bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in Symptom Clusters Among Asian American Breast Cancer Survivors in Technology-Based Coaching Intervention
Authors: Min Se Hee , Chee Wonshik , Im Eun-Ok 
Published: January 2024

Background
Limited research studies have focused on examining the impact of technology-based interventions in changing symptom clusters among Asian American breast cancer survivors.

Objective
The aim of this study was to understand the longitudinal impact of a technology-based program on the symptom cluster experience of Asian American breast cancer survivors.

Methods
This is a secondary data analysis that used exploratory factor analysis at each time point (baseline, post–1 month, post–3 months) for the control and intervention groups (N = 199).

Results
The number of symptom clusters remained the same, and the same symptoms remained in similar clusters across the 2 groups. The control group experienced psychological cluster, fatigue cluster, and neck/skin cluster at baseline; psychological cluster, fatigue/dizzy cluster, and neck/skin cluster at post–1 month; and psychological cluster, fatigue/dizzy cluster, and somatic cluster at post–3 months. The intervention group experienced psychological cluster, neck cluster, and appetite/itching cluster at baseline; somatic/anticholinergic cluster, psychological/sexual cluster, and appetite cluster at post–1 month; and psychological cluster, neck cluster, and itching cluster at post–3 months. The psychological and neck clusters shared similar core symptoms of feeling nervous, dry mouth, and cough between the control and intervention groups.

Conclusion
The different symptom cluster experiences may be due to the technology-based intervention where the intervention group receives individual/group coaching/support that may have changed symptom clusters over time. Yet, the true efficacy of the intervention on symptom clusters warrants further investigation.

Implications for Practice
Clinicians should understand the changes in symptom clusters as well as the presence of core symptoms and take a targeted symptom cluster approach in clinical settings.
Female Homicide Victims in Cook County, Illinois
Authors: Gitto Lorenzo , Tarozzi Ilaria , Arunkumar Ponni 
Published: January 2024

Abstract
Female homicide is a broad term that includes any homicide in which the victim is a female, representing the most extreme form of violence against women. This study investigated the characteristics of female homicides to determine the types and characteristics of injury, circumstances of the events, and other aspects in this specific population. The Cook County Medical Examiner's Office files were searched for homicides in female subjects between January 2017 and January 2022, with no limits for age, race, or cause of death. A total of 527 cases met the criteria. Most homicides occurred in Chicago during the summer. The most common cause of death was firearm(s) wounds, followed by sharp force traumas, asphyxia, and blunt force injuries. The remaining deaths were due to combined and “other” mechanisms. Different patterns of injuries were observed at the autopsy. Alleged offenders were mostly male subjects and were frequently in a romantic relationship with the victim, and the reasons for homicide were related to jealousy and personal conflicts. This study offers an overview of homicidal deaths in female subjects in a large metropolitan area.
Pneumocystis jirovecii in solid organ transplant recipients: updates in epidemiology, diagnosis, treatment, and prevention
Authors: Saadatzadeh Tirajeh , Angarone Michael , Stosor Valentina 
Published: January 2024

Purpose of review
This review highlights the epidemiology of Pneumocystis jirovecii pneumonia in solid organ transplant recipients, advancements in the diagnostic landscape, and updates in treatment and prevention.

Recent findings
The increasing use of immune-depleting agents in the context of solid organ transplantation has given rise to P. jirovecii pneumonia in this population. The use of prophylaxis has dramatically reduced risk of infection; however, late-onset infections occur after cessation of prophylaxis and in the setting of lymphopenia, advancing patient age, acute allograft rejection, and cytomegalovirus infection. Diagnosis requires respiratory specimens, with PCR detection of Pneumocystis replacing traditional staining methods. Quantitative PCR may be a useful adjunct to differentiate between infection and colonization. Metagenomic next-generation sequencing is gaining attention as a noninvasive diagnostic tool. Trimethoprim-sulfamethoxazole remains the drug of choice for treatment and prevention of Pneumocystis pneumonia. Novel antifungal agents are under investigation.

