bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leveraging natural language processing to augment structured social determinants of health data in the electronic health record
Authors: Lybarger Kevin , Dobbins Nicholas J , Long Ritche , Singh Angad , Wedgeworth Patrick , Uzuner Özlem , Yetisgen Meliha 
Published: May 2023

Abstract

Objective
Social determinants of health (SDOH) impact health outcomes and are documented in the electronic health record (EHR) through structured data and unstructured clinical notes. However, clinical notes often contain more comprehensive SDOH information, detailing aspects such as status, severity, and temporality. This work has two primary objectives: (1) develop a natural language processing information extraction model to capture detailed SDOH information and (2) evaluate the information gain achieved by applying the SDOH extractor to clinical narratives and combining the extracted representations with existing structured data.

Materials and Methods
We developed a novel SDOH extractor using a deep learning entity and relation extraction architecture to characterize SDOH across various dimensions. In an EHR case study, we applied the SDOH extractor to a large clinical data set with 225 089 patients and 430 406 notes with social history sections and compared the extracted SDOH information with existing structured data.

Results
The SDOH extractor achieved 0.86 F1 on a withheld test set. In the EHR case study, we found extracted SDOH information complements existing structured data with 32% of homeless patients, 19% of current tobacco users, and 10% of drug users only having these health risk factors documented in the clinical narrative.

Conclusions
Utilizing EHR data to identify SDOH health risk factors and social needs may improve patient care and outcomes. Semantic representations of text-encoded SDOH information can augment existing structured data, and this more comprehensive SDOH representation can assist health systems in identifying and addressing these social needs.
Development and Validation of a Modified QuEChERS protocol Coupled to Liquid Chromatography–Tandem Mass Spectrometry for the Rapid and Accurate Determination of Acrylamide in Cereal-Based Baby Foods
Authors: Marzouk Abdelrahman M , Shendy Amr H , Aboelhassan AlaaEldean Fathy Ahmed , Gomaa Ahmed M , El-Shahat M F 
Published: May 2023

Abstract

Background
With the widespread consumption by children of cereal-based baby food, acrylamide contamination is a prevalent risk that may have carcinogenic consequences.

Objective
This study aims to develop and validate a modified QuEChERS protocol (quick, easy, cheap, effective, rugged, and safe) without solvent exchange, followed by rapid separation and accurate determination of acrylamide in cereal-based baby foods using reversed-phase (RP)-LC–MS/MS.

Methods
Samples were extracted using a modified QuEChERS protocol of the AOAC version and cleaned up with basic alumina. Separation was performed on a Phenomenex® Kinetex C18 column (100 Å × 3.5 µm × 4.6 mm × 150 mm) using a gradient elution program with a mobile phase of 10 mM ammonium formate–methanol. Determinations were conducted using electrospray ionization (ESI)-MS/MS in positive-ion mode.

Results
Basic alumina yielded clean extracts, resulting in acceptable recovery percentages and a tolerable matrix effect (ME) &lt;5%. This allowed extraction without a solvent exchange step. Efficient separation was achieved at a retention time (tR) of 3.39 ± 0.05 min employing an RP-C18 column with core-shell properties in a relatively short analysis run time of only 5 min. Trueness, precision, LOD, LOQ, linearity range, and R2 results were 92.5–104.6%, RSD ≤12.2%, 5 µg/kg, 20 µg/kg, 4.0–1000.0 µg/kg, and &gt; 0.9999, respectively. The test method applicability was demonstrated by proficiency testing (PT) and 50 real samples of cereal-based baby foods. Most of the tested samples were in violation of acrylamide’s established European Union benchmark (40 µg/kg).

Conclusion
Acetate-buffered QuEChERS protocol in conjunction with optimized amounts of basic alumina was confirmed as an efficient extraction protocol for acrylamide from cereal-based baby foods resulting in optimal method performance. Successful selection of the RP-C18 column is key for selective separation for acrylamide in a relatively short analysis run time.

