bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developing State Health Improvement Plans: Exploring States' Use of Healthy People
Authors: Fromknecht Catharine Q. , Hallman Victoria A. , Heffernan Megan 
Published: September 2021

Background:
While Healthy People outlines a national framework for improving the health of the nation, many states develop State Health Improvement Plans (SHIPs) to set priorities to improve the health of their residents. The purpose of this study was to understand the processes that states use to develop their SHIPs, how states align their SHIPs with Healthy People, and challenges that states face using Healthy People.

Methods:
NORC conducted semistructured interviews with 9 state health department representatives who were responsible for SHIPs. The responses were analyzed using qualitative thematic analysis.

Results:
State health departments used similar approaches to develop their SHIPs. Generally, states began the SHIP development process by performing community health assessments and then assembling diverse stakeholders to recommend key priority areas that should be addressed in the SHIP. States used a similar framework for their SHIPs, outlining priority areas, indicators, and targets. All respondents reported that they referenced Healthy People during the development of their SHIPs. Some states reported aligning their state plans with the Healthy People Framework, while others focused more on the specific Healthy People objectives or target setting guidance.

Conclusions:
Both the federal government and state public health agencies rely on input from stakeholders and cross-sector collaboration to ensure their initiatives reflect the diverse needs of their population. Stakeholder engagement is increasingly important as public health professionals are shifting toward a health equity approach that considers social determinants outside of the health care sector. Healthy People continues to strengthen this perspective by outlining national priorities on well-being while incorporating language around health equity issues. Reinforcing relationships between the federal government and state public health can help states better understand the role of Healthy People as well as encourage further dissemination of creative strategies and best practices.
A uniform benchmark for testing ssrA-derived degrons in the Escherichia coli ClpXP pathway
Authors: Klimecka Maria Magdalena , Antosiewicz Anna , Izert Matylda Anna , Szybowska Patrycja Emanuela , Twardowski Piotr Krzysztof , Delaunay Clara , Górna Maria Wiktoria 
Published: September 2021

ABSTRACTThe ssrA degron is commonly used in fusion proteins to control protein stability in bacteria or as an interaction module. These applications often rely on the modular activities of the ssrA tag in binding to the SspB adaptor and in engaging the ClpXP protease. However, a comparison of these activities for a substantial standard set of degron variants has not been conducted previously, which may hinder developments of new variants optimized exclusively for one application. Here, we strive to establish a benchmark that will facilitate the comparison of ssrA variants under uniform conditions. In our workflow, we included methods for expression and purification of ClpX, ClpP, SspB and eGFP-degrons, assays of ClpX ATPase activity, of eGFP-degron binding to SspB and for measuring eGFP-degron degradation in vitro and in vivo. Using uniform, precise and sensitive methods under the same conditions on a range of eGFP-degrons allowed us to determine subtle differences in their properties that can affect their potential applications. Our findings can serve as a reference and a resource for developing targeted protein degradation approaches.SUMMARYThis work lays standards for assays used to compare engagement of SspB and ClpXP by a set of ssrA-derived degrons that can be used to fine-tune tools for protein stability control.
Association of Initial Clinical Characteristics with the Need for the Intensive Care Unit and Hospitalization in Patients Presenting to the Emergency Department with Acute Symptomatic COVID-19
Authors: Zollinger Benjamin , Newton Sophia , Freeman Jincong Q. , Moran Seamus , Montano Vargas Nataly , Ma Yan , Meltzer Andrew C. 
Published: September 2021

