bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development, Evaluation, and Initial Findings of New York State Department of Health Community Drug Checking Pilot Programs
Authors: Payne Emily R. , Thomas Guy J. , Fallico Matthew , Clear Allan , Gogia Maka , Zamboni Lucila 
Published: October 2024

Context:
The illicit drug landscape in the United States is dynamic, featuring a risky and erratic drug supply. Drug checking programs (DCP) have been successfully implemented and studied extensively in Canada and Europe but are scarce in the United States. Integrating DCP at harm reduction programs provides an opportunity to engage people at the point-of-care and deliver a combination of harm reduction services, access to healthcare services, and linkages to treatment.

Program:
The New York State Department of Health (NYSDOH) developed and supports operation of 8 pilot community DCP sites throughout the state. The DCP were trained to utilize Fourier-transform infrared spectroscopy (FTIR) technology to deliver real-time results to participants.

Implementation:
The NYSDOH community DCP pilot began development in 2022. Partnerships were formed across multiple domains including other DCP, universities, forensic laboratories, syringe service and harm reduction programs, and legal and regulatory offices within the NYSDOH. The first pilot sites began operating in mid-2023 and program expansion is on-going.

Evaluation:
Evaluation staff were extensively engaged in development and implementation phases. Qualitative evaluation focused on barriers, facilitators, and lessons learned from program staff and technicians. Quantitative evidence was gathered to assess the reach of the DCP and accuracy of results attained by drug checking technicians during their training periods. Drug checking results helped characterize the illicit drug supply.

Discussion:
Development and implementation of DCP in NYS was facilitated by strong partnerships across sectors including public health and harm reduction. DCP may involve diverse partners who do not regularly collaborate, and health departments are positioned to build relationships and convene partners for program implementation. Evaluation findings highlight the importance of facilitating on-going training and technical assistance to DCP for quality assurance. The initial successes and lessons learned from the NYSDOH DCP demonstrate state public health departments’ ability to successfully deploy this innovative harm reduction strategy.
Breast Metastasis From Sigmoid Adenocarcinoma Revealed by FDG PET/CT
Authors: Liu Yanlin , Dai Hongyuan , Su Minggang , Huang Rui 
Published: October 2024

Abstract
Breast metastasis from sigmoid carcinoma is rare. A 32-year-old woman, who had a history of sigmoid carcinoma, was found a hypermetabolic soft tissue mass in the left breast and a lymph node with moderate uptake on FDG PET/CT. Final pathology supported that the breast mass and lymph node were both metastases from the sigmoid carcinoma.
FDG PET/CT in a Case of Esophageal Schwannoma
Authors: Zhang Jun , Ji Xia , Dong Aisheng 
Published: October 2024

Abstract
Esophageal schwannoma is very rare. We describe FDG PET/CT findings in a case of benign esophageal schwannoma. Endoscopic ultrasound showed the tumor was located in the muscular layer of the esophagus. FDG PET/CT showed intense FDG uptake with SUVmax of 10 of the tumor mimicking malignancy. This case indicates that schwannoma should be included in the differential diagnosis of esophageal FDG-avid lesions.
Mildly Increased 68Ga-Pentixafor Uptake in Hepatic Hemangioma
Authors: Yang Lixiang , Huang Mingxing , Tian Rong , Li Qianrui 
Published: October 2024

Abstract

68Ga-pentixafor uptake in hemangioma is rare. We report 68Ga-pentixafor PET/MRI findings of a hepatic hemangioma in a 54-year-old woman. The images revealed a hyperintense lesion in the right posterior liver on T2-weighted images, with mild pentixafor uptake. The lesion was consistent with typical presentations of a hemangioma on MRI and contrast-enhanced CT.
Perinephric Extramedullary Disease in Multiple Myeloma
Authors: Koichi Alex , Zemianschi Razvan , Manzil Fathima Fijula Palot , Eichhorn Joshua 
Published: October 2024

