bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preparation Sessions
Authors: Brennan Bill , Belser Alex 
Published: March 2024

AbstractChapter 5 outlines a preparation phase consisting of three 90-minute nondrug sessions. Preparation lays the groundwork for potential benefits across the six EMBARK domains. The therapist’s aims in this phase include building trust, understanding the participant’s experience of depression, identifying participant intentions, and providing psychoeducation about psychedelic therapy. The chapter provides concrete instructions for the preparation sessions in each of the six EMBARK clinical domains. For example, the therapist: (E) aims to create an environment that encourages profound spiritual experiences; (M) teaches techniques for compassionate internal focus and self-soothing; (B) fosters an appreciation for somatic practices; (A) encourages the participant to openly receive their emotions and beliefs; (R) strives to cultivate a therapeutic relationship characterized by safety, acceptance, and empowerment while considering the participant’s trauma history and cultural context; and (K) codevelops strategies to promote continuity of therapeutic gains. Three session agendas are provided.
Secret origins: the disavowal of the comics medium within the promotional rhetoric of film trailers
Authors: Grosvenor Chris 
Published: March 2024

AbstractPredicated upon a corpus of 4,200 films, this article documents, analyses, and interprets the international film industry’s rhetorical disavowal of the comic book medium as a source for adaptation within advertising and promotional rhetoric for the cinematic adaptation of comic book texts. By analysing the statistical trends and patterns for comic book adaptations between 2000 and 2020, examining the language used within promotional trailers to conceptualise or promote the feature adaptation in relation to their comic book source material, and by comparing the type and scope of this rhetoric with other adapted texts of the same period, this article evidences and interrogates the overwhelming disavowal of the comic book medium despite the persistent and widely perceived ubiquity of comic book adaptation franchises. Above all, this article utilises statistical evidence and analysis to evidence clear patterns and trends within the perceived hierarchies of cultural taste or artistic value.
Cracking the black box of deep sequence-based protein–protein interaction prediction
Authors: Bernett Judith , Blumenthal David B , List Markus 
Published: March 2024

Abstract
Identifying protein–protein interactions (PPIs) is crucial for deciphering biological pathways. Numerous prediction methods have been developed as cheap alternatives to biological experiments, reporting surprisingly high accuracy estimates. We systematically investigated how much reproducible deep learning models depend on data leakage, sequence similarities and node degree information, and compared them with basic machine learning models. We found that overlaps between training and test sets resulting from random splitting lead to strongly overestimated performances. In this setting, models learn solely from sequence similarities and node degrees. When data leakage is avoided by minimizing sequence similarities between training and test set, performances become random. Moreover, baseline models directly leveraging sequence similarity and network topology show good performances at a fraction of the computational cost. Thus, we advocate that any improvements should be reported relative to baseline methods in the future. Our findings suggest that predicting PPIs remains an unsolved task for proteins showing little sequence similarity to previously studied proteins, highlighting that further experimental research into the ‘dark’ protein interactome and better computational methods are needed.
The role of the indoleamine 2,3-dioxygenase gene in preventing ovarian transplant rejection in rats
Authors: Long Aizhuan , Zhao Shuyun , Huang Guanyou , Li Xiaoying , Cheng Hui , Chen Zengchunxiao , Hu Zhu , Zhu Leilei , Zhao Danqing , Hu Xiaoyan , Wang Jun 
Published: March 2024

