bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preface
Authors: Stuckey W M , Silberstein Michael , McDevitt Timothy 
Published: July 2024

Abstract
The 2022 Nobel Prize in Physics was awarded “for experiments with entangled photons, establishing the violation of Bell inequalities” that have created tremendous confusion among physicists and philosophers about “how Nature works.” With the violation of Bell inequalities due to quantum entanglement (hereafter just “entanglement”), we now know that Einstein’s view of a universe that functions exclusively according to locally real causal mechanisms is wrong. Ironically, we propose to replace Einstein’s desired “constructive” explanation of entanglement with a “principle” explanation based on his own relativity principle. In other words, we solve Einstein’s mystery of entanglement just like Einstein solved the mystery of length contraction, i.e., using the relativity principle. Chapters that can be skipped based on the interests and background of the reader are recommended.
A Principle Response from Quantum Information Theorists
Authors: Stuckey W M , Silberstein Michael , McDevitt Timothy 
Published: July 2024

Abstract
Chapter 6 explains the axiomatic reconstruction of QM via information-theoretic principles. Hardy’s reconstruction is featured because it shows that the quantum probability theory of QM obtains by adding the word “continuous” to the fifth axiom of classical probability theory. As explained in Chapter 0, continuity is responsible for superposition, so the quantum bit (qubit) differs from the classical bit because the states of a qubit are superpositions. The Planck postulate is shown to follow from Brukner and Zeilinger’s principle of Information Invariance & Continuity at the foundation of their reconstruction, so QM can be understood as a principle theory based on NPRF + h. We show that ‘average-only’ projection is one way to characterize the ‘weirdness’ of the qubit. Grinbaum’s reconstruction based on relational quantum mechanics is introduced.
Superquantum Probabilities: Why No PR-Box?
Authors: Stuckey W M , Silberstein Michael , McDevitt Timothy 
Published: July 2024

Abstract
Chapter 8 introduces Popescu and Rohrlich’s no-signalling PR-box of superquantum joint probabilities violating the CHSH Bell inequality more strongly than QM. We present Mermin’s derivation of the CHSH Bell inequality. Using Tanya and Jeff Bub’s quantum guessing game, we show how the PR-box violates conservation per NPRF whence Bell state entanglement. This is shown to be the reason the PR-box violates the CHSH-Bell inequality more strongly than QM. Therefore, we conclude that the PR-box is akin to a perpetual motion machine.
What’s Really Going On?
Authors: Stuckey W M , Silberstein Michael , McDevitt Timothy 
Published: July 2024

Abstract
In Chapter 9 we answer Zeilinger’s question, “What’s really going on?” concerning how Nature works. In other words, we present an ontology over which the constraints NPRF + h and NPRF + c range and operate. We contrast contextuality with reductionism and relationalism, then discuss relational quantum mechanics. We explain our version of multiscale contextual emergence called quantum-classical contextuality. Accordingly, bodily (classical) objects interact via the exchange of quanta of energy-momentum. NPRF + c constrains the distribution of worldtubes of bodily objects in spacetime while NPRF + h constrains the distribution of quanta exchanged between bodily objects. Thus, NPRF + h is an “all-at-once” or “atemporal” constraint on the distribution of quanta among bodily objects in spacetime. We call such a constraint an adynamical global constraint (AGC). Feynman’s path integral formalism for QM is contrasted with Schrödinger’s equation. We present our Poincaré symmetric ontology.
Interpreting Quantum Mechanics in a Realist Fashion
Authors: Stuckey W M , Silberstein Michael , McDevitt Timothy 
Published: July 2024

Abstract
In Sub-Chapter 9A we explain what makes an interpretation of QM realist and how our interpretation of QM is realist and psi-epistemic. We contrast this with relational quantum mechanics. What is fundamental in our interpretation is 4D quantum–classical contextuality as given by “all-at-once” AGCs.
Young Adult Patient and Caregiver Perspectives on Transition Readiness in an Inflammatory Bowel Disease Clinic
Authors: Strobel Thomas M , Narayani Nikita A , Nicholson Maribeth R , Riera Diana C , Rakos Tanner G , Fulton Nisa P , Trotter-Busing Jordan A , Horst Sara N , Dalal Robin L , Pabla Baldeep S , Scoville Elizabeth A , Schwartz David A , Beaulieu Dawn B 
Published: July 2024

Abstract

Background
When it comes to readiness to transition to an adult subspecialty clinic, perspectives between patients with inflammatory bowel disease (IBD) and their caregivers may differ and influence the ability to successfully transition. Patients with IBD have been shown to suffer from poor transfers of care. There is a need to more efficiently and accurately assess transition readiness to improve the transfer process.