Summary

P. jirovecii is a fungal opportunistic pathogen that remains a cause of significant morbidity and mortality in solid organ transplant recipients. Early detection and timely treatment remain the pillars of management.
Proposal of New ypStage Grouping System for Patients With Esophageal Squamous Cell Carcinoma Who Underwent Neoadjuvant Chemoradiotherapy Followed by Surgery
Authors: Park Seong Yong , Park Boram , Yun Jae Kwang , Kim Hyeong Ryul , Kim Yong-Hee , Jeon Yeong Jeong , Lee Junghee , Cho Jong Ho , Choi Yong Soo , Zo Jae Il , Shim Young Mog , Kim Hong Kwan 
Published: January 2024

Objective:
To propose a new ypTNM grouping system to address limitations and improve prognostic relevance.

Background:
The current eighth edition of the American Joint Committee on Cancer (AJCC) ypStage system shows unsatisfactory prognostic relevance in patients with esophageal squamous cell carcinoma (ESCC) treated with neoadjuvant chemoradiotherapy (nCRT), followed by esophagectomy.

Methods:
The study cohort included 501 patients with ESCC who received nCRT, followed by esophagectomy at the Samsung Medical Center in Korea between 1994 and 2018 (development cohort), and 422 patients treated at Asan Medical Center (validation cohort). Recursive partitioning with a tree-structured regression model was used to develop and validate a new ypStage grouping system.

Results:
In the new ypStage grouping system, ypStage I include ypT0N0 only, ypStage II includes ypTis–T2N0 or ypT0–T2N1, ypStage III includes ypT3N0–N1, and ypStage IV includes ypT4N0–N1 or ypTanyN2–3. This system adequately addressed the limitations of the existing AJCC classification system, including overlapping and reversal of survival rates. Moreover, the discrimination ability of the new system was higher than that of the existing system [concordance-index (C-index): 61.9%] in the development (C-index: 66.6%) and validation (C-index: 66.0%) cohorts. NRIe was 0.17 (95% CI: 0.09–0.26, P < 0.001) and 0.18 (95% CI: 0.10–0.27, P <0.001) in the development and validation cohorts, respectively.

Conclusions:
The current study proposes a clear revised version of the eighth edition of the AJCC ypStage grouping system that exhibits superior prognostic stratification in patients with ESCC treated with nCRT, followed by esophagectomy.
Kufor-Rakeb Syndrome-Associated Psychosis: A Novel Loss-of-FunctionATP13A2Variant and Response to Treatment
Authors: Colijn Mark , Vrijsen Stephanie , Au Ping Yee Billie , El Asrar Rania Abu , Houdou Marine , Van den haute Chris , Sarna Justyna , Montgomery Greg , Vangheluwe Peter 
Published: January 2024

AbstractBiallelic (autosomal recessive) pathogenic variants in ATP13A2 cause a form of juvenile-onset parkinsonism, termed Kufor-Rakeb syndrome. In addition to motor symptoms, a variety of other neurological and psychiatric symptoms may occur in affected individuals, including supranuclear gaze palsy, spasticity, and cognitive decline. Although psychotic symptoms are often reported, response to antipsychotic therapy is not well described in previous case reports/series. As such, we describe treatment response in an individual with Kufor-Rakeb syndrome-associated psychosis. His disease was caused by a homozygous novel loss-of-function ATP13A2 variant (NM_022089.4, c.1970_1975del) that was characterized in this study. Our patient exhibited a good response to quetiapine monotherapy, which he has so far tolerated well. We also reviewed the literature and summarized all previous descriptions of antipsychotic treatment response. Although its use has infrequently been described in Kufor-Rakeb syndrome, quetiapine is commonly used in other degenerative parkinsonian disorders, given its lower propensity to cause extrapyramidal symptoms. As such, quetiapine should be considered in the treatment of Kufor-Rakeb syndrome-associated psychosis, when antipsychotic therapy is deemed necessary.
DR-GPT: a large language model for medical report analysis of diabetic retinopathy patients
Authors: Jaskari Joel , Sahlsten Jaakko , Summanen Paula , Moilanen Jukka , Lehtola Erika , Aho Marjo , Säpyskä Elina , Hietala Kustaa , Kaski Kimmo 
Published: January 2024