Abstract
Indoleamine 2,3-dioxygenase (IDO) plays important roles in maternal immune tolerance. Female Sprague Dawley rats (9–11 weeks old) were randomly divided into an autoplastic transplantation group (n = 75) and an allograft transplantation group (n = 300) was further divided into subgroups of ovarian transplantation, allograft ovarian transplantation, allograft ovarian transplantation with cyclosporine A treatment, allograft ovarian transplantation and transfection with IDO-expressing lentiviruses, and allograft ovarian transplantation and transfection with control lentiviruses. IDO was successfully transfected into the transplanted ovarian tissue. The survival rate, success rate of ovarian transplantation, period until estrous cycle restoration, and estrogen levels of rats that received IDO-expressing lentiviruses were significantly different from those of rats that underwent allograft transplantation and with control transfection (all P &lt; 0.05), but not significantly different from those rats that received autoplastic transplantation (all P &gt; 0.05). The number of ovarian follicles in the transplanted ovarian tissue of rats that received IDO-expressing lentiviruses was also significantly higher. The expression level of IDO protein detected by immunohistochemistry and western blotting was especially high in ovaries that had received IDO-containing lentiviruses. Naturally pregnant rats were found in each group postoperatively. These results indicated that IDO-expressing lentiviruses were successfully transfected into transplanted ovarian tissues of rats and that IDO was stably expressed within a certain time. These findings suggest that the expression level of IDO protein is associated with an enhanced success rate of ovarian tissue transplantation and a short restoration period of endocrine function.
The role of remnant cholesterol in patients with ST-segment elevation myocardial infarction
Authors: Zhou Yan , Madsen Jasmine Melissa , Özbek Burcu Tas , Køber Lars , Bang Lia Evi , Lønborg Jacob Thomsen , Engstrøm Thomas 
Published: March 2024

Abstract

Aims
Remnant cholesterol (RC) is the cholesterol content within triglyceride-rich lipoproteins. It promotes atherosclerotic cardiovascular disease beyond LDL cholesterol (LDL-C). The prognostic role of RC in patients with ST-segment elevation myocardial infarction (STEMI) is unknown. We aimed to estimate RC-related risk beyond LDL-C in patients with STEMI.

Methods and results
A total of 6602 consecutive patients with STEMI treated with primary percutaneous coronary intervention (PCI) from 1999 to 2016 were included. Remnant cholesterol was calculated as total cholesterol minus LDL-C minus HDL cholesterol. Adjusted Cox models were used to estimate the association between continuous RC levels and all-cause mortality, cardiovascular death, ischaemic stroke, and recurrent myocardial infarction (MI) at long-term (median follow-up of 6.0 years). Besides, discordance analyses were applied to examine the risk of the discordantly high RC (RC percentile rank minus LDL-C percentile rank &gt; 10 units) compared with the discordantly low RC (LDL-C percentile rank minus RC percentile rank &gt; 10 units). The concordance was defined as the percentile rank difference between RC and LDL-C ≤ 10 units. The median age of patients was 63 years [interquartile range (IQR) 54–72] and 74.8% were men. There were 2441, 1651, and 2510 patients in the discordantly low RC group, concordant group, and discordantly high RC group, respectively. All outcomes in the discordantly high RC group were higher than the other groups, and the event rate of all-cause mortality in this group was 31.87%. In the unadjusted analysis, the discordantly high RC was associated with increased all-cause mortality [hazard ratio (HR) 1.82, 95% confidence interval (CI) 1.63–2.04] and increased cardiovascular death (HR 1.79, 95% CI 1.55–2.06) compared with the discordantly low RC. In an adjusted model, RC was associated with higher all-cause mortality (HR 1.14, 95% CI 1.07–1.22). The discordantly high RC was associated with increased all-cause mortality (adjusted HR 1.55, 95% CI 1.37–1.75) and increased cardiovascular death (adjusted HR 1.47, 95% CI 1.25–1.72) compared with the discordantly low RC. There were no associations between RC and ischaemic stroke or recurrent MI.