Abstract
Extramedullary disease represents an aggressive form of multiple myeloma occurring outside the skeleton and is a poor prognostic indicator. Extramedullary disease most commonly involves the skin, muscle, pleura, lymph nodes, liver, and central nervous system. Infrequently, extramedullary disease can involve the kidneys or perirenal space. We present 3 cases of perirenal involvement of extramedullary disease on 18F-FDG PET/CT confirmed with tissue sampling as plasma cell infiltration. Within the limitation of physiologic activity in the kidneys due to 18F-FDG excretion, close consideration is essential when evaluating multiple myeloma patients for genitourinary involvement as it can resemble other malignancies, hemorrhage, or renal injury.
FDG Uptake in Brown Adipose Tissue Activated by a Long-Acting β2-Adrenergic Receptor Agonist Inhaler Prescribed for Bronchial Asthma
Authors: Nitta Akira , Kotani Tomoya , Okuyama Chio 
Published: October 2024

Abstract
We herein report a case of an elderly woman in whom brown adipose tissue (BAT) was visible on 18F-FDG PET imaging performed in the summer. In this patient, none of the well-known factors that induce BAT activation in adults, including cold exposure, catecholamine-producing tumors, or β3-adrenergic receptor agonists administration, were present. Daily inhalation of a long-acting β2-adrenergic agonist for treatment of her bronchial asthma was considered the cause of her BAT visualization. This case suggests the need to consider β2-adrenergic receptor agonists as a cause of BAT visualization.
Residual Ultrasound-Enhancing Agents Mimicking Portal Venous Gas
Authors: Bitar Ryan , Langdon Jonathan , Kaur Manroop , Crandall Ian , McNamara Robert , Revzin Margarita 
Published: October 2024

Abstract
Sonographic detection of mobile echogenic foci within the main portal vein and its branches or within the liver parenchyma extending along the portal triads to the periphery of the liver is an alarming finding that has been associated with portal venous gas in the setting of bowel ischemia. Ultrasound-enhancing agents (UEAs) have been widely utilized in abdominal ultrasound for evaluation of organ neoplasms and vascular patency as well as in echocardiography for the evaluation of cardiac function. The appearance of UEAs on abdominal ultrasound can resemble gas like that seen in the portal venous system and liver in patients with bowel ischemia; therefore, UEA residuals should always be a part of the differential diagnosis of echogenic foci when seen on abdominal ultrasounds with preceding recent UEA administration. In this observational study, we present a series of cases with suspected portal venous gas suspicious for bowel ischemia that turned out to be a result of residual or persistent UEA from the recent contrast-enhanced echocardiography. Discussion of this phenomenon and its potential explanation is provided.
Injectable Janus Base Nanomatrix (JBNm) in Maintaining Long-Term Homeostasis of Regenerated Cartilage for Tissue Chip Applications
Authors: Yau Anne , Sands Ian , Zhang Wuxia , Chen Yupeng 
Published: October 2024

AbstractEngineered cartilage tissues have wide applications in in vivo cartilage repair as well as in vitro models, such as cartilage-on-a-chip or cartilage tissue chips. Currently, most cartilage tissue engineering approaches focus on promoting chondrogenesis of stem cells to produce regenerated cartilage. However, this regenerated cartilage can dedifferentiate into fibrotic tissue or further differentiate into hypertrophic or calcified cartilage. One of the most challenging objectives in cartilage tissue engineering is to maintain long-term cartilage homeostasis. Since the microenvironment of engineered cartilage tissue is crucial for stem cell adhesion, proliferation, differentiation, and function, we aim to develop a novel scaffold that can maintain the long-term homeostasis of regenerated cartilage. Therefore, we developed a library of Janus base nanomatrices (JBNms), composed of DNA-inspired Janus nanotubes (JBNts) as well as cartilage extracellular matrix (ECM) proteins. The JBNms were developed to selectively promote chondro-lineage cell functions while inhibiting bone and endothelial cell growth. More importantly, the JBNm can effectively promote chondrogenesis while inhibiting hypertrophy, osteogenesis, angiogenesis, and dedifferentiation. Additionally, the JBNm is injectable, forming a solid scaffold suitable for producing and maintaining regenerated cartilage tissue in microfluidic chips, making it ideal for tissue chip applications. In this study, we successfully created cartilage tissue chips using JBNms. These chips can model cartilage tissue even after long-term culture and can also mimic arthritis progression, making them useful for drug screening. Thus, we have developed a novel nanomaterial approach for improved cartilage tissue engineering and cartilage tissue chip applications.
Arabidopsis 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthases of the shikimate pathway display both manganese- and cobalt-dependent activities
Authors: Yokoyama Ryo , Maeda Hiroshi A 
Published: October 2024