AbstractObjectiveTo evaluate the association of initial clinical symptoms with need for hospitalization, intensive care, or death in ED patients within 30 days after presenting with acute symptomatic COVID-19.MethodsThis study is a retrospective case-series of patients presenting to a single ED with acute symptomatic COVID-19 from March 7–August 9, 2020. Symptomatic patients with laboratory-confirmed SARS-CoV-2 infection were eligible for this study. Patients who tested positive for COVID-19 due to screening tests but had no reasonably associated symptoms were excluded. Participants were analyzed by three categories representative of clinical severity: intensive care unit (ICU) care/death, general ward admission, and ED discharge/convalescence at home. Outcomes were ascertained 30 days after initial presentation to account for escalation in severity after the ED visit. We conducted univariate and multivariable logistic regression analyses to report odds ratios (OR) with 95% confidence intervals (CI) between hospital or ICU care/death versus convalescence at home and between ICU care/death versus general ward admission.ResultsIn total, 994 patients were included in the study, of which, 551 (55.4%) patients convalesced at home, 314 (31.6%) patients required general ward admission, and 129 (13.0%) required ICU care or died. In the multivariable models, ED patients requiring hospital admission were more likely to be aged ≥ 65 years (adjusted OR [aOR] 7.4, 95% CI: 5.0, 10.8), Black/African American (aOR 3.0, 95% CI: 1.6, 5.8) or Asian/American Indian/Alaska Native/Other (aOR 2.2, 95% CI: 1.1, 4.3), and experience dyspnea (aOR 2.7, 95% CI: 2.0, 3.7) or diarrhea (aOR 1.6, 95% CI: 1.1, 2.2). However, they were less likely to experience sore throat (aOR 0.4, 95% CI: 0.2, 0.6), myalgia (aOR 0.5, 95% CI: 0.4, 0.7), headache (aOR 0.5, 95% CI: 0.4, 0.8), or olfactory/taste disturbance (aOR 0.5, 95% CI: 0.3, 0.8). ED patients who required ICU care or died were more likely to experience altered mental status (aOR 3.8, 95% CI: 2.1, 6.6), but were less likely to report history of fever (0.5, 95% CI: 0.3, 0.8).ConclusionsCOVID-19 presents with a multitude of clinical symptoms and an understanding of the association of symptoms with clinical severity may be useful for predicting ultimate patient outcomes.
The impact of armed conflict on the prevalence and transmission dynamics of HIV Infection in Libya
Authors: Daw Mohamed Ali , El-Bouzedi Abdallah Hussean , Ahmed Mohamed Omar 
Published: September 2021

ABSTRACTThe interrelationships between HIV/AIDS and armed conflict are a complex phenomenon and studies are rarely devoted to this area of research. Libya is the second-largest country in Africa that has been evoked with war since NATO intervention in 2011. The country has also experienced one of the largest HIV outbreaks associated with the Bulgarian Nurses saga. The effect of the armed conflict on the dynamic spread of HIV is not well known. The objectives of this study were to determine the impact of armed conflict on the epidemiological situation of HIV infection in Libya and analyze the transmission dynamics of HIV strains during the conflict. We investigated the movement of HIV-infected people during the Libyan armed conflict and analyzed the HIV subtypes reported from 2011 to 2020 and followed up the infected cases all over the country. The patterns of HIV spread within the Libyan regions were traced and risk factors were determined during the conflict period. A total of 4539 HIV/AIDS patients were studied from the four regions during the Libyan conflict. Our data analysis indicated that Benghazi the biggest city in the Eastern region was the significant exporter of the virus to the rest of the country. Viral dissemination changes were observed within the country particularly after 2015. A major virus-flow from the Eastern region during the armed conflict associated with internally displaced people. This resulted in a dissemination of new HIV strains and accumulations of HIV cases in Western and Meddle regions. Although, there were no significant changes in the national prevalence of HIV/AIDS. Our data highlights the factors that complicated the spread and dissemination of HIV during the armed conflict which provides a better understanding of the interaction between them. This could be used to plan for effective preventive measures in tackling the spread of HIV in conflict and post-conflict settings.
Galvanic current activates the NLRP3 inflammasome to promote type I collagen production in tendon
Authors: Peñín-Franch Alejandro , Antonio García-Vidal José , Martínez Carlos Manuel , Escolar-Reina Pilar , I.Gómez Ana , Minaya-Muñoz Francisco , Valera-Garrido Fermín , Medina-Mirapeix Francesc , Pelegrín Pablo 
Published: September 2021