AbstractDiabetic retinopathy (DR) is a sight-threatening condition caused by diabetes. Screening programmes for DR include eye examinations, where the patient’s fundi are photographed, and the findings, including DR severity, are recorded in the medical report. However, statistical analyses based on DR severity require structured labels that calls for laborious manual annotation process if the report format is unstructured. In this work, we propose a large language model DR-GPT for classification of the DR severity from unstructured medical reports. On a clinical set of medical reports, DR-GPT reaches 0.975 quadratic weighted Cohen’s kappa using truncated Early Treatment Diabetic Retinopathy Study scale. When DR-GPT annotations for unlabeled data are paired with corresponding fundus images, the additional data improves image classifier performance with statistical significance. Our analysis shows that large language models can be applied for unstructured medical report databases to classify diabetic retinopathy with a variety of applications.
Bacterial exonuclease III expands its enzymatic activities on single-stranded DNA
Authors: Wang Hao , Ye Chen , Lu Qi , Jiang Zhijie , Jiang Chao , Zhou Chun , Li Na , Zhang Caiqiao , Zhao Guoping , Yue Min , Li Yan 
Published: January 2024

AbstractBacterial exonuclease III (ExoIII), widely acknowledged for specifically targeting double-stranded DNA (dsDNA), has been documented as a DNA repair-associated nuclease with apurinic/apyrimidinic (AP)-endonuclease and 3′→5′ exonuclease activities. Due to these enzymatic properties, ExoIII has been broadly applied in molecular biosensors. Here, we demonstrate that ExoIII (Escherichia coli) possesses highly active enzymatic activities on ssDNA. By using a range of ssDNA fluorescence-quenching reporters and fluorophore-labelled probes coupled with mass spectrometry analysis, we found ExoIII cleaved the ssDNA at 5′-bond of phosphodiester from 3′ to 5′ end by both exonuclease and endonuclease activities. Additional point mutation analysis identified the critical residues for the ssDNase action of ExoIII and suggested the activity shared the same active center with the dsDNA-targeted activities of ExoIII. Notably, ExoIII could also digest the dsDNA structures containing 3′-end ssDNA. Considering most ExoIII-assisted molecular biosensors require the involvement of single-stranded DNA (ssDNA) or nucleic acid aptamer containing ssDNA, the activity will lead to low efficiency or false positive outcome. Our study revealed the multi-enzymatic activity and the underlying molecular mechanism of ExoIII on ssDNA, illuminating novel insights for understanding its biological roles in DNA repair and the rational design of ExoIII-ssDNA involved diagnostics.
Utilizing Natural Language Processing and Large Language Models in the Diagnosis and Prediction of Infectious Diseases: A Systematic Review
Authors: Omar Mahmud , Brin Dana , Glicksberg Benjamin , Klang Eyal 
Published: January 2024

AbstractBackgroundNatural Language Processing (NLP) and Large Language Models (LLMs) hold largely untapped potential in infectious disease management. This review explores their current use and uncovers areas needing more attention.MethodsThis analysis followed systematic review procedures, registered with PROSPERO. We conducted a search across major databases including PubMed, Embase, Web of Science, and Scopus, up to December 2023, using keywords related to NLP, LLM, and infectious diseases. We also employed the QUADAS-2 tool for evaluating the quality and robustness of the included studies.ResultsOur review identified 15 studies with diverse applications of NLP in infectious disease management. Notable examples include GPT-4’s application in detecting urinary tract infections and BERTweet’s use in Lyme Disease surveillance through social media analysis. These models demonstrated effective disease monitoring and public health tracking capabilities. However, the effectiveness varied across studies. For instance, while some NLP tools showed high accuracy in pneumonia detection and high sensitivity in identifying invasive mold diseases from medical reports, others fell short in areas like bloodstream infection management.ConclusionThis review highlights the yet-to-be-fully-realized promise of NLP and LLMs in infectious disease management. It calls for more exploration to fully harness AI’s capabilities, particularly in the areas of diagnosis, surveillance, predicting disease courses, and tracking epidemiological trends.
Leveraging Multi-Echo EPI to Enhance BOLD Sensitivity in Task-based Olfactory fMRI
Authors: Zhao Ludwig Sichen , Raithel Clara U. , Tisdall M. Dylan , Detre John A. , Gottfried Jay A. 
Published: January 2024

