bluuebunny/crossref_metadata_2025_split huggingface dataset:
hictk: blazing fast toolkit to work with .hic and .cool files
Authors: Rossini Roberto , Paulsen Jonas 
Published: June 2024

Abstract

Motivation
Hi-C is gaining prominence as a method for mapping genome organization. With declining sequencing costs and a growing demand for higher-resolution data, efficient tools for processing Hi-C datasets at different resolutions are crucial. Over the past decade, the .hic and Cooler file formats have become the de-facto standard to store interaction matrices produced by Hi-C experiments in binary format. Interoperability issues make it unnecessarily difficult to convert between the two formats and to develop applications that can process each format natively.

Results
We developed hictk, a toolkit that can transparently operate on .hic and .cool files with excellent performance. The toolkit is written in C++ and consists of a C++ library with Python and R bindings as well as CLI tools to perform common operations directly from the shell, including converting between .hic and .mcool formats. We benchmark the performance of hictk and compare it with other popular tools and libraries. We conclude that hictk significantly outperforms existing tools while providing the flexibility of natively working with both file formats without code duplication.

Availability and implementation
The hictk library, Python bindings and CLI tools are released under the MIT license as a multi-platform application available at github.com/paulsengroup/hictk. Pre-built binaries for Linux and macOS are available on bioconda. Python bindings for hictk are available on GitHub at github.com/paulsengroup/hictkpy, while R bindings are available on GitHub at github.com/paulsengroup/hictkR.
Optimizing data integration improves gene regulatory network inference in Arabidopsis thaliana
Authors: Cassan Océane , Lecellier Charles-Henri , Martin Antoine , Bréhélin Laurent , Lèbre Sophie 
Published: June 2024

Abstract

Motivations
Gene regulatory networks (GRNs) are traditionally inferred from gene expression profiles monitoring a specific condition or treatment. In the last decade, integrative strategies have successfully emerged to guide GRN inference from gene expression with complementary prior data. However, datasets used as prior information and validation gold standards are often related and limited to a subset of genes. This lack of complete and independent evaluation calls for new criteria to robustly estimate the optimal intensity of prior data integration in the inference process.

Results
We address this issue for two regression-based GRN inference models, a weighted random forest (weigthedRF) and a generalized linear model estimated under a weighted LASSO penalty with stability selection (weightedLASSO). These approaches are applied to data from the root response to nitrate induction in Arabidopsis thaliana. For each gene, we measure how the integration of transcription factor binding motifs influences model prediction. We propose a new approach, DIOgene, that uses model prediction error and a simulated null hypothesis in order to optimize data integration strength in a hypothesis-driven, gene-specific manner. This integration scheme reveals a strong diversity of optimal integration intensities between genes, and offers good performance in minimizing prediction error as well as retrieving experimental interactions. Experimental results show that DIOgene compares favorably against state-of-the-art approaches and allows to recover master regulators of nitrate induction.

Availability and implementation
The R code and notebooks demonstrating the use of the proposed approaches are available in the repository https://github.com/OceaneCsn/integrative_GRN_N_induction
Problems in Commercial Kits of 25-Hydroxy Vitamin D and the Development of Simple, Robust and Faster HPLC Method
Authors: Saad Syed Muhammad , Khan Abdul Rafiq , Khan Khalid Mohammed , Al-Othaim Ali 
Published: June 2024

Abstract
Vitamin D is a lipid-soluble compound that plays a key role in bone mineral metabolism. The commercial current kits and several published assay methods (High-performance liquid chromatography (HPLC) and Immunoassay) are complicated due to the use of multiple reagents, larger sample volume, high backpressure, longer extraction time, evaporation under nitrogen after extraction, significant interference and antibody cross-reactivity. Here we report a new HPLC method for the determination of 25-hydroxyvitamin D2 (25-OHD2) and 25-hydroxyvitamin D3 (25-OHD3) that is simple (no evaporation), rapid (10-minute run time) and robust. Serum sample (300 μl) is mixed with 300 μl acetonitrile containing lauraphenone as internal standard. After vortexing and centrifugation, the supernatant was loaded into C18 extraction cartridges, washed with 70% methanol and then eluted with 200 μl of a mixture of 70% ethanol and 30% isopropyl alcohol (IPA). The eluent was mixed with 50 μl of water and injected into the HPLC-UV system for analysis. The method proved to be linear in the range of 10–750 nmol/L of 25-OHD2 and 25-OHD3. The intra- and inter-assay precision was less than 10 for both compounds at four different concentrations. The method was compared with (LC–MS/MS) and the correlation coefficients (R2) were 0.9454 and 0.9673 for 25-OHD2 and 25-OHD3 respectively. The proposed HPLC method is simple, rapid, robust and free from the most common problems encountered with commercial kits. It can be used in a high-volume laboratory that uses the HPLC method for the simultaneous determination of 25-OHD2 and 25-OHD3 in serum samples.
Case report of increased left ventricular end-diastolic pressure with pulsatile left ventricular assist device
Authors: de Sá Marchi Mauricio Felippi , Verhemel Sarah , Nuis Rutger-Jan , Van Mieghem Nicolas M 
Published: June 2024

