was replaced by a violent policy of creating collective farms, uniting individual peasant farms into collective ones. An analysis of the events associated with collectivization allowed for the following conclusions: creation of collective farms turned the peasantry into the poorest class, devoid of interest in the results of their labor; the passport system became the second enslavement of the peasantry.
Dual transcriptome based reconstruction of Salmonella-human integrated metabolic network to screen potential drug targets

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

Salmonella enterica serovar Typhimurium ( S . Typhimurium) is a highly adaptive pathogenic bacteria with a serious public health concern due to its increasing resistance to antibiotics. Therefore, identification of novel drug targets for S . Typhimurium is crucial. Here, we first created a pathogen-host integrated genome-scale metabolic network by combining the metabolic models of human and S . Typhimurium, which we further tailored to the pathogenic state by the integration of dual transcriptome data. The integrated metabolic model enabled simultaneous investigation of metabolic alterations in human cells and S . Typhimurium during infection. Then, we used the tailored pathogen-host integrated genome-scale metabolic network to predict essential genes in the pathogen, which are candidate novel drug targets to inhibit infection. Drug target prioritization procedure was applied to these targets, and pabB was chosen as a putative drug target. It has an essential role in 4-aminobenzoic acid (PABA) synthesis, which is an essential biomolecule for many pathogens. A structure based virtual screening was applied through docking simulations to predict candidate compounds that eliminate S . Typhimurium infection by inhibiting pabB. To our knowledge, this is the first comprehensive study for predicting drug targets and drug like molecules by using pathogen-host integrated genome-scale models, dual RNA-seq data and structure-based virtual screening protocols. This framework will be useful in proposing novel drug targets and drugs for antibiotic-resistant pathogens.
Selecting the Type of the Control Setting Composite Cement-Ash Binder

Field: Chemical Engineering (Physical Sciences)

One of the most important technological properties in the technology of concrete and concrete products is the viability of the concrete mix. This property depends on the setting time of the cement used. Therefore, when you create a new binding, it's necessary, in addition to improving the physical and mechanical properties of the hardened concrete binder and on its basis, to optimize the timing of its setting and hardening. It was established that the composite binder consisting of portland cement and fly ash ground Krasnoyarsk CHP (fly ash content of 40-80%) needs a few minutes to grasp and thicken. The study revealed that the most effective retarder composite binder is gypsum.
The uses and abuses of phonological assessment

Field: Health Professions (Health Sciences)

A number of ready-made phonological assessment procedures have become available to the clinical and educational professions over recent years. It is suggested that the scope of most procedures is unnecessarily narrow; there is no justification for the continuing omission of vowels and prosodic systems from such assessments. The impressionistic transcription on which assessments are based is subjective, imprecise and unreliable. The usefulness of the results, particularly with regard to the measurement of intelligibility and the differential diagnosis of disorders, is much exaggerated. Concern is expressed that clinicians' disillusionment over assessment procedures failing to live up to the claims made for them might lead to a reaction against clinical linguistic procedures in general.
Mechanical Properties and Microstructures of Severely Plastic Deformed Pure Titanium by Mechanical Milling and Spark Plasma Sintering

Field: Materials Science (Physical Sciences)

Severe plastic deformation (SPD) was applied to pure titanium powder by mechanical milling (MM) process with stearic acid, added as a process control agent (PCA), by using a vibrational ball mill, and MMed powders possessing large strains were subsequently consolidated into bulk materials by spark plasma sintering (SPS) in order to enhance the hardness and strength of pure titanium. Changes in the hardness and constituent phases of the MMed powders have been examined by microhardness measurements and X-ray diffraction. The hardness and microstructure of the SPS materials have also been studied by hardness measurements and optical microscopy. The Vickers microhardness of the pure titanium powders with PCA 0.25 g increased sharply from 189 HV to 513 HV after 8 h of the mechanical milling (MM) process. Formation of TiH2 as the solid-state reaction product occurred in the MMed powder during 4 and 8 h of the MM process. The near full density was obtained for the SPS materials under the condition of an applied pressure at 49 MPa with a sintering temperature at 1073 K for 0.5 h. The Vickers hardness of the SPS material fabricated from 8 h MMed powder with PCA 0.50 g exhibited a maximum value of 1253 HV.
A Sad and Angry Consolation: Violence, Mourning and Memory in the Late Poetry of Ted Hughes and Geoffrey Hill

Field: Arts and Humanities (Social Sciences)