Methods
Patients transferring to an adult subspecialty clinic and their caregivers were each administered the Transition Readiness Assessment Questionnaire and IBD Self-Efficacy Scale—Adolescent. Differences between patient and caregiver responses and agreement among each dyad were tested.

Results
There were 29 dyads of patients and caregivers who enrolled. There was no difference between patient and caregiver total scores. The average level of agreement between patients and caregivers was 78%. There was no association between patient response and their age, gender, ethnicity, age at time of transfer, age at diagnosis, or number of emergency room visits in the prior year.

Conclusions
Patient-reported readiness to transition to adult care was confirmed by their caregivers using validated readiness assessment tools. As transition clinics must focus on high-yield interventions, a readiness survey of young adult patients without a survey of their caregivers may be adequate. However, as experts in each patient’s journey, caregivers may be utilized when setting goals and priorities for a transition readiness program. The surveys used in this study can be used broadly to aid subspecialty clinics that are trying to improve the transition process.
Enigmatic Pachytene PIWI-Interacting RNAs
Authors: Xu Ming-Min , Li Xin Zhiguo 
Published: July 2024

Abstract
PIWI-interacting RNAs (piRNAs), a class of small RNAs, are renowned for their roles in sequencing-dependent targeting and suppressing transposable elements (TEs). Nevertheless, a majority of mammalian piRNAs, expressing at pachytene stage of meiosis, known as pachytene piRNAs, are devoid of discernible targets, casting a veil of enigma over their functional significance. Overturning the notion that this unusual class of piRNAs functions beyond TE silencing, we recently demonstrated that pachytene piRNAs play an essential and conserved role in silencing young and actively transposing TEs across amniotes. However, only 1% of pachytene piRNAs target active TEs. The biological significance of the abundant non-TE piRNAs, coproduced from the same precursors as TE piRNAs, remains unclear. Here, we provide a comprehensive summary of the potential roles of non-TE piRNAs, and thus propose that these non-TE piRNAs either bolster the action of TE piRNAs or provide the host genome a preexisting mechanism to suppress the potential invasion of novel TEs in the future.
The Young and the Resilient: Investigating Coral Thermal Resilience in Early Life Stages
Authors: Walker Nia S , Isma Lys , García Nepsis , True Aliyah , Walker Taylor , Watkins Joyah 
Published: July 2024

Synopsis
Global ocean warming is affecting keystone species distributions and fitness, resulting in the degradation of marine ecosystems. Coral reefs are one of the most diverse and productive marine ecosystems. However, reef-building corals, the foundational taxa of coral reef ecosystems, are severely threatened by thermal stress. Models predict 40–80% of global coral cover will be lost by 2100, which highlights the urgent need for widespread interventions to preserve coral reef functionality. There has been extensive research on coral thermal stress and resilience, but 95% of studies have focused on adult corals. It is necessary to understand stress during early life stages (larvae, recruits, and juveniles), which will better inform selective breeding programs that aim to replenish reefs with resilient stock. In this review, we surveyed the literature on coral thermal resilience in early life stages, and we highlight that studies have been conducted on relatively few species (commonly Acropora spp.) and in limited regions (mainly Australia). Reef-building coral management will be improved by comprehensively understanding coral thermal resilience and fitness across life stages, as well as in diverse species and regions.
Pathogenesis of IgA nephropathy as a tissue-specific autoimmune disease
Authors: Nihei Yoshihito , Kitamura Daisuke 
Published: July 2024