Abstract

Background
Left ventricular assist devices (LVADs) are increasingly utilized in cardiogenic shock and high-risk percutaneous coronary interventions (PCIs). These devices aspirate and expel blood from the left ventricle (LV) into the aorta, consequently reducing left ventricular end-diastolic pressure (LVEDP). We report a case of unexpected LVEDP rise under LV-to-aorta LVAD in the context of transcatheter aortic valve implantation (TAVI) and concomitant multi-vessel PCI.

Case summary
A patient with acute heart failure, severely depressed systolic LV function, severe aortic stenosis, and multi-vessel coronary artery disease underwent TAVI and concomitant PCI under pulsatile LVAD. Notably, the patient experienced unexpected shortness of breath and elevated LVEDP while under LVAD, which normalized immediately upon LVAD removal.

Discussion
Pulsatile LVAD enhances cardiac output by providing pulsatile support through a percutaneous bi-directional flow catheter. Despite expectations of reduced LVEDP and improved myocardial oxygen supply under LVAD support, we observed high LVEDP and clinical complaints of shortness of breath following TAVI and multi-vessel PCI. This case illustrates that an LVAD across the aortic valve may immobilize aortic leaflets and generate acute aortic regurgitation.
Genomic Consequences of Isolation and Inbreeding in an Island Dingo Population
Authors: Leon-Apodaca Ana V , Kumar Manoharan , del Castillo Andres , Conroy Gabriel C , Lamont Robert W , Ogbourne Steven , Cairns Kylie M , Borburgh Liz , Behrendorff Linda , Subramanian Sankar , Szpiech Zachary A 
Published: June 2024

Abstract
Dingoes come from an ancient canid lineage that originated in East Asia around 8,000 to 11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K’gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K’gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequence data is lacking from this population. Here, we include five new whole-genome sequences of K’gari dingoes. We analyze a total of 18 whole-genome sequences of dingoes sampled from mainland Australia and K’gari to assess the genomic consequences of their demographic histories. Long (&gt;1 Mb) runs of homozygosity (ROHs)—indicators of inbreeding—are elevated in all sampled dingoes. However, K’gari dingoes showed significantly higher levels of very long ROH (&gt;5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K’gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.
Pathways to hypermutation in high-grade gliomas: Mechanisms, syndromes, and opportunities for immunotherapy
Authors: Haynes Tuesday , Gilbert Mark R , Breen Kevin , Yang Chunzhang 
Published: June 2024

Abstract
Despite rapid advances in the field of immunotherapy, including the success of immune checkpoint inhibition in treating multiple cancer types, clinical response in high-grade gliomas (HGGs) has been disappointing. This has been in part attributed to the low tumor mutational burden (TMB) of the majority of HGGs. Hypermutation is a recently characterized glioma signature that occurs in a small subset of cases, which may open an avenue to immunotherapy. The substantially elevated TMB of these tumors most commonly results from alterations in the DNA mismatch repair pathway in the setting of extensive exposure to temozolomide or, less frequently, from inherited cancer predisposition syndromes. In this review, we discuss the genetics and etiology of hypermutation in HGGs, with an emphasis on the resulting genomic signatures, and the state and future directions of immuno-oncology research in these patient populations.
Surviving the Game
Authors: Rebillard Fanny 
Published: June 2024

Abstract
Fanny Rebillard discusses the issues surrounding the archiving of video game music. Building over the preexisting research about game preservation and music preservation through recordings in popular music studies and ethnomusicology, Rebillard identifies a number of problems, including those of changes in audio format and the loss of elements related to interactivity and graphics. She discusses how the resolving of these issues during the archiving process, especially through published soundtracks, can provide new perspectives on the wider place of game music. The organization of tracks in such archives is important, and Rebillard closes the chapter with some suggestions for published game music typologies, focusing on the broad categories of completion level and track list organization.
Ludomusical Narrativity
Authors: Grasso Julianne 
Published: June 2024

