bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning
Authors: Caufield J Harry , Hegde Harshad , Emonet Vincent , Harris Nomi L , Joachimiak Marcin P , Matentzoglu Nicolas , Kim HyeongSik , Moxon Sierra , Reese Justin T , Haendel Melissa A , Robinson Peter N , Mungall Christopher J 
Published: February 2024

Abstract

Motivation
Creating knowledge bases and ontologies is a time consuming task that relies on manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrarily complex nested knowledge schemas.

Results
Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against an LLM to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for matched elements. We present examples of applying SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease relationships. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction methods, but greatly surpasses an LLM’s native capability of grounding entities with unique identifiers. SPIRES has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any new training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM.

Availability and implementation
SPIRES is available as part of the open source OntoGPT package: https://github.com/monarch-initiative/ontogpt.
Intrauterine exposure to SARS-CoV-2 infection and early newborn brain development
Authors: Andescavage Nickie , Lu Yuan-Chiao , Wu Yao , Kapse Kushal , Keller Jennifer , Von Kohorn Isabelle , Afifi Ashraf , Vezina Gilbert , Henderson Deidtra , Wessel David L , du Plessis Adre J , Limperopoulos Catherine 
Published: February 2024

Abstract
Epidemiologic studies suggest that prenatal exposures to certain viruses may influence early neurodevelopment, predisposing offspring to neuropsychiatric conditions later in life. The long-term effects of maternal COVID-19 infection in pregnancy on early brain development, however, remain largely unknown. We prospectively enrolled infants in an observational cohort study for a single-site study in the Washington, DC Metropolitan Area from June 2020 to November 2021 and compared these infants to pre-pandemic controls (studied March 2014–February 2020). The primary outcomes are measures of cortical morphometry (tissue-specific volumes), along with global and regional measures of local gyrification index, and sulcal depth. We studied 210 infants (55 infants of COVID-19 unexposed mothers, 47 infants of COVID-19-positive mothers, and 108 pre-pandemic healthy controls). We found increased cortical gray matter volume (182.45 ± 4.81 vs. 167.29 ± 2.92) and accelerated sulcal depth of the frontal lobe (5.01 ± 0.19 vs. 4.40 ± 0.13) in infants of COVID-19-positive mothers compared to controls. We found additional differences in infants of COVID-19 unexposed mothers, suggesting both maternal viral exposures, as well as non-viral stressors associated with the pandemic, may influence early development and warrant ongoing follow-up.
Weak identification with many instruments
Authors: Mikusheva Anna , Sun Liyang 
Published: February 2024

Summary
Linear instrumental variable regressions are widely used to estimate causal effects. Many instruments arise from the use of ‘technical’ instruments and more recently from the empirical strategy of ‘judge design’. This paper surveys and summarises ideas from recent literature on estimation and statistical inferences with many instruments for a single endogenous regressor. We discuss how to assess the strength of the instruments and how to conduct weak identification robust inference under heteroskedasticity. We establish new results for a jack-knifed version of the Lagrange Multiplier test statistic. Furthermore, we extend the weak identification robust tests to settings with both many exogenous regressors and many instruments. We propose a test that properly partials out many exogenous regressors while preserving the re-centring property of the jack-knife. The proposed tests have correct size and good power properties.
White Matter Plasticity Underpins Cognitive Gains After Multidomain Adaptive Computerized Cognitive Training
Authors: Dai Xiangwei , Liu Sihan , Li Yumeng , Long Shijie , Li Xin , Chen Chuansheng , Yang Caishui , Zhang Junying , Han Zhuo Rachel , Li He , Wang Jun , Zhang Zhanjun 
Published: February 2024

Abstract

Background
This study aims to evaluate the effectiveness of computerized cognitive training (CCT) on white matter (WM) neuroplasticity and neuropsychological performance.

Methods
A total of 128 community older adults (64.36 ± 6.14 years) were recruited and randomly assigned to the intervention or control group. Participants in the intervention group received a home-based, multidomain, and adaptive CCT for 30 minutes, 2 days per week for 1 year. Neuropsychological assessments, diffusion magnetic resonance imaging (MRI), and T1-weighted structural MRI were performed at the pre- and post-intervention visits.