Abstract
Glomerulonephritis (GN) is a group of heterogeneous immune-mediated kidney diseases that causes inflammation within the glomerulus. Autoantibodies (auto-Abs) are considered to be central effectors in the pathogenesis of several types of GN. Immunoglobulin A nephropathy (IgAN) is the most common GN worldwide and is characterized by the deposition of IgA in the glomerular mesangium of the kidneys, which is thought to be mediated by immune complexes containing non-specific IgA. However, we recently reported that IgA auto-Abs specific to mesangial cells (anti-mesangium IgA) were found in the sera of gddY mice, a spontaneous IgAN model, and patients with IgAN. We identified two autoantigens (β2-spectrin and CBX3) that are selectively expressed on the mesangial cell surface and targeted by anti-mesangial IgA. Our findings redefined IgAN as a tissue-specific autoimmune disease. Regarding the mechanisms of production of anti-mesangium IgA, studies using gddY mice have revealed that the production of anti-CBX3 IgA is induced by particular strains of commensal bacteria in the oral cavity, possibly through their molecular mimicry to CBX3. Here, we discuss a new concept of IgAN pathogenesis from the perspective of this disease as autoimmune GN caused by tissue-specific auto-Abs.
Antibacterial characteristics and mechanistic insights of combined tea polyphenols, Nisin, and epsilon-polylysine against feline oral pathogens: a comprehensive transcriptomic and metabolomic analysis
Authors: Bai Huasong , Liu Tong , Wang Hengyan , Wang Zhanzhong 
Published: July 2024

Abstract

Aims
This study evaluates the antibacterial characteristics and mechanisms of combined tea polyphenols (TPs), Nisin, and ε-polylysine (PL) against Streptococcus canis, Streptococcus minor, Streptococcus mutans, and Actinomyces oris, common zoonotic pathogens in companion animals.

Methods and results
Pathogenic strains were isolated from feline oral cavities and assessed using minimum inhibitory concentration (MIC) tests, inhibition zone assays, growth kinetics, and biofilm inhibition studies. Among single agents, PL exhibited the lowest MIC values against all four pathogens. TP showed significant resistance against S. minor, and Nisin against S. mutans. The combination treatment (Comb) of TP, Nisin, and PL in a ratio of 13:5:1 demonstrated broad-spectrum antibacterial activity, maintaining low MIC values, forming large inhibition zones, prolonging the bacterial lag phase, reducing growth rates, and inhibiting biofilm formation. RNA sequencing and metabolomic analysis indicated that TP, Nisin, and PL inhibited various membrane-bound carbohydrate-specific transferases through the phosphoenolpyruvate-dependent phosphotransferase system in S. canis, disrupting carbohydrate uptake. They also downregulated glycolysis and the citric acid cycle, inhibiting cellular energy metabolism. Additionally, they modulated the activities of peptidoglycan glycosyltransferases and d-alanyl-d-alanine carboxypeptidase, interfering with peptidoglycan cross-linking and bacterial cell wall stability.

Conclusions
The Comb therapy significantly enhances antibacterial efficacy by targeting multiple bacterial pathways, offering potential applications in food and pharmaceutical antimicrobials.
Determination of Toxic Elements in Botanical Dietary Supplement Ingredient Reference Materials
Authors: Fong Sam Jennifer , Kuszak Adam J , Gray Patrick J , Wise Stephen A 
Published: July 2024

Abstract

Background
The National Institute of Standards and Technology (NIST) has produced over 40 botanical dietary supplement Standard Reference Materials (SRMs) and reference materials (RMs) with values assigned for chemical markers and/or active compounds. Although environmental accumulation or inadvertent introduction of toxic elements (arsenic, cadmium, lead, and mercury) is a potential source of exposure in botanical dietary supplement products, the majority of the dietary supplement SRMs/RMs do not have values assigned for the four major toxic elements.

Objective
To determine As, Cd, Pb, and Hg content in the current inventory of NIST botanical dietary supplement SRMs/RMs.

Methods
Fifteen SRMs/RMs suites of plant part, extract, and finished products (i.e., solid oral dosage form [SODF]) were analyzed for As, Cd, Pb, and Hg using nitric acid microwave-assisted digestion followed by quantification using inductively coupled plasma–mass spectrometry.

Results
Results for control samples were in good agreement with certified values indicating that the analyses of 38 individual botanical SRMs/RMs were in control. Characterization of linked plant/extract SRMs/RMs derived from the same source materials demonstrated that while extraction processes can often yield extracts with lower toxic element content for Hg or As, it is also possible for mass fraction levels to remain unchanged or even to increase after extraction.

Conclusions
The results fill significant knowledge gaps in toxic element content ranges for SRMs/RMs where no NIST assigned values existed, in particular for Hg content and for extract and SODF matrixes. With comprehensive toxic element content now available, researchers can better select appropriate dietary supplement SRMs/RMs for use as controls in the analysis of dietary supplement ingredients and products.