ABSTRACTThe NLRP3 inflammasome coordinates inflammation in response to different pathogen- and damage-associated molecular patterns, being implicated in different infectious, chronic inflammatory, metabolic and degenerative diseases. In chronic tendinopathies lesions, different non-resolving mechanisms produce a degenerative condition that impairs tissue healing, complicating their clinical management. Percutaneous needle electrolysis consist in the application of a galvanic current and is emerging as a novel treatment for tendinopathies. Here we found that galvanic current activates the NLRP3 inflammasome and the induction of an inflammatory response promoting a collagen-mediated regeneration of the tendon. This study establish the molecular mechanism of percutaneous electrolysis for the treatment of chronic lesions and the beneficial effects of an induced inflammasome-related response.
Seeing the Forest for the trees: Assessing genetic offset predictions with Gradient Forest
Authors: Láruson Áki Jarl , Fitzpatrick Matthew C. , Keller Stephen R. , Haller Benjamin C. , Lotterhos Katie E. 
Published: September 2021

ABSTRACTGradient Forest (GF) is increasingly being used to forecast climate change impacts, but remains mostly untested for this purpose. We explore its robustness to assumption violations, and relationship to measures of fitness, using SLiM simulations with explicit genome architecture and a spatial metapopulation. We evaluate measures of GF offset in: (1) a neutral model with no environmental adaptation; (2) a monogenic “population genetic” model with a single environmentally adapted locus; and (3) a polygenic “quantitative genetic” model with two adaptive traits, each adapting to a different environment. Although we found GF Offset to be broadly correlated with fitness offsets under both single locus and polygenic architectures. It could also be confounded by neutral demography, genomic architecture, and the nature of the adaptive environment. GF Offset is a promising tool, but it is important to understand its limitations and underlying assumptions, especially when used in the context of forecasting maladaptation.
LOICA: Logical Operators for Integrated Cell Algorithms
Authors: Vidal Gonzalo , Vidal-Céspedes Carlos , Rudge Timothy James 
Published: September 2021

1ABSTRACTMathematical and computational modeling is essential to genetic design automation and for the synthetic biology design-build-test-learn cycle. The construction and analysis of models is enabled by abstraction based on a hierarchy of components, devices, and systems that can be used to compose genetic circuits. These abstract elements must be parameterized from data derived from relevant experiments, and these experiments related to the part composition of the abstract components of the circuits measured. Here we present LOICA (Logical Operators for Integrated Cell Algorithms), a Python package for modeling and characterizing genetic circuits based on a simple object-oriented design abstraction. LOICA uses classes to represent different biological and experimental components, which generate models through their interactions. High-level designs are linked to their part composition via SynBioHub. Furthermore, LOICA communicates with Flapjack, a data management and analysis tool, to link to experimental data, enabling abstracted elements to characterize themselves.
Controlling fibroblast fibrinolytic activity allows for the bio-engineering of stable connective tissue equivalents
Authors: Boucard Elea , Coulon Flora , Vidal Luciano , Hascoët Jean-Yves , Mota Carlos Domingues , Halary Franck 
Published: September 2021

AbstractIn tissue engineering, cell origin is important to ensure outcome quality. However, the impact of the cell type chosen for seeding in a biocompatible matrix has been less investigated. Here, we investigated the capacity of primary and immortalized fibroblasts of distinct origins to degrade a gelatin/alginate/fibrin (GAF)-based biomaterial. We further established that fibrin was targeted by degradative fibroblasts through the secretion of fibrinolytic matrix-metalloproteinases (MMPs) and urokinase, two types of serine protease. Finally, we demonstrated that besides aprotinin, specific targeting of fibrinolytic MMPs and urokinase led to cell-laden GAF stability for at least several days. These results support the use of specific strategies to tune fibrin-based biomaterials degradation over time. It emphasizes the need to choose the right cell type and further bring targeted solutions to avoid the degradation of fibrin-containing hydrogels or bioinks.
The genes controlling normal function of citrate and spermine secretion is lost in aggressive prostate cancer and prostate model systems
Authors: Rye Morten Beck , Krossa Sebastian , Hall Martina , van Mourik Casper , Bathen Tone F. , Drabløs Finn , Tessem May-Britt , Bertilsson Helena 
Published: September 2021