Results
Eighty-one of 128 participants (41 in the intervention group and 40 in the control group) completed the 1-year intervention, and 61 of them (27 in the intervention group and 34 in the control group) underwent MRI scans twice. After excluding attrition bias, a significant time-by-group interaction on the Stroop Color-Word Test (SCWT; F = 51.85, p &lt; .001) was found, showing improvement in the intervention group and a decline in the control group. At the brain level, the intervention group exhibited increased axial diffusivity in the left posterior thalamic radiation, and this increase was significantly correlated with reduced SCWT reaction time (r = ‒0.42, p = .029). No significant time-by-group interactions were found for gray matter volume.

Conclusions
Our findings suggest that conducting multidomain adaptive CCT is an effective and feasible method to counteract cognitive decline in older adults, with WM neuroplasticity underpinning cognitive improvements. This study contributes to the understanding of the neural basis for the beneficial effect of CCT for older adults.
Does Consumer Credit Precede or Follow Health Among Older Adults? An Investigation in the Advanced Cognitive Training for Independent and Vital Elderly (ACTIVE) Trial
Authors: Dean Lorraine T , Chung Shang-En , Gross Alden L , Clay Olivio J , Willis Sherry L , McDonough Ian M , Thomas Kelsey R , Marsiske Michael , Aysola Jaya , Thorpe Roland J , Felix Cynthia , Berkowitz Melissa , Coe Norma B 
Published: February 2024

Abstract

Background and Objectives
Consumer credit has shown increasing relevance to the health of older adults; however, studies have not been able to assess the extent to which creditworthiness influences future health or health influences future creditworthiness. We assessed the relationships between 4-year pre and postmorbid consumer credit history and self-rated physical and mental health outcomes among older adults.

Research Design and Methods
Generalized estimating equations models assessed pre and postmorbid credit history (credit scores, derogatory accounts, and unpaid accounts in collections) and the onset of poor self-rated health (SF-36 score &lt;50) among 1,740 participants aged 65+ in the Advanced Cognitive Training for Independent and Vital Elderly study from 2001 to 2017, linked to TransUnion consumer credit data.

Results
In any given year, up to 1/4 of participants had a major derogatory, unpaid, or collections account, and up to 13% of the sample had poor health. Each 50-point increase in credit score trended toward a 5% lower odds of poor health in the next 1 year, a 6% lower odds in the next 2 years, and a statistically significant finding of 13% lower odds by 3 years. A drop in credit score was associated with a 10% greater odds of poor health in the next year, and having a major derogatory account was associated with an 86% greater odds of poor health in the next 3 years. After poor health onset, credit scores continued to see significant losses up to the 3 years, with larger decrements over time.

Discussion and Implications
Having a major derogatory account or a sudden loss in credit may be a time to monitor older adults for changes in health. After a downturn in health, supporting older adults to manage their debt may help stabilize their credit.
A survey on perceived medication guide reading and comprehension ease among US adults
Authors: Jones Paul R , Santiago Jonas , Pearsall Bryon M , Chu Dan-My , Wolff Carolyn , Kearsley Aaron 
Published: February 2024