Highlights
Results for As, Cd, Pb, and Hg are reported for 38 dietary supplement SRMs/RMs including six suites of plant, extract, and SODF and nine pairs of plant and extract from the same batch of plant material.
Operations of a Student-Run Asylum Clinic: Frameworks, Challenges, and Recommendations
Authors: Gu Kathleen , Kim Dylan K , Kleidermacher Lauren E , Berhe Anne D , Sanjurjo Alexander D , Leone Ryan M , Dreux Simone R , Lin Allison P , Yuan Mina , Yang Eunice , Viswanathan Ashwin , Lorence Isabella M , Wang Melissa , Molyneux Kevin , Saha Prantik , Devlin Michael J 
Published: July 2024

Abstract
Student-run asylum clinics within medical schools represent a promising alternative to costly medicolegal services for people seeking asylum by providing pro bono forensic medical evaluations. However, there exist significant operational barriers to creating and developing such clinics, which depend largely on volunteerism and limited financial budgets. This policy and practice note not only presents a framework aimed at navigating these barriers in developing a student-run asylum clinic but also outlines critical challenges and recommendations for addressing them. We describe three principal components of clinic structure: community outreach and service, administration of forensic medical evaluations, and continuity of care. We also highlight challenges, such as access to a physical space for evaluations, maintenance of interpreter access and quality, standardization of clinician evaluator expectations, clinician evaluator availability, and evaluator wellbeing. Recommendations include the incorporation of a diversity of referral sources, opportunities for clinician-clinician shadowing, evaluation quality assessment, affidavit standardization, and development of interdisciplinary partnership.
Durations of Antibiotic Treatment for Acute Otitis Media and Variability in Prescribed Durations Across Two Large Academic Health Systems
Authors: Katz Sophie E , Jenkins Timothy C , Stein Amy B , Thomas Gale , Koenig Nancy , Starnes Gary Lucas , Newland Jason G , Banerjee Ritu , Frost Holly M 
Published: July 2024

Abstract

Background
Acute otitis media (AOM) accounts for roughly 25% of antibiotics prescribed to children annually. Despite national guidelines that recommend short (5–7 days) durations of antibiotics for children 2 years and older with AOM, most receive long (10 day) courses. This study aims to evaluate antibiotic durations prescribed for children aged 2–17 years with uncomplicated AOM across two pediatric academic health systems, and to assess the variability in prescribed durations between and within each system.

Methods
Electronic medical record data from 135 care locations at two health systems were retrospectively analyzed. Outpatient encounters for children aged 2–17 years with a diagnosis of AOM from 2019 to 2022 were included. The primary outcome was the percent of 5-day prescriptions. Secondary outcomes included the proportion of 7-day prescriptions, 10-day prescriptions, prescriptions for nonfirst-line antibiotics, cases associated with treatment failure, AOM recurrence, and adverse drug events.

Results
Among 73 198 AOM encounters for children 2 years and older, 61 612 (84%) encounters resulted in an antibiotic prescription. Most prescriptions were for 10 days (45 689; 75%), 20% were for 7 days (12 060), and only 5% were for 5 days (3144). Treatment failure, AOM recurrence, adverse drug events, hospitalizations, and office, emergency department or urgent-care visits for AOM within 30 days after the index visit were rare.

Conclusions
Despite national guidelines that recommend shorter durations for children with uncomplicated AOM, 75% of our cohort received 10-day durations. Shortening durations of therapy for AOM could reduce antibiotic exposure and should be a priority of pediatric antibiotic stewardship programs.
Fluoroquinolone Prophylaxis in Children With Cancer: A Pro/Con Discussion
Authors: Vasileiadi Eleana , Lloyd Kevin M , Fisher Brian T , Hanisch Benjamin 
Published: July 2024

Abstract
There are conflicting recommendations on whether to use or not to use fluoroquinolone prophylaxis in pediatric oncology patients. An international pediatric clinical practice guideline (CPG) recommends administering levofloxacin prophylaxis in patients with acute myeloblastic leukemia and relapsed acute lymphoblastic leukemia receiving intensive chemotherapy as this practice has been found to reduce episodes of fever and bacteremia. A separate European CPG does not recommend levofloxacin prophylaxis because of concerns for adverse effects, including potentiation of fluoroquinolone resistance and possible increased resistance to other classes of antibiotics. The nuance of the decision to give or not give prophylaxis is discussed in the context of published evidence defining the risks and benefits of levofloxacin prophylaxis for pediatric leukemia patients at high risk for bacterial infection. Knowledge gaps are also identified to guide further investigations to optimize the use of fluoroquinolone prophylaxis in pediatric patients receiving chemotherapy for cancer or undergoing a hematopoietic cell transplantation.
Evolution of drought and frost responses in cool season grasses (Pooideae): was drought tolerance a precursor to frost tolerance?
Authors: Stolsmo Sylvia Pal , Lindberg Camilla Lorange , Ween Rebekka Eriksen , Schat Laura , Preston Jill Christine , Humphreys Aelys Muriel , Fjellheim Siri 
Published: July 2024