AbstractBackgroundSecretion of the metabolites citrate and spermine into prostate lumen is a unique hallmark for normal prostate epithelial cells. However, the identity of the genes controlling citrate and spermine secretion remains mostly unknown despite their obvious relevance for progression to aggressive prostate cancer.Materials & MethodsIn this study, we have correlated simultaneous measurement of citrate/spermine and transcriptomics data. We have refined these gene correlations in 12 prostate cancer cohorts containing 2915 tissue samples to create a novel gene signature of 150 genes connected with citrate and spermine secretion. We further explored the signature in public data, interrogating over 18 000 samples from various tissues and model systems, including 3826 samples from prostate and prostate cancer.ResultsIn prostate cancer, the expression of this gene signature is gradually lost in tissue from normal epithelial cells through PIN, low grade (Gleason <= 7), high grade cancer (Gleason >= 8) and metastatic lesions. The accuracy of the signature is validated by its unique enrichment in prostate compared to other tissues, and its strong enrichment in epithelial tissue compartments compared to stroma. Several zinc-binding proteins that are not previously investigated in the prostate are present in the gene signature, suggesting new mechanisms for controlling zinc homeostasis in citrate/spermine secretion. However, the absence of the gene signature in all common prostate normal and cancer cell-lines, as well as prostate organoids, underlines the challenge to study the role of these genes during prostate cancer progression in model systems.ConclusionsA large collection of transcriptomics data integrated with metabolomics identifies the genes related to citrate and spermine secretion in the prostate, and show that the expression of these genes gradually decreases on the path towards aggressive prostate cancer. In addition, the study questions the relevance of currently available model systems to study metabolism in prostate cancer development.
High permeability of the CSF flow in the juvenile mouse brain by brain-wide DCE-MRI
Authors: Wada Yayoi , Imai Hirohiko , Yamawaki Yuki , Parvez Md Sorwer Alam , Matsui Sae , Ohtsuki Gen 
Published: September 2021

AbstractThe vasculature system with a lymphatic function in the brain is manifested as meningeal lymphatic vessels and the glymphatic system, which drain waste products from cerebrospinal fluid (CSF) and produce interstitial fluid. Invasion of stimulated immune cells or inflammatory cytokines during the maturation is regarded as a sign of the disruption of brain functions through excessive immune stresses. However, it is unclear when the lymphatic system is functionally completed and in which parts of the organ the brain immunity is privileged (i.e., the blood-brain barrier is fully established). Here, we visualized the whole-head signal of gadolinium (Gd) contrast agents in mouse brains to investigate the CSF flow from the signals of Gd-contrast agents using magnetic resonance imaging (MRI) in the course of developmental stages. We found higher Gd-signals in the olfactory bulbs, prefrontal cortex, parietal surface regions of the neocortex along with dorsal meningeal lymphatic vessels, ventral midbrain, and a part of cerebellum, as well as in the basal brain regions, at the immature stage of postnatal (P) 4 weeks, compared to the P8-12 weeks. Our results suggest that the barrier of the vasculature system in mouse brains is still permeable until P1-month and small molecules can leak into the parenchyma.
PharmacoDB 2.0 : Improving scalability and transparency ofin vitropharmacogenomics analysis
Authors: Feizi Nikta , Nair Sisira Kadambat , Smirnov Petr , Beri Gangesh , Eeles Christopher , Esfahani Parinaz Nasr , Nakano Minoru , Tkachuk Denis , Mammoliti Anthony , Gorobets Evgeniya , Mer Arvind Singh , Lin Eva , Yu Yihong , Martin Scott , Hafner Marc , Haibe-Kains Benjamin 
Published: September 2021