Abstract
Medication guides (MGs) provide patients with important information about certain prescription drugs to help them take these drugs safely. We surveyed US residents about their perceptions of MG readability and understandability. We randomly sampled 5204 US residents (age 18+) from Ipsos’s KnowledgePanel to complete a two-part survey. Only respondents who reported receiving an MG with their prescription drugs (n = 3852) completed part 2, which included two key items: How easy to [(1)read/(2)understand] are the MGs that you have received from a pharmacy along with your prescription medicines? (1 = Very easy, 5 = Very difficult; reverse-coded). Health literacy (HL) and demographic data were also collected. After weighting our data, we found that 85% of respondents who reported receiving an MG perceived this information as ‘very easy’ (27.3%), ‘somewhat easy’ (28.3%) or ‘about average’ (29.3%) to read. Eighty-seven percent of respondents who reported receiving an MG perceived it as ‘very easy’ (27.6%), ‘somewhat easy’ (30.2%) or ‘about average’ (29.5%) to understand. ANOVAs revealed higher average perceived MG reading and comprehension ease scores among respondents presumed to have adequate versus inadequate HL (ps ≤ 0.0006). Younger or less-educated respondents and non-Hispanic Blacks perceived MGs as easier to read and understand, on average, than their counterparts (ps ≤ 0.0001). Many of these relationships remained intact in models predicting perceived MG reading and comprehension ease (ps ≤ 0.001). Adjusted R2 values across models were small, however (≤0.06). Our findings suggest most US residents (18+) who received MGs perceived them to be ‘about average’ to ‘very easy’ to read and understand.
Vcp overexpression and leucine supplementation extend lifespan and ameliorate neuromuscular junction phenotypes of a SOD1G93A-ALS mouse model
Authors: Huang Tzyy-Nan , Shih Yu-Tzu , Yen Tzu-Li , Hsueh Yi-Ping 
Published: February 2024

Abstract
Many genes with distinct molecular functions have been linked to genetically heterogeneous amyotrophic lateral sclerosis (ALS), including SuperOxide Dismutase 1 (SOD1) and Valosin-Containing Protein (VCP). SOD1 converts superoxide to oxygen and hydrogen peroxide. VCP acts as a chaperon to regulate protein degradation and synthesis and various other cellular responses. Although the functions of these two genes differ, in the current report we show that overexpression of wild-type VCP in mice enhances lifespan and maintains the size of neuromuscular junctions (NMJs) of both male and female SOD1G93A mice, a well-known ALS mouse model. Although VCP exerts multiple functions, its regulation of ER formation and consequent protein synthesis has been shown to play the most important role in controlling dendritic spine formation and social and memory behaviors. Given that SOD1 mutation results in protein accumulation and aggregation, it may direct VCP to the protein degradation pathway, thereby impairing protein synthesis. Since we previously showed that the protein synthesis defects caused by Vcp deficiency can be improved by leucine supplementation, to confirm the role of the VCP-protein synthesis pathway in SOD1-linked ALS, we applied leucine supplementation to SOD1G93A mice and, similar to Vcp overexpression, we found that it extends SOD1G93A mouse lifespan. In addition, the phenotypes of reduced muscle strength and fewer NMJs of SOD1G93A mice are also improved by leucine supplementation. These results support the existence of crosstalk between SOD1 and VCP and suggest a critical role for protein synthesis in ASL. Our study also implies a potential therapeutic treatment for ALS.
Safety and Immunogenicity of an mRNA-Based RSV Vaccine Including a 12-Month Booster in a Phase 1 Clinical Trial in Healthy Older Adults
Authors: Shaw Christine A , Essink Brandon , Harper Charles , Mithani Runa , Kapoor Archana , Dhar Rakesh , Wilson Lauren , Guo Ruiting , Panozzo Catherine A , Wilson Eleanor , Simorellis Alana K , Reuter Caroline , Stoszek Sonia K , Chen Grace L , Das Rituparna , Goswami Jaya 
Published: February 2024

Abstract

Background
An mRNA-based respiratory syncytial virus (RSV) vaccine, mRNA-1345, is under clinical investigation to address RSV disease burden in older adults.

Methods
Based on a randomized, observer-blind, placebo-controlled design, this phase 1 dose-ranging study evaluated the safety, reactogenicity, and immunogenicity of mRNA-1345 in adults aged 65 to 79 years. Participants were randomized to receive 1 dose of mRNA-1345 (12.5, 25, 50, 100, or 200 µg) or placebo and matched mRNA-1345 booster or placebo at 12 months.

