bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying the impact of rainfall variability on conflicts at the monthly level
Authors: Coulibaly Thierry Yerema , Managi Shunsuke 
Published: October 2022

AbstractResearch on the relationship between rainfall variability and conflicts has yielded contradictory results. This study is the first to show that the significance of the impact of rainfall variability on conflicts depends on the temporal unit of analysis. We prove this point by comparing the statistical significance of the linkages between georeferenced conflicts and rainfall variabilities at the monthly and annual levels with panel data analyses from 1989 to 2020. We find that a 10 percent increase in monthly rainfall decreases the risk of conflict incidence by 0.0298 percent, but annual rainfall variability is not statistically linked to conflict outbreaks. These statistically significant disparities result from the aggregation of data dispersion and the disregard for the timing of the impact of rainfall on conflicts. These findings highlight the importance of information on monthly rainfall variation when estimating the impact of rainfall on conflicts.
Comparisons of quantitative approaches for assessing microglial morphology reveal inconsistencies, ecological fallacy, and a need for standardization
Authors: Green Tabitha R. F. , Murphy Sean M. , Rowe Rachel K. 
Published: October 2022

AbstractMicroglial morphology is used to measure neuroinflammation and pathology. For reliable inference, it is critical that microglial morphology is accurately quantified and that results can be easily interpreted and compared across studies and laboratories. The process through which microglial morphology is quantified is a key methodological choice and little is known about how this choice may bias conclusions. We applied five of the most commonly used ImageJ-based methods for quantifying the microglial morphological response to a stimulus to identical photomicrographs and individual microglial cells isolated from these photomicrographs, which allowed for direct comparisons of results generated using these approaches. We found a lack of comparability across methods that analyzed full photomicrographs, with significant discrepancies in results among the five methods. Quantitative methods to analyze microglial morphology should be selected based on several criteria, and combinations of these methods may give the most biologically accurate representation of microglial morphology.
On the morphology of electrostatic solitary waves in the Earth’s aurora
Authors: Varghese Steffy Sara , Singh Kuldeep , Kourakis Ioannis 
Published: October 2022

AbstractElectrostatic solitary waves (ESWs) have been detected in abundance in Space plasma observations, both by satellites in near-Earth plasma environments as well as by planetary missions, e.g. Cassini in Saturn or MAVEN in Mars. In their usual form, these are manifested as a bipolar electric field corresponding to a bell-shaped pulse in the electrostatic potential. Recent studies have suggested the existence of alternative forms of ESWs, including flat-top solitary waves (FTSWs) and supersolitary waves (SSWs), both of which are often encountered in Space observations such as in polar cap boundary layer, the auroral acceleration region and elsewhere. This article focuses on the existence and characterization of different types of electrostatic solitary waves in multicomponent Space plasmas. Relying on a multi-fluid plasma model, comprising two types of ions and two different electron populations, we have identified the conditions for existence of flat-top solitary waves and supersolitons, in contrast to “standard" solitary waves. Both ion species are models as cold fluids, for simplicity. Our analysis reveals that the coexistence of the two electron populations is pivotal for the formation of such non-standard electrostatic structures, and that their characteristic parameters (temperature, density ratio) plays a decisive role in their generation and structural characteristics. Nonetheless, while supersolitary waves may exist in a wide range of parameter values (as confirmed by earlier theoretical studies), it appears that flat-top solitary waves will occur in a narrow window in the parameter region, which may explain their scarce (but non-negligible) frequency of observation. Our theoretical findings confirm and validate the existence of alternative (non-conventional) ESW waveforms in auroral plasma (in addition to the ubiquitous bipolar electric field form), where such an electron coexistence is typically observed.
Combinatorial gene targeting in primary human hematopoietic stem and progenitor cells
Authors: Bäckström Alexandra , Yudovich David , Žemaitis Kristijonas , Nilsén Falck Ludvig , Subramaniam Agatheeswaran , Larsson Jonas 
Published: October 2022