Highlights
The modified AOAC QuEChERS protocol with a dispersive solid phase extraction (d-SPE) of basic alumina assisted in reducing the ME to tolerable levels while maintaining acceptable method performance. The use of an RP-C18 column with core-shell properties enabled a rapid and accurate acrylamide determination.
A new form of corruption
Authors: Prince Michael of Liechtenstein H S H 
Published: May 2023

Abstract
For some years now, a new form of corruption has been rampant, having a negative influence on both the economy and citizens. This article examines how the decisions of the G20 relate to this and what impacts this new form of corruption has. It is necessary for fiduciaries to understand this development so that they can continue to fulfil their ancestral role which is to protect clients, their families, their businesses, assets and values.
Computed Tomography Scan Versus Saline Load Test for Detection of Traumatic Shoulder Arthrotomy: A Cadaveric Study
Authors: Villacres Mori Benjamin , Lakra Akshay , Gheewala Rohan A. , Carroll Jeremy D. , Bibicheff Darrel , Smith Michael P. , Mulligan Michael T. 
Published: May 2023

Objectives:
Traumatic shoulder arthrotomy (TSA) is a rare injury that is commonly detected through saline load test (SLT). There are no studies that have studied the ability of computed tomography (CT) scan to detect a TSA. The purpose of this study is to determine the ability of CT scan to detect a TSA and compare it with the SLT.

Methods:
Twelve cadaveric shoulders were included in the study. Before intervention, a CT scan was conducted to determine presence of intra-articular air. After confirmation that no air was present, an arthrotomy was made at the anterior or posterior portal site. A CT was obtained postarthrotomy to evaluate for intra-articular air. Each shoulder then underwent an SLT to assess the sensitivity of SLT and the volume needed for extravasation.

Results:
Twelve shoulders were included after a pre-intervention CT scan. Six shoulders received an arthrotomy through the anterior portal and six shoulders received an arthrotomy through the posterior portal. After the arthrotomy, air was visualized on CT scan in 11 of the 12 shoulders (92%). All 12 shoulders demonstrated extravasation during SLT. The mean volume of saline needed for extravasation was 29 mL with an SD of 10 and range of 18–50 mL.

Conclusions:
CT scan is a sensitive modality (sensitivity of 92%) for detection of TSA. In comparison, SLT is more sensitive (sensitivity of 100%) and outperforms CT scan for the diagnosis of TSA in a cadaveric model. Further research is needed to solidify the role that CT imaging has in the diagnosis of TSAs.
Opioid Use in Pediatric Patients After Common Orthopaedic Surgeries
Authors: Perkins Crystal A. , Murata Asahi , Kim Jason , Willimon Samuel Clifton 
Published: May 2023

Background:
The use and misuse of opioid medications is an epidemic and public health emergency. There are currently no standard guidelines for treating perioperative pain in the pediatric population. The purpose of this study is to describe opioid use among pediatric patients after common orthopaedic surgeries.

Methods:
Patients between 5 and 20 years of age undergoing one of 7 common orthopaedic surgeries between the years 2018 to 2020 were prospectively studied. Patients and their families completed a medication logbook to track all doses of pain medication and associated pain scores.

Results:
Three hundred forty-two patients completed the study, including 174 females and 168 males with a mean age of 14.0 years (range, 5 to 20 y). A total of 4351 tablets or liquid doses of the narcotic medication, 44% of the total prescribed, were consumed. Of the prescribed medication,56% remained unused. Nonsteroidal anti-inflammatory drug use was identified to be the only independent predictor of less narcotic use, with a mean of 5.1 tablets (P = 0.003) and 1.7 days (P < 0.01) less opioid consumed among these patients. Thirty-two (9.4%) patients consumed 100% of their prescriptions. Nonmedicinal methods of pain control, most commonly ice, were used by 77% of patients, and this was highly variable between procedures. Physicians were cited as a source of medication information by only 50% of patients, with high variability between procedures.

Conclusions:
Opioid medication use in children and adolescents after orthopaedic surgery is significantly less than the number of tablets prescribed, with 56% of the medication prescribed remaining unused in the postoperative period. Duration of narcotic use was longer than anticipated with a wide SD (4.7 d +/−3 d).
We recommend orthopaedic surgeons responsibly prescribe pain medications using evidence-based data or the results of their own experience monitoring medication consumption. In addition, and important in the setting of the “opioid epidemic,” physicians must counsel patients and families on postoperative pain expectations and appropriate medication use.

Level of Evidence:
Level IV, prospective case series.
Relationship of Ethinylestradiol/Drospirenone Prescription on Work Productivity and Activity Impairment Among Women With Menstruation-Related Symptoms
Authors: Ikeda Yumie , Egawa Miho , Ohsuga Takuma , Mandai Masaki , Takahashi Yoshimitsu , Nakayama Takeo 
Published: May 2023

Objective
The aim of the study is to examine changes in work productivity and daily activity impairment among women by starting ethinylestradiol (EE)/drospirenone (DRSP) for perimenstrual symptoms.