Results
Overall, 298 participants received the first injection and 247 received the 12-month booster injection. mRNA-1345 was generally well tolerated after both injections, with the most frequently reported solicited adverse reactions being injection site pain, fatigue, headache, arthralgia, and myalgia. Reactogenicity was higher after the booster injection but with severity, time to onset, and duration similar to the first injection. A single mRNA-1345 injection boosted RSV-A and RSV-B neutralizing antibody titers and prefusion F binding antibody (preF bAb) concentrations at 1 month (geometric mean fold rises: RSV-A, 10.2–16.5; RSV-B, 5.3–12.5; preF bAb, 7.2–12.1). RSV antibody levels remained above baseline through 12 months, indicating immune persistence. A 12-month booster injection also increased RSV-A and RSV-B neutralizing antibody titers and preF bAb concentrations; titers after booster injection were numerically lower than those after the first dose, with overlapping 95% CIs.

Conclusions
mRNA-1345 was well tolerated and immunogenic following a single injection and a 12-month booster.

Clinical Trials Registration
NCT04528719 (ClinicalTrials.gov).
The New Creatinine-Based Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) 2021 Equation: Potential Impact on Screening for Chronic Kidney Disease in an Asymptomatic Black African Population
Authors: Omuse Geoffrey , Maina Daniel , Sokwala Ahmed 
Published: February 2024

Abstract

Background
In 2021, a new Chronic Kidney Disease Epidemiology (CKD-EPI) Collaboration equation was introduced that excluded race correction. We set out to compare estimated glomerular filtration rate (eGFR) determined using the creatinine-based CKD-EPI 2009 and 2021 equations and the reclassification of chronic kidney disease (CKD) eGFR staging to explore the potential ramifications of adopting the 2021 equation on reported eGFR and CKD staging.

Methods
We analyzed secondary data previously utilized to determine reference intervals among Black African individuals residing in urban towns in Kenya. Serum creatinine was measured using a standardized modified Jaffé kinetic method on a Beckman AU5800 analyzer. Glomerular filtration rate (GFR) was estimated using both the 2009 and 2021 CKD-EPI creatinine equations. Classification of CKD based on eGFR was performed using the Kidney Disease: Improving Global Outcomes (KDIGO) practice guidelines.

Results
Using 533 study samples, the median eGFR was highest when determined using the race-corrected CKD-EPI 2009 equation. The CKD-EPI 2021 equation yielded a median eGFR that was similar to the non-race–corrected CKD-EPI 2009 equation. The race-corrected CKD-EPI 2009 equation classified 93.6% of participants into CKD stage G1 compared with 85.6% by the CKD-EPI 2021 equation. The CKD-EPI 2021 equation classified 14.3% of participants into CKD stage G2 compared to 6.4% by the race-corrected CKD-EPI 2009 equation.

Conclusions
The CKD-EPI 2021 equation gave a comparable eGFR to the non-race–corrected CKD-EPI 2009 equation and its implementation in laboratories reporting eGFR in Kenya will help in identifying patients with an appropriate decrease in renal function.
Cardiovascular problems
Authors: Currow David , Clark Katherine , Kleinig Paul 
Published: February 2024

Abstract
Cardiovascular disease is associated with acute changes requiring emergency responses. In people with life-limiting illnesses, the same urgency is required when evaluating the options that should be discussed with the person and their family. The range of problems more often relate to comorbid illnesses than the life-limiting illness itself, given the risk factor that many people bring to their life-limiting illness. Simultaneously evaluating the person’s clinical condition, managing their symptoms, and discussing options for investigations and definitive treatments typify the challenges of clinical care for people with life-limiting illnesses.
Renal and metabolic disorders
Authors: Currow David , Clark Katherine , Kleinig Paul 
Published: February 2024

Abstract
Renal impairment is relatively prevalent in people with life-limiting illnesses. Reduced hydration and the many medications prescribed account for much of the renal impairment seen late in life. Other frequently encountered metabolic disorders include hypo- and hypernatraemia, and hypo- and hyperkalaemia. Although aggressive supportive care measures can be implemented, care should be taken to understand a person’s overall prognosis, and the wishes that they have for their future care.
Endocrine problems
Authors: Currow David , Clark Katherine , Kleinig Paul 
Published: February 2024