AbstractFunctional magnetic resonance imaging (fMRI) using blood-oxygenation-level-dependent (BOLD) contrast relies on gradient echo echo-planar imaging (GE-EPI) to quantify dynamic susceptibility changes associated with the hemodynamic response to neural activity. However, acquiring BOLD fMRI in human olfactory regions is particularly challenging due to their proximity to the sinuses where large susceptibility gradients induce magnetic field distortions. BOLD fMRI of the human olfactory system is further complicated by respiratory artifacts that are highly correlated with event onsets in olfactory tasks.Multi-echo EPI (ME-EPI) acquires gradient echo data at multiple echo times (TEs) during a single acquisition and can leverage signal evolution over the multiple echo times to enhance BOLD sensitivity and reduce artifactual signal contributions. In the current study, we developed a ME-EPI acquisition protocol for olfactory task-based fMRI and demonstrated significant improvement in BOLD signal sensitivity over conventional single-echo EPI (1E-EPI). The observed improvement arose from both an increase in BOLD signal changes through aT2*-weighted echo combination and a reduction in non-BOLD artifacts through the application of the Multi-Echo Independent Components Analysis (ME-ICA) denoising method. This study represents one of the first direct comparisons between 1E-EPI and ME-EPI in high-susceptibility regions and provides compelling evidence in favor of using ME-EPI for future task-based fMRI studies.
Staphylococcus aureuscounters organic acid anion-mediated inhibition of peptidoglycan cross-linking through robust alanine racemase activity
Authors: Panda Sasmita , Jayasinghe Yahani P. , Shinde Dhananjay D. , Bueno Emilio , Stastny Amanda , Bertrand Blake P. , Chaudhari Sujata S. , Kielian Tammy , Cava Felipe , Ronning Donald R. , Thomas Vinai C. 
Published: January 2024

AbstractWeak organic acids are commonly found in host niches colonized by bacteria, and they can inhibit bacterial growth as the environment becomes acidic. This inhibition is often attributed to the toxicity resulting from the accumulation of high concentrations of organic anions in the cytosol, which disrupts cellular homeostasis. However, the precise cellular targets that organic anions poison and the mechanisms used to counter organic anion intoxication in bacteria have not been elucidated. Here, we utilize acetic acid, a weak organic acid abundantly found in the gut to investigate its impact on the growth ofStaphylococcus aureus. We demonstrate that acetate anions bind to and inhibit D-alanyl-D-alanine ligase (Ddl) activity inS. aureus. Ddl inhibition reduces intracellular D-alanyl-D-alanine (D-Ala-D-Ala) levels, compromising staphylococcal peptidoglycan cross-linking and cell wall integrity. To overcome the effects of acetate-mediated Ddl inhibition,S. aureusmaintains a substantial intracellular D-Ala pool through alanine racemase (Alr1) activity and additionally limits the flux of D-Ala to D-glutamate by controlling D-alanine aminotransferase (Dat) activity. Surprisingly, themodus operandiof acetate intoxication inS. aureusis common to multiple biologically relevant weak organic acids indicating that Ddl is a conserved target of small organic anions. These findings suggest thatS. aureusmay have evolved to maintain high intracellular D-Ala concentrations, partly to counter organic anion intoxication.SignificanceUnder mildly acidic conditions, weak organic acids like acetic acid accumulate to high concentrations within the cytosol as organic anions. However, the physiological consequence of organic anion accumulation is poorly defined. Here we investigate how the acetate anion impactsS. aureus. We show that acetate anions directly bind Ddl and inhibit its activity. The resulting decrease in intracellular D-Ala-D-Ala pools impacts peptidoglycan integrity. Since acetate is a weak inhibitor of Ddl, mechanisms that maintain a high intracellular D-Ala pools are sufficient to counter the effect of acetate-mediated Ddl inhibition inS. aureus.
The threshold for intracranial self-stimulation does not increase in rats exposed to chronic unpredictable stress - a systematic review and meta–analysis
Authors: Berrio Jenny P. , Wilzopolski Jenny , Hohlbaum Katharina , Kalliokoski Otto 
Published: January 2024