AbstractThe plant shikimate pathway directs a significant portion of photosynthetically assimilated carbon into the downstream biosynthetic pathways of aromatic amino acids (AAA) and aromatic natural products. 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase (DHS) catalyzes the first step of the shikimate pathway, playing a critical role in controlling the carbon flux from central carbon metabolism into the AAA biosynthesis. Previous biochemical studies suggested the presence of manganese- and cobalt-dependent DHS enzymes (DHS-Mn and DHS-Co, respectively) in various plant species. Unlike well-studied DHS-Mn, however, the identity of DHS-Co is still unknown. Here, we show that all three DHS isoforms ofArabidopsis thalianaexhibit both DHS-Mn and DHS-Co activitiesin vitro. A phylogenetic analysis of various DHS orthologs and related sequences showed that Arabidopsis 3-deoxy-D-manno-octulosonate-8-phosphate synthase (KDOPS) proteins were closely related to microbial Type I DHSs. Despite their sequence similarity, these Arabidopsis KDOPS proteins showed no DHS activity. Meanwhile, optimization of the DHS assay conditions led to the successful detection of DHS-Co activity from Arabidopsis DHS recombinant proteins. Compared to DHS-Mn, DHS-Co activity displayed the same redox dependency but distinct optimal pH and cofactor sensitivity. Our work provides biochemical evidence that the DHS isoforms of Arabidopsis possess DHS-Co activity.
Unique belowground ecological strategies of subtropical and tropical plant species expand the root trait space
Authors: Guerrero-Ramírez Nathaly R. , Weemstra Monique , Addo-Danso Shalom D. , Andersen Kelly , Arnaud Marie , Cordeiro Amanda L. , Cusack Daniela F. , Kotowska Martyna M. , Lee Ming Yang , Leroy Céline , Lugli Laynara F. , Pierick Kerstin , Smith-Martin Chris M. , Toro Laura , Umaña María Natalia , Valverde-Barrantes Oscar J , Wong Michelle , Fortunel Claire 
Published: October 2024

AbstractRoot trait variation may reflect the ecological and evolutionary processes shaping biodiversity, but remains poorly quantified in the (sub)tropics. Here, we aim to further complete our knowledge of belowground functional strategies by assessing the contributions of subtropical and tropical species to global root trait diversity. We gathered root data for 1618 temperate, 341 subtropical, and 775 tropical species. We compared functional diversity among biomes and calculated the unique contribution of each biome to the global root economics space. Further, we determined if the within-variation of subtropical and tropical biomes is shaped by species’ niches and/or differences in evolutionary history. Root trait expressions differed among biomes, but root functional diversity did not. Furthermore, subtropical and tropical biomes accounted for 40% of the unique root functional space within the global traits space. Species’ climate niches and phylogenetic turnover explained variation in root traits (e.g., denser root tissue was associated with drier sites) among subtropical but not tropical species. Through their unique root traits, sub(tropical) species strongly expand the current ‘global’ root trait space. This work underwrites their importance in conceptual models for more complete insights into how various belowground strategies drive plant functional biogeography and biodiversity globally.
Assessing the Alignment of Biomedical Research and Clinical Translation
Authors: Sun Mengyi , Stoeger Thomas , Nunes Amaral Luís A 
Published: October 2024

AbstractMore than half of all drug clinical trials fail due to lack of efficacy, highlighting gaps in our understanding of disease-target relationships. While it is widely believed that scientific research is essential for identifying drug-targets, whether scientists can allocate their research attention according to the clinical potential of disease-target relationships is unknown. To answer this question, we analyzed data from Open Targets, a comprehensive disease-target relationship platform. By building an open pipeline that follows drugs through consecutive clinical trial phases, we demonstrate that research attention in the disease-specific primary literature can predict trial success. However, research attention toward specific targets are not predictive for overall trial success across diseases. Our study thus highlights the crucial, yet complex, role of the primary research literature in steering clinical trials, encouraging a more nuanced approach to translational medicine.
James-Stein estimator improves accuracy and sample efficiency in human kinematic and metabolic data
Authors: Alwan Aya , Srinivasan Manoj 
Published: October 2024