Methods
Participants were women who were newly prescribed EE/DRSP at 25 gynecological clinics in Japan. Eligible participants recorded daily intake of EE/DRSP and the Work Productivity Activity Impairment Questionnaire General Health every 2 weeks for 3 months by smartphone app. A linear mixed-effects model was used to see changes in work productivity impairment and activity impairment relative to baseline.

Results
A total of 222 participants were eligible. Work productivity impairment recovered by 20.0% (95% confidence interval, 14.1%–26.0%) at 1 m and maintained for 2 months. Activity impairment recovered by 20.1% (95% confidence interval, 15.5%–24.7%) at 1 m and thereafter.

Conclusions
Improvements in work productivity and daily activities were observed at 1 m after EE/DRSP initiation, with a sustained effect thereafter.
Current challenges and perspectives in lung cancer care during COVID-19 waves
Authors: Mariniello Domenica Francesca , Aronne Luigi , Vitale Maria , Schiattarella Angela , Pagliaro Raffaella , Komici Klara 
Published: May 2023

Purpose of review
In the era of the SARS-Cov2 pandemic, the multidisciplinary care of patients with lung cancer is the main challenge for clinicians. The depiction of complex networking between SARS-CoV2 and cancer cells is crucial to understanding the downstream signalling pathways leading to more severe clinical behaviour of COVID-19 among lung cancer patients.

Recent findings
The immunosuppressive status caused by both blunted immune response and active anticancer treatments (e.g. radiotherapy, chemotherapy) affects also the response to vaccines. Furthermore, the COVID-19 pandemic has significantly influenced early detection, therapeutic management, and clinical research for patients with lung cancer.

Summary
SARS-CoV-2 infection does undoubtedly represent a challenge for care of patients with lung cancer. Since symptoms of infection may overlap with underlying condition, diagnosis must be reached and treatment should start as soon as possible. Although any cancer treatment should be procrastinated as long as infection is not cured, every choice must be pondered on individual basis, according to clinical conditions. Underdiagnosis should be avoided, and both surgical and medical treatment must be tailored to each patient. Therapeutic scenario standardization represents a major challenge for clinicians and researchers.
COVID AMP: An Open Access Dataset of COVID-19 Response Policies
Authors: Katz Rebecca , Toole Kate , Robertson Hailey , Case Alaina , Kerr Justin , Robinson-Marshall Siobhan , Schermerhorn Jordan , Orsborn Sarah , Van Maele Michael , Zimmerman Ryan , Stevens Tess ,   COVID AMP Coding Team, Phelan Alexandra , Carlson Colin , Graeden Ellie 
Published: May 2023

AbstractAs the COVID-19 pandemic unfolded in the spring of 2020, governments around the world began to implement policies to mitigate and manage the outbreak. Significant research efforts were deployed to track and analyse these policies in real-time to better inform the response. While much of the policy analysis focused narrowly on social distancing measures designed to slow the spread of disease, here, we present a dataset focused on capturing the breadth of policy types implemented by jurisdictions globally across the whole-of-government. COVID Analysis and Mapping of Policies (COVID AMP) includes nearly 50,000 policy measures from 150 countries, 124 intermediate areas, and 235 local areas between January 2020 and June 2022. With up to 40 structured and unstructured characteristics encoded per policy, as well as the original source and policy text, this dataset provides a uniquely broad capture of the governance strategies for pandemic response, serving as a critical data source for future work in legal epidemiology and political science.
Astrocytic Foxo1 regulates hippocampal spinogenesis and synaptic plasticity to enhance fear memory
Authors: Viana João Filipe , Guerra-Gomes Sónia , Abreu Daniela Sofia , Machado João Luís , Barsanti Sara , Gonçalves Mariana , Martín-Monteagudo Cristina , Sardinha Vanessa Morais , Marques Nascimento Diana Sofia , Tavares Gabriela , Irmler Martin , Beckers Johannes , Korostynski Michal , Sousa Nuno , Navarrete Marta , Teixeira-Castro Andreia , Pinto Luísa , Oliveira João Filipe 
Published: May 2023