AbstractThe chronic unpredictable stress model is a laboratory rodent model of stress-induced anhedonia. The sucrose preference test, often used to validate it, suffers from being unreliable. Intracranial self-stimulation offers an alternative and is often cited as supporting evidence of the validity of the model. Our aim was to assess whether an increased self-stimulation threshold is found after stress and if such a change correlates with decreases in sweet consumption. We searched PubMed, Embase, and Web of Science for studies in rats exposed to chronic unpredictable stress that employed intracranial self-stimulation. Thresholds, for stressed and control animals, in 23 experiments (11 studies) were pooled. Over 50% of the data was contributed by one research group, so a three-level meta-analytical random effects model was fit to account for methodological differences between different networks of researchers. After this adjustment, we did not find that the self-stimulation thresholds were increased in stressed rats. Pioneering experiments with positive results failed to be replicated by others, although no specific factor could be pointed to as a likely explanation. What is more, the available evidence suggests a lack of connection between sweet preference and self-stimulation, although this relationship has been seldom investigated. Methods known to mitigate biases were frequently absent, as was a transparent report of crucial study details. Our findings challenge the claim made in support of the validity of the model. Further efforts would be well-invested in assessing how reliably other tests of anhedonia have found the effects of the chronic unpredictable stress model.
Fusion of blood vessel organoids with human pancreatic islets improves insulin response over time
Authors: Tubbs Emily , Mehanovic Mahira , Lopes Mélanie , Quintard Clément , Combe Stéphanie , Armanet Mathieu , Domet Thomas , Sabatier Julia , Granziera Sabrina , Penninger Josef , Freida Delphine , Gidrol Xavier 
Published: January 2024

AbstractPancreatic islet transplantation is a promising treatment strategy for type 1 diabetes, however there are still major challenges to overcome, including vascularization. Novel strategies for the generation of prevascularized islets with native microvessels have reported improved islet functionality, vascularization and engraftment emphasizing integral role of microvascular bed. Recently a new model of self-organizing three-dimensional human blood vessel organoids (BVOs) has been developed from human pluripotent stem cells (hPSCs), composed of both endothelial and mural cells. BVO recapitulate key features of human microvasculature such as formation of vascular network, vascular lumen and basement membrane, and have been shown to be perfusable. Here, we report a new strategy to construct prevascularized islets by fusion with hPSC-derived BVOs. We demonstrate that islets and BVOs in co-culture leads to fusion and improved insulin secretion over time, on two independent human islet donors, suggesting a new therapeutic approach for pancreatic islet transplantation and type 1 diabetes modeling.
Adsorption-driven deformation and landing-footprints of the RBD proteins in SARS-CoV-2 variants onto biological and inanimate surfaces
Authors: Bosch Antonio , Guzman Horacio V. , Pérez Rubén 
Published: January 2024

AbstractRespiratory viruses, carried through airborne microdroplets, frequently adhere to surfaces, including plastics and metals. However, our understanding of the interactions between viruses and materials remains limited, particularly in scenarios involving polarizable surfaces. Here, we investigate the role of receptor-binding domain (RBD) mutations on the adsorption of SARS-CoV-2 to hydrophobic and hydrophilic surfaces employing molecular simulations. To contextualize our findings, we contrast the interactions on inanimate surfaces with those on native-biological interfaces, specifically the ACE2 receptor. Notably, we identify a twofold increase in structural deformations for the protein’s receptor binding motif onto the inanimate surfaces, indicative of enhanced shock-absorbing mechanisms. Furthermore, the distribution of amino acids (landing-footprints) on the inanimate surface reveals a distinct regional asymmetry relative to the biological interface. In spite of the H-bonds formed at the hydrophilic substrate, the simulations consistently show a higher number of contacts and interfacial area with the hydrophobic surface, with the WT RBD adsorbed more strongly than the delta or omicron RBDs. In contrast, the adsorption of delta and omicron to hydrophilic surfaces was characterized by a distinctive hopping-pattern. The novel shock-absorbing mechanisms identified in the virus adsorption on inanimate surfaces could lead current experimental efforts in the design of virucidal surfaces.