AbstractHuman biomechanical data are often accompanied with measurement noise and behavioral variability. Errors due to such noise and variability are usually exaggerated by fewer trials or shorter trial durations, and could be reduced using more trials or longer trial durations. Speeding up such data collection by lowering number of trials or trial duration, while improving the accuracy of statistical estimates, would be of particular interest in wearable robotics applications and when the human population studied is vulnerable (e.g., the elderly). Here, we propose the use of the James-Stein estimator (JSE) to improve statistical estimates with a given amount of data, or reduce the amount of data needed for a given accuracy. The JSE is a shrinkage estimator that produces a uniform reduction in the summed squared errors when compared to the more familiar maximum likelihood estimator (MLE), simple averages, or other least squares regressions. When data from multiple human participants are available, an individual participant’s JSE can improve upon MLE by incorporating information from all participants, improving overall estimation accuracy on average. Here, we apply the JSE to multiple time-series of kinematic and metabolic data from the following parameter estimation problems: foot placement control during level walking, energy expenditure during circle walking, and energy expenditure during resting. We show that the resulting estimates improve accuracy — that is, the James-Stein estimates have lower summed squared error from the ‘true’ value compared to more conventional estimates.
Species-specific loss of genetic diversity and exposure of deleterious mutations following agricultural intensification
Authors: Nolen Zachary J. , Jamelska Patrycja , Lara Ana Sofia Torres , Wahlberg Niklas , Runemark Anna 
Published: October 2024

AbstractAgriculture driven land-use change is a major contributor to insect declines globally. As a result of population decline and subdivision, species lose genetic diversity, potentially reducing adaptive potential and increasing genetic load, reinforcing decline. We examine how genetic diversity has changed over the past century in three Polyommatinae butterfly species in Sweden, leveraging genome sequencing of specimens from museum collections. Based on 63 historical and 92 contemporary genomes, we document a general decline in genetic diversity and reveal that the extent of decline depends on habitat specialization. The habitat generalist has retained most of its genetic diversity and connectivity. In contrast, the two specialists have declined sufficiently that even common variation is being eroded by drift, with up to a 3.3% reduction in heterozygosity per decade in the strongly grassland associatedCyaniris semiargus. While this sharp decline has reduced the burden of strongly deleterious mutations in the specialist species, increased population isolation has led to inbreeding inCy. semiargus, exposing a greater proportion of weakly deleterious mutations in homozygous state. This realized burden likely reduces mean fitness and reinforces population decline, highlighting the need for well-connected grassland landscapes to maintain grassland specialist functional connectivity and genetic diversity. We complement these analyses with seven additional Polyommatinae species, uncovering that declines are common across the group, with alarming rates of genetic decline in species listed as viable. This study highlights the urgency of incorporating genetic data into conservation planning, as threats from genetic erosion are not captured by current conservation assessment.
RELEASE: REdressing Long-tErm Antidepressant uSE in adults in general practice (RELEASE): A two-arm parallel-group cluster RCT effectiveness-implementation hybrid type-1 study
Authors:   a pragmatic multicentre, superiority, parallel group, controlled study of participants allocated to a multi-strategy intervention vs Usual Care, Wallis Katharine , Donald Maria , Horowitz Mark , Ware Rob , Byrnes Joshua , Moncrieff Joanna , Zwar Nicholas , Scott Ian , Morgan Mark , Freeman Christopher , Gill Neeraj , Sturman Nancy , Geraghty Adam , Partanen Riitta , Lynch Johanna 
Published: October 2024