Conclusion
In patients with STEMI treated with primary PCI, elevated RC levels beyond LDL-C and discordantly high RC were independently associated with increased all-cause mortality.
Fas2EB112: a tale of two chromosomes
Authors: Finegan Tara M , Cammarota Christian , Mendoza Andrade Oscar , Garoutte Audrey M , Bergstralh Dan T 
Published: March 2024

Abstract
The cell–cell adhesion molecule Fasciclin II (Fas2) has long been studied for its evolutionarily conserved role in axon guidance. It is also expressed in the follicular epithelium, where together with a similar protein, Neuroglian (Nrg), it helps to drive the reintegration of cells born out of the tissue plane. Remarkably, one Fas2 protein null allele, Fas2G0336, demonstrates a mild reintegration phenotype, whereas work with the classic null allele Fas2EB112 showed more severe epithelial disorganization. These observations raise the question of which allele (if either) causes a bona fide loss of Fas2 protein function. The problem is not only relevant to reintegration but fundamentally important to understanding what this protein does and how it works: Fas2EB112 has been used in at least 37 research articles, and Fas2G0336 in at least three. An obvious solution is that one of the two chromosomes carries a modifier that either suppresses (Fas2G0336) or enhances (Fas2EB112) phenotypic severity. We find not only the latter to be the case, but identify the enhancing mutation as Nrg14, also a classic null allele.
Repeated Hyposalinity Pulses Immediately and Persistently Impair the Sea Urchin Adhesive System
Authors: Garner Austin M , Moura Andrew J , Narvaez Carla A , Stark Alyssa Y , Russell Michael P 
Published: March 2024

Synopsis
Climate change will increase the frequency and intensity of extreme climatic events (e.g., storms) that result in repeated pulses of hyposalinity in nearshore ecosystems. Sea urchins inhabit these ecosystems and are stenohaline (restricted to salinity levels ∼32‰), thus are particularly susceptible to hyposalinity events. As key benthic omnivores, sea urchins use hydrostatic adhesive tube feet for numerous functions, including attachment to and locomotion on the substratum as they graze for food. Hyposalinity severely impacts sea urchin locomotor and adhesive performance but several ecologically relevant and climate change-related questions remain. First, do sea urchin locomotion and adhesion acclimate to repeated pulses of hyposalinity? Second, how do tube feet respond to tensile forces during single and repeated hyposalinity events? Third, do the negative effects of hyposalinity exposure persist following a return to normal salinity levels? To answer these questions, we repeatedly exposed green sea urchins (Strongylocentrotus droebachiensis) to pulses of three different salinities (control: 32‰, moderate hyposalinity: 22‰, severe hyposalinity: 16‰) over the course of two months and measured locomotor performance, adhesive performance, and tube foot tensile behavior. We also measured these parameters 20 h after sea urchins returned to normal salinity levels. We found no evidence that tube feet performance and properties acclimate to repeated pulses of hyposalinity, at least over the timescale examined in this study. In contrast, hyposalinity has severe consequences on locomotion, adhesion, and tube foot tensile behavior, and these impacts are not limited to the hyposalinity exposure. Our results suggest both moderate and severe hyposalinity events have the potential to increase sea urchin dislodgment and reduce movement, which may impact sea urchin distribution and their role in marine communities.
Seasonal Variations in the Toughness of Leaves: A Case Study Using Griselinia littoralis
Authors: Taylor David 
Published: March 2024

Synopsis
Potential effects of climate change include greater extremes of temperature and increased severity of storms. Many plants have evolved to resist the challenges of winter (freezing, dehydration, and wind) in a process known as cold hardening. Sensing reducing temperatures, they make structural changes at the cellular level to increase their mechanical resistance and prevent damage. Previous work on this topic, though extensive, has been conducted under laboratory conditions rather than in the field, and while many workers have observed changes to cell wall thickness and composition, which imply increased mechanical strength, few have actually measured strength or any other parameter describing structural integrity. This paper describes experiments on a model system designed to measure the structural integrity of leaf laminae from plants growing naturally in the field over extended periods, allowing seasonal variations to be captured. Standard engineering properties—tensile strength and fracture toughness—were measured for leaves of Griselinia littoralis on 19 separate occasions over a 12-month period. Toughness (rather than strength) was found to be the controlling mechanical property. Toughness values were found to change significantly during the year, by more than a factor of 2. Toughness correlated strongly with average daily soil temperature, but with a lag of about 1–2 weeks, suggesting that this is the time needed for structural adjustments to take place. Highest toughness values occurred in winter, confirming cold hardening. Increasing temperature in the spring was associated with decreasing toughness, but in the summer, when highest temperatures occurred, toughness increased again. This apparent “hot hardening” may be a response to dehydration. Results imply that a given leaf is able to both increase and decrease its toughness in response to temperature changes, demonstrating excellent plasticity of response. This case study of a single species establishes a method of reliably measuring changes in a plant’s structural integrity due to cold hardening and other seasonal variations, which may be used to investigate the effects of climate change and other variables.
High niche specificity and host genetic diversity of groundwater viruses
Authors: Gios Emilie , Mosley Olivia E , Hoggard Michael , Handley Kim M 
Published: March 2024