AbstractThe CRISPR/Cas9 system offers enormous versatility for functional genomics but many applications have proven to be challenging in primary human cells compared to cell lines or mouse cells. Here, to establish a paradigm for multiplexed gene editing in primary human cord blood-derived hematopoietic stem and progenitor cells (HSPCs), we used co-delivery of lentiviral sgRNA vectors expressing either Enhanced Green Fluorescent Protein (EGFP) or Kusabira Orange (KuO), together with Cas9 mRNA, to simultaneously edit two genetic loci. The fluorescent markers allow for tracking of either single- or double-edited cells, and we could achieve robust double knockout of the cell surface molecules CD45 and CD44 with an efficiency of ~ 70%. As a functional proof of concept, we demonstrate that this system can be used to model gene dependencies for cell survival, by simultaneously targeting the cohesin genes STAG1 and STAG2. Moreover, we show combinatorial effects with potential synergy for HSPC expansion by targeting the Aryl Hydrocarbon Receptor (AHR) in conjunction with members of the CoREST complex. Taken together, our traceable multiplexed CRISPR/Cas9 system enables studies of genetic dependencies and cooperation in primary HSPCs, and has important implications for modelling polygenic diseases, as well as investigation of the underlying mechanisms of gene interactions.
Live slow-frozen human tumor tissues viable for 2D, 3D, ex vivo cultures and single-cell RNAseq
Authors: Restivo Gaetana , Tastanova Aizhan , Balázs Zsolt , Panebianco Federica , Diepenbruck Maren , Ercan Caner , Preca Bodgan-T. , Hafner Jürg , Weber Walter P. , Kurzeder Christian , Vetter Marcus , Soysal Simone Münst , Beisel Christian , Bentires-Alj Mohamed , Piscuoglio Salvatore , Krauthammer Michael , Levesque Mitchell P. 
Published: October 2022

AbstractBiobanking of surplus human healthy and disease-derived tissues is essential for diagnostics and translational research. An enormous amount of formalin-fixed and paraffin-embedded (FFPE), Tissue-Tek OCT embedded or snap-frozen tissues are preserved in many biobanks worldwide and have been the basis of translational studies. However, their usage is limited to assays that do not require viable cells. The access to intact and viable human material is a prerequisite for translational validation of basic research, for novel therapeutic target discovery, and functional testing. Here we show that surplus tissues from multiple solid human cancers directly slow-frozen after resection can subsequently be used for different types of methods including the establishment of 2D, 3D, and ex vivo cultures as well as single-cell RNA sequencing with similar results when compared to freshly analyzed material.
Affinity microfluidics enables high-throughput protein degradation analysis in cell-free extracts
Authors: Brio Lev , Wasserman Danit , Michaely-Barbiro Efrat , Barazany-Gal Gal , Gerber Doron , Tzur Amit 
Published: October 2022

AbstractProtein degradation mediated by the ubiquitin-proteasome pathway regulates signaling events in many physiological and pathological conditions. In vitro degradation assays have been instrumental in the understanding of how cell proliferation and other fundamental cellular processes are regulated. These assays are direct, time-specific and highly informative but also laborious, typically relying on low-throughput polyacrylamide gel-electrophoresis followed by autoradiography or immunoblotting. We present protein degradation on chip (pDOC), a MITOMI-based integrated microfluidic technology for discovery and analysis of proteins degradation in cell-free extracts. The platform accommodates hundreds of microchambers on which protein degradation is assayed quickly, simultaneously and using minute amounts of reagents in one or many physiochemical environments. Essentially, pDOC provides a sensitive multiplex alternative to the conventional degradation assay, with relevance to biomedical and translational research associated with regulated proteolysis.
The Blob marine heatwave transforms California kelp forest ecosystems
Authors: Michaud Kristen M. , Reed Daniel C. , Miller Robert J. 
Published: October 2022

AbstractOcean warming has both direct physiological and indirect ecological consequences for marine organisms. Sessile animals may be particularly vulnerable to anomalous warming given constraints in food acquisition and reproduction imposed by sessility. In temperate reef ecosystems, sessile suspension feeding invertebrates provide food for an array of mobile species and act as a critical trophic link between the plankton and the benthos. Using 14 years of seasonal benthic community data across five coastal reefs, we evaluated how communities of sessile invertebrates in southern California kelp forests responded to the “Blob”, a period of anomalously high temperatures and low phytoplankton production. We show that this event had prolonged consequences for kelp forest ecosystems. Changes to community structure, including species invasions, have persisted six years post-Blob, suggesting that a climate-driven shift in California kelp forests is underway.
Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide
Authors: Schnee Philipp , Choudalakis Michel , Weirich Sara , Khella Mina S. , Carvalho Henrique , Pleiss Jürgen , Jeltsch Albert 
Published: October 2022