Abstract
Endocrine problems are often long term, but need considered management when someone is become frailer and losing weight late in life. Managing these difficult transitions will minimize the risks of acute changes that become symptomatic. Even with optimal management, there will be times that there are changes in the well-being of a person because of endocrine dysfunction. A low threshold for considering endocrine sources for otherwise unexplained changes or symptoms is often productive, especially those with gradual onset.
Neurology
Authors: Currow David , Clark Katherine , Kleinig Paul 
Published: February 2024

Abstract
Any neurological change is frightening. In the face of advanced illness, it is especially frightening with thoughts of whether this is the beginning of the end. History and physical examination that are sensitive to the fears and concerns of the person with the life-limiting illness are critical when there are neurological changes. The urgency of response is dictated by the speed with which irreversible damage can be done to neural tissue. Embolic stroke is now a neurological emergency given the opportunity to manage the clot and restore normal blood flow. Optimizing functional outcomes is critical to good care for neurological changes, even late in life.
Orthopaedic disorders
Authors: Currow David , Clark Katherine , Kleinig Paul 
Published: February 2024

Abstract
Orthopaedic problems require basic first aid of immobilizing above and below any fracture of a long bone and, with all fractures, analgesia while issues are being investigated. Careful imaging where a fracture is suspected will often disclose pathology that may not, at first, be apparent. Even in late-stage disease, surgical fixation may be indicated as the best way to palliate a fracture.
Neuroleptic Malignant Syndrome Versus Serotonin Syndrome
Authors: Gentry Jasmine , Lippert Katie 
Published: February 2024

Abstract
Serotonin syndrome and neuroleptic malignant syndrome (NMS) are iatrogenic syndromes that arise from the use of serotonin modulators and psychotropic drugs, respectively. Serotonin syndrome presents as mental status changes, autonomic nervous system disturbances, neurologic manifestations, and hyperthermia. Similarly, NMS presents as muscle rigidity, hyperpyrexia, mental status changes, and autonomic instability. Both are associated with high morbidity and potentially high mortality, making the diagnosis and discernment between the two critical. As clinical diagnoses, the constellation of features, associated offending agents, and progression of each syndrome over time are the keys to differentiating the two. Furthermore, the stabilization and treatment of both is focused on the management of an elevated temperature along with its ensuing effects on various organ systems.
To Chelate or Not to Chelate: When Too Much Iron Is Too Much
Authors: Hallett T. Christy 
Published: February 2024

Abstract
Iron is a transitional metal that plays an essential role in body processes. The GI tract regulates iron absorption. In overdoses, iron can be absorbed down a concentration gradient without hindrance due to the cytotoxic effects on the GI epithelium. Symptoms are unlikely to occur with ingestions of elemental iron less than 20 mg/kg. Initial symptoms include nausea, vomiting, and diarrhea. Iron overdoses inhibit oxidative phosphorylation and cause metabolic acidosis. Besides supportive care, treatment can include decontamination with whole-bowel irrigation, trending serum iron levels, and chelation therapy with IV deferoxamine at serum levels greater than 500 mcg/dL as well as for those with systemic symptoms of hypotension, multiorgan failure, or lethargy. Patients requiring prolonged deferoxamine therapy are at risk of Yersinia enterocolitica sepsis.
Beyond Benzos: Alcohol and Sedative-Hypnotic Withdrawal
Authors: Suen Kyle 
Published: February 2024

Abstract
Alcohol withdrawal syndrome is frequently encountered in EDs and managed by healthcare providers in the hospital. Alcohol withdrawal syndrome can vary in severity; milder cases can be managed outside a healthcare facility, and more serious cases should be managed in the hospital. Severity of alcohol withdrawal syndrome can be determined using severity scales. Serious manifestations of alcohol withdrawal syndrome can occur, such as alcohol withdrawal seizures and delirium tremens. Management of alcohol withdrawal syndrome involves administration of benzodiazepines, and dosing depends on clinical severity. Alcohol withdrawal syndrome may become resistant to first-line medications used, and additional medications may be required to prevent morbidity and mortality. Phenobarbital is recommended for benzodiazepine-resistant alcohol withdrawal syndrome and may also be used in delirium tremens.