Abstract
Viruses are key members of microbial communities that exert control over host abundance and metabolism, thereby influencing ecosystem processes and biogeochemical cycles. Aquifers are known to host taxonomically diverse microbial life, yet little is known about viruses infecting groundwater microbial communities. Here, we analysed 16 metagenomes from a broad range of groundwater physicochemistries. We recovered 1571 viral genomes that clustered into 468 high-quality viral operational taxonomic units. At least 15% were observed to be transcriptionally active, although lysis was likely constrained by the resource-limited groundwater environment. Most were unclassified (95%), and the remaining 5% were Caudoviricetes. Comparisons with viruses inhabiting other aquifers revealed no shared species, indicating substantial unexplored viral diversity. In silico predictions linked 22.4% of the viruses to microbial host populations, including to ultra-small prokaryotes, such as Patescibacteria and Nanoarchaeota. Many predicted hosts were associated with the biogeochemical cycling of carbon, nitrogen, and sulfur. Metabolic predictions revealed the presence of 205 putative auxiliary metabolic genes, involved in diverse processes associated with the utilization of the host’s intracellular resources for biosynthesis and transformation reactions, including those involved in nucleotide sugar, glycan, cofactor, and vitamin metabolism. Viruses, prokaryotes overall, and predicted prokaryotic hosts exhibited narrow spatial distributions, and relative abundance correlations with the same groundwater parameters (e.g. dissolved oxygen, nitrate, and iron), consistent with host control over viral distributions. Results provide insights into underexplored groundwater viruses, and indicate the large extent to which viruses may manipulate microbial communities and biogeochemistry in the terrestrial subsurface.
Development of an experimental model for liver abscess induction in Holstein steers using an acidotic diet challenge and bacterial inoculation
Authors: McDaniel Zach S , Hales Kristin E , Salih Harith , Deters Alyssa , Shi Xiaorong , Nagaraja Tiruvoor G , Lawrence Ty E , Tennant Travis C , Amachawadi Raghavendra G , Carroll Jeff A , Burdick Sanchez Nicole C , Galyean Michael L , Smock Taylor M , Ballou Michael A , Machado Vinicius S , Davis Emily , Broadway Paul R 
Published: March 2024