This essay considers the changes that have taken place in the conceptualizing of a history of English poetry, as exemplified in two editions of The Oxford Book of English Verse. The first Edition, which appeared in 1900, was edited by Sir Arthur Quiller-Couch, founding father of Cambridge English, while the most recent version published in 1999 is edited by Christopher Ricks. The author contextualizes both anthologies, considering not only the ways in which they reflect contemporary tastes in poetry, but also the ways in which they represent different concepts of the discipline of English literature. Whereas the idea of literature in 1900 was that it served as a civilizing force abroad and as part of a mission for national renewal at home, the essay suggests that by the end of the century the role of literature was less clear. The decisions taken by both editors in terms of what to exclude or to include and which poets to select are considered in terms of reader expectations at each end of the century. Quiller-Couch’s revised edition of 1939 is also discussed, since it marks a half-way house between the exuberant confidence of the first edition and Ricks’ more cerebral anthology that strives for greater inclusivity as the parameters of what constitutes English poetry are seen to have broadened as the century has progressed.
Racial dignity framework: Advancing dignity-led thinking and practice in Australia

Field: Social Sciences (Social Sciences)

Abstract The 1948 Universal Declaration of Human Rights Charter recognizes that all human beings have ‘inherent dignity’; they are ‘born free and have equal and inalienable rights’ (Universal Declaration of Human Rights Charter, 1948). This article explores an important contradiction: the idea that all people possess equal, inherent dignity versus the reality that race, a social construct, creates categories that assign unequal worth to those who are racialized within colonial modernities. To grapple with this contradiction, this article introduces the concept of Racial Dignity, which demonstrates how race profoundly shapes who is afforded dignity as a given and who must struggle for it. The Racial Dignity Framework (RDF) functions as both a theoretical lens and a practical approach to analyse how racialized experiences of exclusion and (non)belonging impact a person’s sense of worth. Drawing from critical theories and, in particular, Jacobsen's conceptualization of bodily dignity, the RDF is operationalized through an examination of how dignity is fostered or undermined through micro-practices of i) humanization, ii) affirming everyday relational practices, iii) sociocultural experiences, and iv) self-determination.
PARAMETRIC SURFACES FOR AUGMENTED ARCHITECTURE REPRESENTATION

Field: Computer Science (Physical Sciences)

Abstract. Augmented Reality (AR) represents a growing communication channel, responding to the need to expand reality with additional information, offering easy and engaging access to digital data. AR for architectural representation allows a simple interaction with 3D models, facilitating spatial understanding of complex volumes and topological relationships between parts, overcoming some limitations related to Virtual Reality. In the last decade different developments in the pipeline process have seen a significant advancement in technological and algorithmic aspects, paying less attention to 3D modeling generation. For this, the article explores the construction of basic geometries for 3D model’s generation, highlighting the relationship between geometry and topology, basic for a consistent normal distribution. Moreover, a critical evaluation about corrective paths of existing 3D models is presented, analysing a complex architectural case study, the virtual model of Villa del Verginese, an emblematic example for topological emerged problems. The final aim of the paper is to refocus attention on 3D model construction, suggesting some "good practices" useful for preventing, minimizing or correcting topological problems, extending the accessibility of AR to people engaged in architectural representation.
Social representations and social conflict in the marketplace: The “war” against illicit alcohol in Kenya

Field: Social Sciences (Social Sciences)

Using social representation theory, this paper examines public communications around illicit alcohol in Kenya to demonstrate how the emergence of a misleading metaphor in such communications can lead to undesirable harmful consequences.This paper is based on an ethnography of the illicit alcohol market in Kenya through immersion in a longitudinal media analysis of news articles on illicit alcohol. Data was collected from three Kenyan newspapers namely, The Daily Nation, The Standard and The Star, for the period June-November 2016.The study findings demonstrate that the “war” metaphor has a direct bearing on the course and consequences of action taken by the different market players actors.The article contributes to the analysis of communication and social representation theory.
Financial performance and Outreach: A Global Analysis of Leading Microbanks

Field: Economics, Econometrics and Finance (Social Sciences)

Microfinance promises to reduce poverty by employing profit-making banking practices in low-income communities. Many microfinance institutions have secured high loan repayment rates but, so far, relatively few earn profits. We examine why this promise remains unmet. We explore patterns of profitability, loan repayment, and cost reduction with unusually high-quality data on 124 institutions in 49 countries. The evidence shows the possibility of earning profits while serving the poor, but a trade-off emerges between profitability and serving the poorest. Raising fees to very high levels does not ensure greater profitability and the benefits of cost-cutting diminish when serving better-off customers. Copyright 2007 The Author(s). Journal compilation Royal Economic Society 2007.