bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intellectual property issues for open science practices in genomic-related health research and innovation in Africa
Authors: Adaji Aishatu Eleojo , Abdulrauf Lukman Adebisi 
Published: December 2024

ABSTRACT
This paper considers the applicability and implications of intellectual property rights (IPRs) for open science practices in the context of genomic-related health research and innovation in Africa. The first part provides a brief background of the gaps in genomics and health research in Africa, highlighting the possible role of open science in facilitating collaborative research to address the peculiar health needs of the continent. The second part examines intellectual property protection in genomic-related health research and innovation in Africa, outlining some of the existing legal instruments and policies guiding the application of IPRs, focusing on patents and copyrights. Thereafter, the paper examined how intellectual property standards could impact the adoption of open science in genomics health research in Africa. In doing this, the paper considers the role they could play as enablers of open science practices in genomics health research and innovation and the potential challenges they pose. The paper concludes with recommendations regarding aspects of the intellectual property policies and legal frameworks in Africa that could be calibrated to overcome potential challenges and, thereby, stimulate the adoption of an open science model and promote open, collaborative genomics health research and innovation in the continent.
Drinking pattern and time lag of alcohol consumption with colorectal cancer risk in US men and women
Authors: Li Xinyi , Hur Jinhee , Zhang Yin , Song Mingyang , Smith-Warner Stephanie A , Liang Liming , Mukamal Kenneth J , Rimm Eric B , Giovannucci Edward L 
Published: December 2024

Abstract

Background
Association between light to moderate alcohol consumption and colorectal cancer (CRC) incidence remains understudied, especially regarding drinking pattern, beverage type, and temporal aspects.

Methods
Hazard ratios (HRs) and 95% confidence intervals (CIs) for time to CRC diagnosis were estimated among 137 710 participants. Estimates based on remote (eg, &gt;10 years before follow-up) and recent (eg, the preceding 10 years before follow-up) alcohol intake, using different cutoffs (eg, 8, 10, 12 years) and mutual adjustment, enabled separating independent effects and investigating time lag of alcohol–CRC association.

Results
In total, 3599 CRC cases were documented over 3 decades. Light to moderate drinking was associated with an increased CRC risk only in men: HR (95% CI) for 5-14.9 and 15-29.9 vs 0 g/day of alcohol intake was 1.19 (1.01 to 1.41) and 1.38 (1.13 to 1.67). In women, that for 0.1-4.9 and 5-14.9 vs 0 g/day of alcohol was 1.07 (0.96 to 1.20) and 1.05 (0.91 to 1.20). Drinkers with both high drinking frequency and daily intake had the highest CRC risk, suggesting total alcohol intake was the critical factor. We estimated the time lag between alcohol consumption and CRC occurrence to be 8 to 12 years. Former drinkers did not experience a significant reduction in CRC risk even after 10 years of quitting or reducing consumption.

Conclusions
Based on 2 cohorts of health professionals, our findings suggest that the increased risk of CRC associated with alcohol intake is driven mainly by total quantity and remote intake. Former drinkers did not experience an immediate reduction in CRC risk after quitting or reducing consumption.
miPEPs and cPEPs as tools to monitor plant gene expression and to develop alternative strategies in agriculture
Authors: Thuleau Patrice , Ormancey Mélanie , Plaza Serge , Combier Jean-Philippe 
Published: December 2024

Abstract
In order to develop a sustainable agriculture respecting the environment and to reduce chemical inputs, a new strategy has emerged in recent years, based on the use of products targeting plant natural defense and growth mechanisms. In this context, a few years ago we demonstrated the existence in plants of regulatory peptides called miPEPs for ‘microRNA-encoded peptides’. miRNAs are small RNAs that down-regulate the expression of numerous genes in eukaryotes. miPEPs increase the amount of their cognate miRNA, resulting in an even greater decrease in the expression of genes targeted by these miRNAs. Thus, the application of an artificial miPEP to plants causes a phenotype associated with a change in the genes targeted by the corresponding miRNA. More recently we also identified new regulatory peptides, namely cPEPs for ‘complementary peptides’, capable of enhancing the activity of a given protein, independently of any increase in transcriptional activity. Moreover, as for the miPEPs, the external application of these new peptides makes it possible to regulate the phenotypes associated with the targeted proteins. This review highlights the most recent advances in the potential use of miPEPs and cPEPs in agronomy to improve plant development and stress tolerance.
Is the repeat worth it? Optimizing syndromic panel pathogen detection protocols
Authors: Cerqueira Filipe M , Do Linh , Enderle Janet , Ren Ping 
Published: December 2024

Abstract

Objective
The aim of the study was to compare the cost and clinical impact of repeating BioFire FilmArray gastrointestinal (GI) and respiratory (RP) panel assays with 3 vs 4 pathogen targets positive.