AbstractProtein lysine methyltransferases have important regulatory functions in cells, but mechanisms determining their activity and specificity are incompletely understood. Naturally, SETD2 introduces H3K36me3, but previously an artificial super-substrate (ssK36) was identified, which is methylated >100-fold faster. The ssK36-SETD2 complex structure cannot fully explain this effect. We applied molecular dynamics (MD) simulations and biochemical experiments to unravel the mechanistic basis of the increased methylation of ssK36, considering peptide conformations in solution, association of peptide and enzyme, and formation of transition-state (TS) like conformations of the enzyme-peptide complex. We observed in MD and FRET experiments that ssK36 adopts a hairpin conformation in solution with V35 and K36 placed in the loop. The hairpin conformation has easier access into the active site of SETD2 and it unfolds during the association process. Peptide methylation experiments revealed that introducing a stable hairpin conformation in the H3K36 peptide increased its methylation by SETD2. In MD simulations of enzyme-peptide complexes, the ssK36 peptide approached TS-like structures more frequently than H3K36 and distinct, substrate-specific TS-like structures were observed. Hairpin association, hairpin unfolding during association, and substrate-specific catalytically competent conformations may also be relevant for other PKMTs and hairpins could represent a promising starting point for SETD2 inhibitor development.
Characterizing COVID-19 waves in urban and rural districts of India
Authors: Pandey Bhartendu , Gu Jianyu , Ramaswami Anu 
Published: October 2022

AbstractUnderstanding spatial determinants, i.e., social, infrastructural, and environmental features of a place, which shape infectious disease is critically important for public health. We present an exploration of the spatial determinants of reported COVID-19 incidence across India’s 641 urban and rural districts, comparing two waves (2020–2021). Three key results emerge using three COVID-19 incidence metrics: cumulative incidence proportion (aggregate risk), cumulative temporal incidence rate, and severity ratio. First, in the same district, characteristics of COVID-19 incidences are similar across waves, with the second wave over four times more severe than the first. Second, after controlling for state-level effects, urbanization (urban population share), living standards, and population age emerge as positive determinants of both risk and rates across waves. Third, keeping all else constant, lower shares of workers working from home correlate with greater infection risk during the second wave. While much attention has focused on intra-urban disease spread, our findings suggest that understanding spatial determinants across human settlements is also important for managing current and future pandemics.
cfr and fexA genes in methicillin-resistant Staphylococcus aureus from humans and livestock in the Netherlands
Authors: Schouls Leo M. , Veldman Kees , Brouwer Michael S. M. , Dierikx Cindy , Witteveen Sandra , van Santen-Verheuvel Marga , Hendrickx Antoni P. A. , Landman Fabian , Hengeveld Paul , Wullings Bart , Rapallini Michel , Wit Ben , van Duijkeren Engeline ,   the Dutch MRSA surveillance study group, Maijer-Reuwer A. , Leversteijn-van Hall M. A. , van den Bijllaardt W. , van Mansfeld R. , van Dijk K. , Zwart B. , Diederen B. M. W. , Dorigo-Zetsma J. W. , Notermans D. W. , Ott Certe A. , Ang W. , da Silva J. , Vlek A. L. M. , Buiting A. G. M. , Bode L. , Paltansing S. , van Griethuysen A. J. , den Reijer M. , van Trijp M. J. C. A. , Wong M. , Muller A. E. , van der Linden M. P. M. , van Rijn M. , Debast S. B. , Waar K. , Kolwijck E. , Alnaiemi N. , Schulin T. , Dinant S. , van Mens S. P. , Melles D. C. , Stuart J. W. T. Cohen , Gruteke P. , Overdevest I. T. M. A. , van Dam A. , Maat I. , Maraha B. , Sinnige J. C. , Mattsson E. E. , van Meer M. , Stam A. , de Jong E. , Vainio S. J. , Heikens E. , Steingrover R. , Troelstra A. , Bathoorn E. , Trienekens T. A. M. , van Dam D. W. , de Brauwer E. I. G. B. , Berkhout H. 
Published: October 2022

Abstract
Background
Although the Netherlands is a country with a low endemic level of methicillin-resistant Staphylococcus aureus (MRSA), a national MRSA surveillance has been in place since 1989. In 2003 livestock emerged as a major reservoir of MRSA and currently livestock-associated MRSA (clonal complex CC398) make up 25% of all surveillance isolates. To assess possible transfer of resistant strains or resistance genes, MRSA obtained from humans and animals were characterized in detail.