Abstract
Julianne Grasso’s chapter provides a means to account for music in video games through a narrative perspective. While ludic structures in games (challenges, exploration) are often understood in opposition to narrative structures (story, characters), musical forms help reconcile these experiences for the player. Her aim is to show that, within the perception that musical loops and repetitions (particularly in early video games) promote a feeling of timelessness, the use of music implies narrative form and so enhances the narrativization of the play experience. Indeed, Grasso argues with the aid of case studies, music can be used to shape interactive play and, in some cases, “the enacted narrative is fundamentally musical.”
Hard Limitations and Soft Possibilities
Authors: Burke Kevin R. 
Published: June 2024

Abstract
Kevin R. Burke provides a survey and assessment of the hardware and software that powered early video game sound and analyzes how the hardware limitations and innovative software led to specific compositional styles across platform developers. Throughout, Burke’s focus is on the home consoles of the chiptune era, and he develops a “systematic” approach for the analysis of the audio hardware and software systems, systems that determine the challenges posed, and the possibilities afforded the games’ composers. Burke provides also a glossary of selected digital audio terminology pertinent to the video games industry, a list of video game audio formats, and a table of programmable sound generators used in the video games industry detailing their developer, the number of channels they have, and significant console and PC video games producers using these generators.
Claude Debussy’s Piano Music and the Evocation of Atmosphere and Humor in Video Games
Authors: Bhogal Gurminder Kaur 
Published: June 2024

Abstract
Gurminder Kaur Bhogal’s chapter is an exploration of the influence and direct use of Claude Debussy’s piano music: for instance, how his ethereal “floating sounds” as found in works such as “Clair de Lune” have directed game designers’ attentions toward the creation of various atmospheres and moods in video games, as well as the possibilities that these afford the player. For Bhogal, Debussy’s music and video game compositions that draw from it are effective in creating the virtual spaces players are invited to inhabit, where atmospheres and moods fashioned by the music can touch the player and make them feel.
Music and Sound in Early Film-to-Game Adaptations
Authors: O’Hara William 
Published: June 2024

Abstract
William O’Hara’s chapter examines the use and transformation of sound and music in film-to-game adaptations, focusing on the format’s rise in popularity during the 1980s. O’Hara contends that, rather than assessing the game’s fidelity to the film, game adaptations are best viewed as a new form of media convergence. Using archival evidence, O’Hara sheds light on cross-media relationships during the adaptation process and uncovers cooperation and tension between different industries—changes and compromises had to be made in the games’ audio design due to the exigencies of different technologies and narrative forms and the requirements of intellectual property law and advertising.
Video Games Alive
Authors: Greenfield-Casas Stefan 
Published: June 2024

Abstract
Stefan Greenfield-Casas reviews the growing phenomenon of live concerts of video game music, both offering a typology of these concerts as well as asking if the experience of attending such concerts has an aesthetic effect on the concertgoer’s personal memory of their experience of the game they have played. Greenfield-Casas’s analysis is rooted in the game fans’ experiences, and he constructs a theory of “ludic liveness” to argue that attendance at such concerts provokes experiences of replaying the games—what he calls “replayful listening.” Ultimately, he argues that video game music, remediated through live concerts by way of concert arrangements, becomes ontologically validated in the real world through this process.
Pop Shove-It, Pop Music
Authors: Millea James 
Published: June 2024

Abstract
James Millea focuses on the Tony Hawk’s Pro Skater series of video games, its use of popular music, and how this transmediality between game culture and music culture shapes the series’ “projection of authenticity.” Millea critiques the vogue for viewing the music of video games through the lens of cinema—the ways in which popular music is used in the series have a markedly different genesis, that of music videos and television and other media depicting the culture of skateboarding. The transmediality of popular music and the series’ games finds purchase in the skateboarding community through the creation of audiovisual relationships that are anything but cinematic.
Valuations of target items are drawn towards unavailable decoy items due to prior expectations
Authors: Izakson Liz , Yoo Minhee , Hakim Adam , Krajbich Ian , Webb Ryan , Levy Dino J 
Published: June 2024

Abstract
When people make choices, the items they consider are often embedded in a context (of other items). How this context affects the valuation of the specific item is an important question. High-value context might make items appear less attractive because of contrast—the tendency to normalize perception of an object relative to its background—or more attractive because of assimilation—the tendency to group objects together. Alternatively, a high-value context might increase prior expectations about the item's value. Here, we investigated these possibilities. We examined how unavailable context items affect choices between two target items, as well as the willingness-to-pay for single targets. Participants viewed sets of three items for several seconds before the target(s) were highlighted. In both tasks, we found a significant assimilation-like effect where participants were more likely to choose or place a higher value on a target when it was surrounded by higher-value context. However, these context effects were only significant for participants’ fastest choices. Using variants of a drift-diffusion model, we established that the unavailable context shifted participants’ prior expectations towards the average values of the sets but had an inconclusive effect on their evaluations of the targets during the decision (i.e. drift rates). In summary, we find that people use context to inform their initial valuations. This can improve efficiency by allowing people to get a head start on their decision. However, it also means that the valuation of an item can change depending on the context.
The Poem on the Door: John Milton’s Sonnet VIII and the Defence of London 1642–1643
Authors: Sawday Jonathan 
Published: June 2024