Method
We analyzed 12,027 GI and RP panels to evaluate our retesting policy, which retested panels with 3 or more detected pathogens (3-pathogen protocol) compared with the manufacturer’s 4-pathogen (4-pathogen protocol) recommendation. We compared the retesting results, calculated the cost implications, and reviewed the clinical impact on antibiotic prescriptions and patient outcomes.

Results
Retesting with our 3-pathogen protocol revealed that 81% (39/48) of GI and 76% (26/34) of RP panels had identical results, whereas 19% (9/48) of GI and 24% (8/34) of RP panels showed discrepancies on retesting. The additional cost incurred by our protocol compared with the manufacturer’s protocol was $9820.32. There was no evidence that our more stringent policy affected antibiotic prescription or clinical outcomes.

Conclusion
Our more stringent 3-pathogen protocol for retesting panels did not improve patient management compared with the manufacturer’s 4-pathogen protocol but resulted in unnecessary costs and increased the risk of depleting testing kits during supply shortages. Consequently, we adopted the manufacturer’s suggestions, highlighting the need to balance clinical rigor with cost-effectiveness in laboratory testing protocols.
Methodology
Authors: Schenone Aldo L. , Reyes Eliana 
Published: December 2024

Abstract
Nuclear cardiology practices have evolved at unprecedented pace in recent years. Advances in camera technology (single-photon emission computed tomography (SPECT) and positron emission tomography (PET)), paired with new methods of imaging reconstruction, filtering, and correction, have resulted in significant improvement in image quality, faster imaging, and lower radiation exposure. In parallel, innovation in imaging acquisition with novel patient-centred protocols has enhanced patient satisfaction and throughput of imaging laboratories, while further reducing radiation exposure. Contemporary radionuclide myocardial perfusion imaging, with ECG-gated cine imaging, hybrid imaging, and parametric imaging, offers a comprehensive and accurate ischaemic evaluation that includes myocardial perfusion, ventricular function, myocardial blood flow, and coronary calcium score. Understanding of these novel technologies, methodologies, and practices is paramount for the optimal conduction and interpretation of nuclear cardiology studies in the current era.
Amyloidosis
Authors: Jaber Wael A. , Gimelli Alessia 
Published: December 2024

Abstract
This chapter delves into the pivotal role of nuclear cardiology techniques in the comprehensive evaluation of cardiac amyloidosis, a challenging and often underdiagnosed condition. The chapter explores the ability of single-photon emission computed tomography (SPECT) and positron emission tomography (PET) with specific radiotracers to provide crucial diagnostic insights, including early detection and subtype differentiation. With the spotlight on integration of multimodal imaging and emerging radiopharmaceuticals, this chapter offers a resource for clinicians navigating through the use of nuclear cardiology in the context of amyloidosis.
Novel Use of Exoskeleton Assist Device in an Ankle Fracture: A Case Report
Authors: Lax John W 
Published: December 2024

ABSTRACT
Lower extremity fractures and musculoskeletal injuries are among the leading causes of morbidity for Special Operations Forces (SOF), frequently resulting in prolonged immobilization and weeks of therapeutic exercises and strength training to return to full status. This is a case of a 34-year-old Caucasian combat rescue officer with a stable right distal fibula (Weber B) fracture managed with early mobilization and assisted plantarflexion using a Dephy Exoboot device. Early mobilization resulted in no adverse events and resulted in a significant reduction in down-time compared with usual care. This case highlights the novel use of a commercially available exoskeleton device to minimize recovery time and speed return to duty for an injured SOF operator. Although further study is required to determine thresholds of safety and applicability, it suggests a potential role for assistive exoskeleton devices in the recovery of injured operators.
The MeerKAT Pulsar Timing Array: the first search for gravitational waves with the MeerKAT radio telescope
Authors: Miles Matthew T , Shannon Ryan M , Reardon Daniel J , Bailes Matthew , Champion David J , Geyer Marisa , Gitika Pratyasha , Grunthal Kathrin , Keith Michael J , Kramer Michael , Kulkarni Atharva D , Nathan Rowina S , Parthasarathy Aditya , Singha Jaikhomba , Theureau Gilles , Thrane Eric , Abbate Federico , Buchner Sarah , Cameron Andrew D , Camilo Fernando , Moreschi Beatrice E , Shaifullah Golam , Shamohammadi Mohsen , Possenti Andrea , Krishnan Vivek Venkatraman 
Published: December 2024