AbstractThe REdressing Long-tErm Antidepressant uSE in general practice (RELEASE) trial is a pragmatic cluster randomized controlled trial (cRCT) that seeks to determine whether a novel multi-strategy intervention that supports safe cessation of long-term antidepressants is superior to Usual Care.1Pragmatic trials are designed to determine how well interventions work in clinical practice under everyday conditions.2The multi-strategy intervention has two forms, known as RELEASE and RELEASE+. RELEASE for patients includes direct patient education and resources3and an invitation to medication review; RELEASE for general practitioners (GPs) includes education, training in the brief intervention (Ask, Advise, Assist) and printable resources via practice management software. RELEASE+ additionally includes for patients links to freely available information online via an App, and for GPs clinical audit and feedback on practice prescribing of antidepressants. Patient directed education material has the potential to support safer prescribing, including in this case improved recognition and management of antidepressant withdrawal symptoms.4, 5Brief interventions have the potential to change GP prescribing behaviour.6The primary comparison of interest is whether any RELEASE intervention is superior to Usual Care. A secondary comparison will be between the two types of RELEASE interventions (RELEASE and RELEASE+).The purpose of this document is to minimise bias and ensure transparency and internal validity for the findings of the trial, by defining and making publicly available the analysis approach prior to reviewing or analysing trial data. The statistical analysis plan (SAP) will inform analysis and reporting of the main effectiveness findings of the trial. It provides a detailed description of the primary and secondary trial outcomes and the methods for statistical comparison.
Evaluation of the Impact of a 90-day Mortality Prediction Model Integrated in the EHR for Advanced Care Planning*
Authors: Rossi Lorenzo A. , Roberts Laura , Olivares Marinel , Christian Amis , Mooney Stefanie , Morse Denise , Zachariah Finly 
Published: October 2024

AbstractMedical centers have begun to integrate AI models for mortality prediction in their electronic health records (EHR) systems to support advance care planning.1There is evidence that advance care planning can reduce suffering and unwanted, costly treatment near the end of life.2To better target patients at a risk of death with advance directive (AD) capture and goals of care (GOC) conversations at our comprehensive cancer center, we developed and integrated a 90-day mortality prediction model in the EHR. The model has been live since February, 2021. Performance in production has matched very closely pre-production pilots, achieving an 85% AUROC (AI Showcase Stage I). We implemented 4 clinical decision support (CDS) tools driven by the model to promote goal concordant care in inpatient and outpatient encounters (AI Showcase Stage II).3In this document, we analyze the impact of one of the aforementioned CDS applications, implemented as an inter-ruptive alert for the clinical social workers (CSWs) to facilitate advance directive (AD) completion in the inpatient setting. We also present preliminary results on volumes of GOC conversations prompted by one of the model-driven alerts. Our analysis is based on 12 months of data, collected between March 1, 2021 and February 28, 2022.The challenges for our assessment included inconsistent EHR documentation practices, coexistence with (traditional) non-AI driven processes tasked for similar goals and many external factors that can affect target outcomes. We believe such challenges to be rather common across healthcare organizations integrating AI in their workflows.
Enhanced RNA-targeting CRISPR-Cas technology in zebrafish
Authors: Moreno-Sanchez Ismael , Hernandez-Huertas Luis , Nahon-Cano Daniel , Gomez-Marin Carlos , Martinez-García Pedro Manuel , Treichel Anthony J. , Tomas-Gallardo Laura , da Silva Pescador Gabriel , Kushawah Gopal , Díaz-Moscoso Alejandro , Cano-Ruiz Alejandra , Walker John A. , Muñoz Manuel J. , Holden Kevin , Galcerán Joan , Nieto María Ángela , Bazzini Ariel , Moreno-Mateos Miguel A. 
Published: October 2024

SummaryCRISPR-Cas13 systems are widely used in basic and applied sciences. However, its application has recently generated controversy due to collateral activity in mammalian cells and mouse models. Moreover, its efficiency could be improved in vivo. Here, we optimized transient formulations as ribonucleoprotein complexes or mRNA-gRNA combinations to enhance the CRISPR-RfxCas13d system in zebrafish. We i) used chemically modified gRNAs to allow more penetrant loss-of-function phenotypes, ii) improved nuclear RNA-targeting, and iii) compared different computational models and determined the most accurate to predict gRNA activity in vivo. Furthermore, we demonstrated that transient CRISPR-RfxCas13d can effectively deplete endogenous mRNAs in zebrafish embryos without inducing collateral effects, except when targeting extremely abundant and ectopic RNAs. Finally, we implemented alternative RNA-targeting CRISPR-Cas systems with reduced or absent collateral activity. Altogether, these findings contribute to CRISPR-Cas technology optimization for RNA targeting in zebrafish through transient approaches and assist in the progression of in vivo applications.