ABSTRACTCancer pharmacogenomics studies provide valuable insights into disease progression and associations between genomic features and drug response. PharmacoDB integrates multiple cancer pharmacogenomics datasets profiling approved and investigational drugs across cell lines from diverse tissue types. The web-application enables users to efficiently navigate across datasets, view and compare drug dose-response data for a specific drug-cell line pair. In the new version of PharmacoDB (version 2.0,https://pharmacodb.ca/), we present: (i) new datasets such as NCI-60, the Profiling Relative Inhibition Simultaneously in Mixtures (PRISM) dataset, as well as updated data from the Genomics of Drug Sensitivity in Cancer (GDSC) and the Genentech Cell Line Screening Initiative (gCSI); (ii) implementation of FAIR data pipelines using ORCESTRA and PharmacoDI; (iii) enhancements to drug response analysis such as tissue distribution of dose-response metrics and biomarker analysis; (iv) improved connectivity to drug and cell line databases in the community. The web interface has been rewritten using a modern technology stack to ensure scalability and standardization to accommodate growing pharmacogenomics datasets. PharmacoDB 2.0 is a valuable tool for mining pharmacogenomics datasets, comparing and assessing drug response phenotypes of cancer models.HIGHLIGHTSPharmacoDB 2.0 includes new and updated large pharmacogenomic datasets. The data processing for PharmacoDB is made fully reproducible through the use of the ORCESTRA platform and automated data ingestion pipelinesThe new release contains enriched annotations for drugs and cell lines via connectivity to external databases, as well as new analytical methods for tissue-specific and pan-cancer biomarker discoveryThe new version of PharmacoDB incorporates a scalable and reproducible framework that can accelerate the implementation of analytical pipelines including machine learning/AI for biomarker discovery in the future
A waveform-independent measure of recurrent neural activity
Authors: Weber Immo , Oehrn Carina R. 
Published: September 2021

AbstractRhythmic neural activity, so called oscillations, play a key role for neural information transmission, processing and storage. Neural oscillations in distinct frequency bands are central to physiological brain function and alterations thereof have been associated with several neurological and psychiatric disorders. The most common methods to analyse neural oscillations, e.g. short-term Fourier transform or wavelet analysis, assume that measured neural activity is composed of a series of symmetric prototypical waveforms, e.g. sinusoids. However, usually the models generating the signal, including waveform shapes of experimentally measured neural activity are unknown. Decomposing asymmetric waveforms of nonlinear origin using these classic methods may result in spurious harmonics visible in the estimated frequency spectra. Here, we introduce a new method for capturing rhythmic brain activity based on recurrences of similar states in phase-space. This method allows for a time-resolved estimation of amplitude fluctuations of recurrent activity irrespective of or specific to waveform-shapes. The algorithm is derived from the well-established field of recurrence analysis, which has rarely been adopted in neuroscience. In this paper, we show its advantages and limitations in comparison to short-time Fourier transform and wavelet convolution using periodic signals of different waveform shapes. Further, we demonstrate its application using experimental data, i.e. intracranial electrophysiological recordings from the human motor cortex of one epilepsy patient.
On the effect of inheritance of microbes in commensal microbiomes
Authors: Zapién-Campos Román , Bansept Florence , Sieber Michael , Traulsen Arne 
Published: September 2021

BackgroundOur current view of nature depicts a world where macroorganisms dwell in a landscape full of microbes. Some of these microbes not only transit but establish themselves in or on hosts. Although hosts might be occupied by microbes for most of their lives, a microbe-free stage during their prenatal development seems to be the rule for many hosts. The questions of who the first colonizers of a newborn host are and to what extent these are obtained from the parents follow naturally.ResultsWe have developed a mathematical model to study the effect of the transfer of microbes from parents to offspring. Even without selection, we observe that microbial inheritance is particularly effective in modifying the microbiome of hosts with a short lifespan or limited colonization from the environment, for example by favouring the acquisition of rare microbes.ConclusionBy modelling the inheritance of commensal microbes to newborns, our results suggest that, in an eco-evolutionary context, the impact of microbial inheritance is of particular importance for some specific life histories.