ABSTRACTAstrocytes are active players in brain circuits, sensing and responding to neuronal activity, impacting behavior production. Activation of astrocytes triggers intracellular calcium elevations displaying complex spatiotemporal properties. Intracellular calcium activity is thought to underlie synaptic transmission, metabolism, and brain homeostasis modulation. However, the calcium-dependent signaling pathways involved in these processes are poorly understood, representing a critical knowledge gap in this field. To reveal calcium-dependent signaling pathways involved in circuit structure and function, we performed a multi-level analysis of the inositol 1,4,5-triphosphate receptor type 2 knockout (IP3R2 KO) mouse model which lacks somatic calcium elevations specifically in astrocytes. We focused on the hippocampus, a brain region responsible for cognitive function and emotional behaviors.The transcriptomic analysis of hippocampal tissue revealed that the lack of astrocytic somatic calcium causes the differential expression of hundreds of genes. Among these, 76 genes are regulated by the astrocyte-specific Foxo1 transcription factor. This transcription factor is over-expressed in the hippocampal astrocytes of this mouse model and regulates the expression of genes involved in spinogenesis and synaptic coverage. A detailed morphological analysis of hippocampal pyramidal neurons revealed dendrites with a shift to a more immature spine profile. This spine profile shift may underlie previously described a reduction of long-term depression and performance in fear memory tasks observed in this mouse model. Indeed, we confirmed that these mice lacking astrocytic somatic calcium display an enhancement of long-term fear memory. To verify a causal relationship between these structural, synaptic, and behavioral observations, we used a viral approach to induce the over-expression of Foxo1 in hippocampal astrocytes in naïve C57BL/6J mice. This viral-driven over-expression of Foxo1 in astrocytes of thestratum radiatumreplicated the shift to an immature spine profile in dendrites of pyramidal neurons crossing the territory of these astrocytes and led to a reduction of long-term depression in the same region. Finally, this manipulation was sufficient to enhance long-term fear memory.The detailed characterization of the mouse model lacking astrocytic somatic calcium revealed that astrocytes modulate hippocampal circuit structure and function through Foxo1 signaling to enhance fear memory.
Phages overcome bacterial immunity via diverse anti-defense proteins
Authors: Yirmiya Erez , Leavitt Azita , Lu Allen , Avraham Carmel , Osterman Ilya , Garb Jeremy , Antine Sadie P. , Mooney Sarah E. , Hobbs Sam J. , Kranzusch Philip J. , Amitai Gil , Sorek Rotem 
Published: May 2023

AbstractIt was recently shown that bacteria employ, apart from CRISPR-Cas and restriction systems, a considerable diversity of phage resistance systems, but it is largely unknown how phages cope with this multilayered bacterial immunity. Here, we analyzed groups of closely relatedBacillusphages that showed differential sensitivity to bacterial defense systems, and identified multiple families of anti-defense proteins that inhibit the Gabija, Thoeris, and Hachiman systems. We show that these proteins efficiently cancel the defensive activity when co-expressed with the respective defense system or introduced into phage genomes. Homologs of these anti-defense proteins are found in hundreds of phages that infect taxonomically diverse bacterial species. We show that an anti-Gabija protein, denoted Gad1, blocks the ability of the Gabija defense complex to cleave phage-derived DNA. Our data further reveal an anti-Thoeris protein, denoted Tad2, which is a “sponge” that sequesters the immune signaling molecules produced by Thoeris TIR-domain proteins in response to phage. Our results demonstrate that phages encode an arsenal of anti-defense proteins that can disable a variety of bacterial defense mechanisms.
Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of a salt marsh foundation plant species
Authors: Rolando J.L. , Kolton M. , Song T. , Liu Y. , Pinamang P. , Conrad R. , Morris J.T. , Konstantinidis K.T. , Kostka J.E. 
Published: May 2023