Abstract
Frost tolerance has evolved many times independently across flowering plants. However, conservation of several frost tolerance mechanisms among distant relatives suggests that apparently independent entries into freezing climates may have been facilitated by repeated modification of existing traits (‘precursor traits’). One possible precursor trait for freezing tolerance is drought tolerance, because palaeoclimatic data suggest plants were exposed to drought before frost and several studies have demonstrated shared physiological and genetic responses to drought and frost stress. Here, we combine ecophysiological experiments and comparative analyses to test the hypothesis that drought tolerance acted as a precursor to frost tolerance in cool-season grasses (Pooideae). Contrary to our predictions, we measured the highest levels of frost tolerance in species with the lowest ancestral drought tolerance, indicating that the two stress responses evolved independently in different lineages. We further show that drought tolerance is more evolutionarily labile than frost tolerance. This could limit our ability to reconstruct the order in which drought and frost responses evolved relative to each other. Further research is needed to determine whether our results are unique to Pooideae or general for flowering plants.
mTOR in Acquired and Genetic Models of Epilepsy
Authors: Wong Michael , Bordey Angelique , Danzer Steve C. 
Published: July 2024

Abstract
Mutations in genes regulating the mechanistic target of rapamycin (mTOR) signaling pathway have emerged as a common cause of childhood epilepsy, including focal cortical dysplasia, hemimegalencephaly, and tuberous sclerosis complex. Dysregulation of mTOR signaling is also implicated in nongenetic causes of epilepsy, such as following status epilepticus or traumatic brain injury. In this chapter, we describe the evidence linking the mTOR pathway to genetic and acquired epilepsies, the variety of animal models developed to examine mTOR pathway signaling in the brain, and the general patterns of brain pathology produced by pathway disruption. We also examine potential mechanisms by which disrupted mTOR signaling regulates brain development, neuronal excitability, and epileptogenesis. The variety of tissues and cellular functions regulated by mTOR, and the breadth of epilepsies linked to disrupted mTOR signaling, all implicate the pathway as an important modulator of epileptogenesis.
GABAA-Receptor Signaling and Ionic Plasticity in the Generation and Spread of Seizures
Authors: Kaila Kai , Trevelyan Andrew , Raimondo Joseph , Ala-Kurikka Tommi , Huberfeld Gilles , Avoli Massimo , de Curtis Marco 
Published: July 2024

Abstract
According to a classical concept in epilepsy research, seizures are triggered by an “imbalance” between excitatory (glutamatergic) and inhibitory (GABAergic) synaptic transmission. Recent work has shown, however, that not only the efficacy but also the qualitative mode of action of GABAergic signaling is controlled by ionic plasticity, which is mediated by activity-dependent changes in the driving force of currents across GABAA receptors (GABAARs). We will briefly describe the basics of neuronal Cl− and pH/HCO3− regulation, and the main functions of neuronal carbonic anhydrases and the Cl− transporters, KCC2 and NKCC1. A major topic of discussion is how depolarizing currents carried by bicarbonate and by sodium across GABAARs and ionotropic glutamate receptors, respectively, act in a synergistic manner, leading to massive neuronal uptake of Cl− and large extracellular K+ transients. These transmembrane ion fluxes form a major constituent of a positive feedback cycle, in which neuronal excitability is boosted by, and contributes to, the ionic shifts. Initially, this leads to an erosion of the inhibitory restraint in the region surrounding the ictal core, followed by a subsequent transformation to functionally excitatory GABA action (which is independent on NKCC1). In line with this, a wealth of evidence shows that intense activation of cortical interneurons often has a seizure-promoting effect. The synaptic and non-synaptic mechanisms associated with GABAergic excitation shed light on the complex spatiotemporal profiles of seizure generation and propagation, and they provide a rational basis for the loss of efficacy of GABA-enhancing antiseizure drugs on ongoing seizure activity.