Abstract
This essay offers a substantial reappraisal and reinterpretation of John Milton’s ‘Sonnet VIII’ (‘Captain or Colonel, or Knight in Arms’) first printed in 1645. Arguing that Milton’s sonnet was written in response to the construction of London’s defences which were built in anticipation of a royalist siege in 1642–1643, the essay: a) analyses the ‘locodescriptive’ character of a poem designed as a ‘found’ text, within a city in which messages of many different kinds were publicly displayed; b) uncovers a hitherto unrecognized classical source for Milton’s sonnet; c) examines the significance of Milton’s deployment of a third-person narrative voice in the poem; d) discusses Milton’s own role within London as the city prepared for an assault by royalist troops; e) considers Milton’s poem as a highly topical protest against parliamentarian property destruction and confiscation in London in 1642–1643; f) identifies the most likely individuals to whom Milton’s sonnet was addressed, while also revising the generally assumed date of the poem’s composition; and finally g) situates the poem within the context of Milton’s evolving political views in the 1640s.
Integration of beta counting system with ORION-DSP coupled to NaI(Tl) detector—a comparative study with an HPGe detector
Authors: Rupa Nyapathy , Kumar Pavan , Shankar Madhavi , Reddy Ram Mohan , Rao Bala Bhaskara , Mahalakshmi Balasubramanian 
Published: June 2024

Abstract
The integration of the ORION digital signal processing-based MCA system coupled with a 3″ × 3″ NaI(Tl) detector assembly with a GM detector for counting beta (β) has eliminated the need for a standalone β-γ method in which U3O8 is determined by gross β and gross γ counting. Uraniferous and mixed U-Th samples were taken up for study and compared with the results obtained from Canberra p-type coaxial high resolution gamma ray spectrometry detector. In uraniferous samples, U3O8 values obtained are within ±10%, whereas in the case of mixed U-Th samples, U3O8 values are within ±15%. Regression graphs drawn between the outcomes from the two analytical systems indicate R2 &gt; 0.95 for Ra(eU3O8) and ThO2. In uraniferous samples, the R2 value for U3O8 was found to be &gt; 0.99, but in mixed U-Th samples, it is 0.92. The closeness of agreement between the results obtained from two methods at various concentrations over the analytical range shows that the integrated system is suitable for the quantitative determination of eU3O8, U3O8, Ra(eU3O8), ThO2 and K in geological rock samples.
Clinicians’ Use of Choice Framing in ICU Family Meetings*
Authors: Hart Joanna L. , Malik Leena , Li Carrie , Summer Amy , Ogunduyile Lon , Steingrub Jay , Lo Bernard , Zlatev Julian , White Douglas B. 
Published: June 2024

OBJECTIVES:
To quantify the frequency and patterns of clinicians’ use of choice frames when discussing preference-sensitive care with surrogate decision-makers in the ICU.

DESIGN:
Secondary sequential content analysis.

SETTING:
One hundred one audio-recorded and transcribed conferences between surrogates and clinicians of incapacitated, critically ill adults from a prospective, multicenter cohort study.

SUBJECTS:
Surrogate decision-makers and clinicians.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
Four coders identified preference-sensitive decision episodes addressed in the meetings, including topics such as mechanical ventilation, renal replacement, and overall goals of care. Prior critical care literature provided specific topics identified as preference-sensitive specific to the critical care context. Coders then examined each decision episode for the types of choice frames used by clinicians. The choice frames were selected a priori based on decision science literature. In total, there were 202 decision episodes across the 101 transcripts, with 20.3% of the decision episodes discussing mechanical ventilation, 19.3% overall goals of care, 14.4% renal replacement therapy, 14.4% post-discharge care (i.e., discharge location such as a skilled nursing facility), and the remaining 32.1% other topics. Clinicians used default framing, in which an option is presented that will be carried out if another option is not actively chosen, more frequently than any other choice frame (127 or 62.9% of decision episodes). Clinicians presented a polar interrogative, or a “yes or no question” to accept or reject a specific care choice, in 43 (21.3%) decision episodes. Clinicians more frequently presented options emphasizing both potential losses and gains rather than either in isolation.

CONCLUSIONS:
Clinicians frequently use default framing and polar questions when discussing preference-sensitive choices with surrogate decision-makers, which are known to be powerful nudges. Future work should focus on designing interventions promoting the informed use of these and the other most common choice frames used by practicing clinicians.