Abstract
Holstein steers (n = 40; initial BW = 84.9 ± 7.1 kg) were used to study the genesis of liver abscesses (LA) using an acidotic diet challenge with or without intraruminal bacterial inoculation. Steers were housed in individual pens inside a barn and randomly assigned to one of three treatments: (1) low-starch control diet comprised primarily of dry-rolled corn and wet corn gluten feed (CON); (2) high-starch acidotic diet with steam-flaked corn (AD); or (3) acidotic diet plus intraruminal inoculation with Fusobacterium necrophorum subsp. necrophorum (9.8 × 108 colony forming units [CFU]/mL), Trueperella pyogenes (3.91 × 109 CFU/mL), and Salmonella enterica serovar Lubbock (3.07 × 108 CFU/mL), previously isolated from LA (ADB). Steers in AD and ADB were fed the acidotic diet for 3 d followed by 2 d of the CON diet, and this cycle was repeated four times. On day 23, ADB steers were intraruminally inoculated with the bacteria. At necropsy, gross pathology of livers, lungs, rumens, and colons was noted. Continuous data were analyzed via mixed models as repeated measures over time with individual steer as the experimental unit. Mixed models were also used to determine the difference in prevalence of necropsy scores among treatments. Ruminal pH decreased in AD and ADB steers during each acidotic diet cycle (P ≤ 0.05). LA prevalence was 42.9% (6 of 14) in ADB vs. 0% in AD or CON treatments (P &lt; 0.01). Ruminal damage was 51.1% greater in ADB than in AD (P ≤ 0.04). Culture of LA determined that 100% of the abscesses contained F. necrophorum subsp. necrophorum, 0% contained T. pyogenes, 50% contained Salmonella, and 50% contained a combination of F. necrophorum subsp. necrophorum and Salmonella. The F. necrophorum subsp. necrophorum was clonally identical to the strain used for the bacterial inoculation based on phylogenetic analysis of the whole genome. This experimental model successfully induced rumenitis and LA in Holstein steers and confirms the central dogma of LA pathogenesis that acidosis and rumenitis lead to the entry of F. necrophorum into the liver to cause abscesses. Our findings suggest that an acidotic diet, in conjunction with intraruminal bacterial inoculation, is a viable model to induce LA. Further research is needed to determine the repeatability of this model, and a major application of the model will be in evaluations of novel interventions to prevent LA.
Five-dimensional facies-driven seismic inversion for igneous reservoirs based on rock-physics modelling
Authors: Gu Wen , Yin Xingyao , Wu Furong , Luo Ying , Liang Hong , Pei Song , Yang Yaming 
Published: March 2024

Abstract
The igneous reservoir has become an important exploration target for increasing reserves and production of oil and gas in the Junggar Basin. However, igneous reservoir exploration is restricted because the seismic exploration of high-quality igneous reservoirs is difficult and the anisotropy induced by high-angle fractures cannot be neglected. To implement the characterization of igneous reservoirs, we first study the correlation between anisotropy parameters and physical properties of igneous rock, and we propose a 5D facies-driven inversion method based on rock physics, which means we employ 3D seismic data at different incidence angles and azimuths to implement the estimation of a hydrocarbon reservoir constrained by the igneous rock facies. We also present an anisotropic igneous rock-physics model, in which micro-petrophysical characteristics, strong heterogeneity of skeleton minerals, and pore structures are considered. As a reasonable initial model is important for seismic inversion, we propose a facies-driven modelling seismic inversion method in which we use facies obtained on the basis of the difference between rock composition, reservoir physical parameters, and elastic parameters of different lithofacies igneous rocks to constrain the seismic inversion. Finally, we present a step seismic inversion method of using seismic data to estimate multi-parameters of horizontal transversely isotropic media. Therefore, the comprehensive processes of rock-physics modelling, inversion model establishment, and reservoir prediction of high-quality igneous rocks are proposed in this study, which demonstrates effective application for igneous reservoirs in China.
A complication of an axillary intra-aortic balloon pump
Authors: Kodack Eileen , Patel Riya , Bonner Carain , Pantin Enrique 
Published: March 2024

Abstract
Intra-aortic balloon pumps (IABPs) are used to mechanically temporize a failing heart by decreasing afterload while increasing coronary perfusion pressure of the heart while more definitive treatment is sought. We report a case of a 65-year-old male with nonischemic cardiomyopathy, atrial fibrillation, thyroiditis, and non-Hodgkin lymphoma who presented with worsening heart failure. He underwent a percutaneous placement of a left axillary IABP with seemingly no complications. Approximately 3 weeks post-placement, the patient was taken for a heart transplant when an intraoperative transesophageal echo showed that the IABP was in the aortic arch and ascending aorta, instead of its proper placement in the descending aorta. The patient’s arterial line showed waveforms appropriate for an IABP patient, and the patient showed no signs indicative of improper placement. This erroneous placement carried the potential to affect the aortic valve function, injure the aortic intima and/or occlude the aortic arch vessels. .