AbstractSymbiotic root microbiota are crucial for plant growth as they assist their hosts in nutrient acquisition. In the roots of coastal marine plants, heterotrophic activity in the rhizosphere by sulfate-reducing microorganisms has been linked to nitrogen fixation. In this study, we recovered 239 high-quality metagenome-assembled genomes (MAGs) from a salt marsh dominated by the foundation plantSpartina alterniflora, including diazotrophic sulfate-reducing and sulfur-oxidizing bacteria thriving in the root compartment. Here we show for the first time that highly-abundant sulfur-oxidizing bacteria in the roots of a coastal macrophyte encode and highly express genes for nitrogen fixation (nifHDK). Further, we leveraged aS. alterniflorabiomass gradient to gain a mechanistic understanding on how root-microbe interactions respond to abiotic stress from anoxia and elevated sulfide concentration. We observed that the roots of the stressedS. alternifloraphenotype exhibited the highest rates of nitrogen fixation and expression levels of both the oxidative and reductive forms of the dissimilatory sulfite reductase gene (dsrAB). Approximately 25% and 15% of all sulfur-oxidizing dsrA and nitrogen-fixing nifK transcripts, respectively, were associated with novel MAGs of theCandidatusThiodiazotropha genus in the roots of the stressedS. alternifloraphenotype. We conclude that the rapid cycling of sulfur in the dynamicS. alternifloraroot zone is coupled to nitrogen fixation during both reductive and oxidative sulfur reactions, and that theS. alterniflora–Ca.Thiodiazotropha symbiosis is an adaptive response to anoxic and sulfidic sediment conditions, whereby the plants benefit from reduced sulfide toxicity and potential nitrogen acquisition.
Photosynthetic living fibers fabrication from algal-bacterial consortia with controlled spatial distribution
Authors: Sun Zitong , Di Zhengao , Zhang Yang , Wen Huilin , Zhang Shaobin , Zhang Zhiqian , Zhang Jing , Yu Ziyi 
Published: May 2023

ABSTRACTLiving materials that combine active cells and synthetic matrix materials have become a promising research field in recent years. While multicellular systems present exclusive benefits in developing living materials over single-cell systems, creating artificial multicellular systems can be challenging due to the difficulty in controlling the multicellular assemblies and the complexity of cell-to-cell interactions. Here, we propose a co-culture platform capable of isolating and controlling the spatial distribution of algal-bacterial consortia, which can be used to construct photosynthetic living fibers. Through coaxial extrusion-based 3D printing, hydrogel fibers containing bacteria or algae can be deposited into designated structures and further processed into materials with precise geometries. In addition, the photosynthetic living fibers demonstrate a significant synergistic catalytic effect resulting from the immobilization of both bacteria and algae, which effectively optimize sewage treatment for bioremediation purposes. The integration of microbial consortia and 3D printing gives functional living materials that have promising applications in biocatalysis, biosensing, and biomedicine. Our approach provides an optimized solution for constructing efficient multicellular systems and opens a new avenue for the development of advanced materials.
High carbohydrate to protein ratio promotes changes in intestinal microbiota and host metabolism in rainbow trout (Oncorhynchus mykiss) fed plant-based diet
Authors: Defaix Raphaël , Lokesh Jep , Ghislain Mylène , Bechec Mickael Le , Marchand Michaël , Véron Vincent , Surget Anne , Biasutti Sandra , Terrier Frederic , Pigot Thierry , Panserat Stéphane , Ricaud Karine 
Published: May 2023

AbstractTo ensure the sustainability of aquaculture, it is necessary to change the “menu” of carnivorous fish such as rainbow trout from a fish-based diet to one with plant-based ingredients. However, there is a major problem with the growth performance decrease of fish fed with a 100% plant-based diet due to the reduction in feed intake and feed efficiency. For the first time, we incorporated high levels of digestible carbohydrates (high-starch diet) in a 100% plant-based diet during a 12-week feeding trial in order to improve protein utilization for growth (protein sparing effect) and reduce nitrogen waste.We measured the changes in the intestinal microbiota, Short-Chain Fatty Acid (SCFA) levels and metabolic responses in liver. Dietary carbohydrates had a strong effect on alpha and beta diversity and abundance of 12 genera, includingRalstoniaandBacillusin digesta associated microbiota whereas mucosa associated microbiota was less affected. The change in microbial diversity might be linked to the change observed in SCFA production. High levels ofMycoplasmawere observed in the intestinal mucosa. Overall, hepatic gene expression was significantly altered by the CHO/protein ratio. Up-regulation of genes involved in glucose metabolism (gcka,gckb,g6pcb2a), down-regulation of genes involved in lipid metabolism (hadh,acox3,srebp2a, andcyp51a) were associated with higher enzymatic activities (such as glucokinase or pyruvate kinase) and higher glycogen levels in the liver, suggesting adequate adaptation to diet. Interestingly, strong correlations were observed between abundances of certain bacterial OTUs and gene expression in the liver.The inclusion of digestible carbohydrates in combination with a 100% plant-based diet, could be a promising way to improve and reduce the use of plant proteins in rainbow trout. In addition, the relationship between intestinal microbiota and host metabolism needs further investigation to better understand fish nutrition.