Methods
The sequenced genomes of 6327 MRSA surveillance isolates from humans and from 332 CC398 isolates from livestock-related samples were analyzed and resistance genes were identified. Several isolates were subjected to long-read sequencing to reconstruct chromosomes and plasmids.

Results
Here we show the presence of the multi-resistance gene cfr in seven CC398 isolates obtained from humans and in one CC398 isolate from a pig-farm dust sample. Cfr induces resistance against five antibiotic classes, which is true for all but two isolates. The isolates are genetically unrelated, and in seven of the isolates cfr are located on distinct plasmids. The fexA gene is found in 3.9% surveillance isolates and in 7.5% of the samples from livestock. There is considerable sequence variation of fexA and geographic origin of the fexA alleles.

Conclusions
The rare cfr and fexA resistance genes are found in MRSA from humans and animals in the Netherlands, but there is no evidence for spread of resistant strains or resistance plasmids. The proportion of cfr-positive MRSA is low, but its presence is worrying and should be closely monitored.
The Role of Orthography and Phonology in Written Word Recognition: Evidence From Eye-Tracking in the Visual World Paradigm
Authors: Kim Jina , Meyer Lindsey , Hendrickson Kristi 
Published: October 2022

Purpose:
There is a long-standing debate about how written words are recognized. Central to this debate is the role of phonology. The objective of this study is to contribute to our collective understanding regarding the role of phonology in written word recognition.

Method:

A total of 30 monolingual adults were tested using a novel written word version of the visual world paradigm (VWP). We compared activation of phonological anadromes (words that are matched for sounds but not letters, e.g.,
JAB-BADGE
) and orthographic anadromes (words that are matched for letters but not sounds, e.g.,
LEG-GEL
) to determine the relative role of phonology and orthography in familiar single-word reading.

Results:
We found that activation for phonological anadromes is earlier, more robust, and sustained longer than orthographic anadromes.

Conclusions:
These results are most consistent with strong phonological theories of single-word reading that posit an early and robust role of phonology. This study has broad implications for larger debates regarding reading instruction.
Exploring the Effects of Literacy Instruction for Children With Cerebral Palsy: A Systematic Review
Authors: Murphy Annemarie , Bailey Benjamin , Arciuli Joanne 
Published: October 2022

Purpose:
Some children with cerebral palsy (CP) have difficulty acquiring conventional reading and writing skills. This systematic review explores the different types of literacy instruction and their effects on the reading and writing skills of children with CP.

Method:
Relevant studies published between 2000 and 2020 were identified using electronic databases and terms related to CP and literacy. Data on participant characteristics, instruction characteristics, and instruction outcomes were extracted. A standardized measure of effect size was used to quantify reported treatment effects.

Results:
The systematic search identified 2,970 potentially relevant studies, of which 24 met inclusion criteria. These studies included 66 children with CP aged 5–18 years. One of the included studies utilized a group research design, whereas the remaining used single-subject designs. Studies investigated literacy instruction methods designed to teach phonics, sight-word recognition, reading fluency, reading comprehension, spelling, or written expression skills, or multicomponent instruction (instruction methods encompassing three or more of these skills). Most instruction methods were associated with gains in reading and writing skills with medium to large effects; however, our analysis of methodological rigor suggests that these findings need to be interpreted with caution.

Conclusions:
We propose that literacy instruction utilizing evidence-based principles can be effective for children with CP, provided instruction is accessible and allows children to demonstrate and receive feedback on their skills; however, further research is greatly needed. Clinical implications and priorities for future research are discussed.

Supplemental Material:

https://doi.org/10.23641/asha.21357558
Is Loud Music in Fitness Classes a Motivator or Demotivator?
Authors: Kammerer Kathleen , Emanuel Diana C. , Kubitz Karla , Pitts Donna 
Published: October 2022

Purpose:
Research has documented hazardous sound levels in group fitness classes; however, perceptions of loud sound by fitness class participants, such as how loud and soft sound impacts motivation, whether participants feel empowered to change sound levels, and how sound impacts motivation compared with other characteristics of fitness classes, has not been examined.

Method:
This study examined online survey responses from 249 participants to gain insights into how music level and other environmental aspects of group fitness classes are perceived by participants.

Results:
Findings indicated nonauditory aspects of fitness classes, such as number of attendees, class schedule, difficulty level, and instructor attitude, tended to have a greater impact on motivation than music level. Participants suggested more control over music selection would improve motivation. Too soft music was perceived as a demotivator more often than too loud music. Participants rarely reported trying to modify the sound environment in fitness classes.

Conclusions:
Findings from this study align with a recent theoretical framework proposed by Welch and Fremaux (2017), called the Conditioning, Adaptation, and Acculturation to Loud Music model, which suggests humans are conditioned to first accept loud music (overcoming natural aversion) and eventually to associate loud music with pleasure. Future research using a modified survey and distributed to large fitness center networks, should be conducted to more fully explore perceptions associated with sound environment in fitness classes.
Gratifikationskrisen, Arbeitsfähigkeit und Wunsch nach
beruflichen Veränderungen – eine Querschnittsstudie bei
Pflegepersonen
Authors: Gräske Johannes , Forbrig Theresa A. , Koppe Louise , Urban Svenja , Neumann Fränze , Boguth Katja 
Published: October 2022

Zusammenfassung
Einleitung Seit der Sars-Cov-2 Pandemie haben sich die Arbeitsbedingungen
beruflich Pflegender verschärft. Dies führt zu einem
erhöhten Wunsch, den Beruf zu verlassen. Da Ausstiegsgedanken von
Faktoren wie Arbeitsfähigkeit und dem Verhältnis von Aufwand und
Belohnung beeinflusst werden, soll beides erhoben und in Bezug zum Wunsch des
Berufsausstieges untersucht werden.
Methodik In einer standardisierten, onlinebasierten Querschnittsstudie
wurden Pflegende aus allen Bereichen zu ihrer Arbeitsfähigkeit
(Work-Ability-Index: WAI), dem Verhältnis von Aufwand und Belohnung
(Effort-Reward-Imbalance: ERI-Ratio) sowie dem Wunsch den Beruf zu verlassen
bzw. den*die Arbeitgeber*in zu wechseln, befragt.
Ergebnisse Insgesamt konnten Fragebögen von 2.689 Pflegenden
(durchschnittlich 41,3 Jahre alt, 75,1% weiblich) ausgewertet werden.
Der WAI indiziert eine durchschnittlich gute Arbeitsfähigkeit (37,9
(6,7)). Pflegende erbringen mehr Aufwand als sie Belohnung erfahren (ERI-Ratio
1,7 (0,5)). 38,3% der Pflegenden denken mehrmals monatlich oder
häufiger daran, den Beruf zu verlassen bzw. 30,6% daran, den
Arbeitgeber zu wechseln. Prädiktoren sind WAI (OR 0,881, 95%-CI
0,866; 0,897 bzw. 0,923, 95%-CI 0,908; 0,938) und ERI-Ratio (OR 4,076,
95%-CI 3,224; 5,149 bzw. 4,203, 95%-CI 3,312; 5,334).
Schlussfolgerung Der Einfluss der Arbeitsfähigkeit und insbesondere
der Wahrnehmung von beruflichem Aufwand und erhaltener Belohnung zeigt sich als
einflussnehmend auf den Gedanken an den Berufsausstieg. Dass dem ERI dabei eine
besondere Bedeutung zukommt, zeigen die vorliegenden Ergebnisse. Entsprechend
gilt es zu ergründen, welche Belohnungsfaktoren sich günstig auf
den Berufsverbleib auswirken. Der überdurchschnittliche Anteil an
Pflegenden mit einem akademischen Abschluss kann die Ergebnisse beeinflusst
haben.