ABSTRACT
Pulsar timing arrays search for nanohertz-frequency gravitational waves by regularly observing ensembles of millisecond pulsars over many years to look for correlated timing residuals. Recently the first evidence for a stochastic gravitational wave background has been presented by the major arrays, with varying levels of significance (${\sim} 2\sigma \!-\! 4\sigma$). In this paper, we present the results of background searches with the MeerKAT Pulsar Timing Array. Although of limited duration (4.5 yr), the ${\sim} 250\,000$ arrival times with a median error of just $3 \, \mu {\rm s}$ on 83 pulsars make it very sensitive to spatial correlations. Detection of a gravitational wave background requires careful modelling of noise processes to ensure that any correlations represent a fit to the underlying background and not other misspecified processes. Under different assumptions about noise processes, we can produce either what appear to be compelling Hellings–Downs correlations of high significance ($3\sigma \!-\! 3.4\sigma$) with a spectrum close to that which is predicted, or surprisingly, under slightly different assumptions, ones that are insignificant. This appears to be related to the fact that many of the highest precision MeerKAT Pulsar Timing Array pulsars are in close proximity and dominate the detection statistics. The sky-averaged characteristic strain amplitude of the correlated signal in our most significant model is $h_{{\rm c}, {\rm yr}} = 7.5^{+0.8}_{-0.9} \times 10^{-15}$ measured at a spectral index of $\alpha =-0.26$, decreasing to $h_{{\rm c}, {\rm yr}} = 4.8^{+0.8}_{-0.9} \times 10^{-15}$ when assessed at the predicted $\alpha =-2/3$. These data will be valuable as the International Pulsar Timing Array project explores the significance of gravitational wave detections and their dependence on the assumed noise models.
The MeerKAT Pulsar Timing Array: Maps of the gravitational wave sky with the 4.5-yr data release
Authors: Grunthal Kathrin , Nathan Rowina S , Thrane Eric , Champion David J , Miles Matthew T , Shannon Ryan M , Kulkarni Atharva D , Abbate Federico , Buchner Sarah , Cameron Andrew D , Geyer Marisa , Gitika Pratyasha , Keith Michael J , Kramer Michael , Lasky Paul D , Parthasarathy Aditya , Reardon Daniel J , Singha Jaikhomba , Venkatraman Krishnan Vivek 
Published: December 2024

ABSTRACT
In an accompanying publication, the MeerKAT Pulsar Timing Array (MPTA) Collaboration reports tentative evidence for the presence of a stochastic gravitational wave background, following observations of similar signals from the European and Indian Pulsar Timing Arrays, the North American Nanohertz Observatory for Gravitational Waves, the Parkes Pulsar Timing Array, and the Chinese Pulsar Timing Array. If such a gravitational wave background signal originates from a population of inspiraling supermassive black hole binaries, the signal may be anisotropically distributed in the sky. In this paper, we evaluate the anisotropy of the MPTA signal using a spherical harmonic decomposition. We discuss complications arising from the covariance between pulsar pairs and the regularization of the Fisher matrix. Applying our method to the $4.5 \hbox{-}\text{yr}$ data set, we obtain two forms of sky maps for the three most sensitive MPTA frequency bins between $7 \ {\rm and} \ 21 \, {\rm nHz}$. Our ‘clean maps’ estimate the distribution of gravitational wave strain power with minimal assumptions. Our radiometer maps answer the question: Is there a statistically significant point source? We find a noteworthy hotspot in the $7 \, \mathrm{nHz}$ clean map with a p-factor of $p=0.015$ (not including trial factors). Future observations are required to determine if this hotspot is of astrophysical origin.
The High Time Resolution Universe Pulsar Survey – XIX. A coherent GPU-accelerated reprocessing and the discovery of 71 pulsars in the Southern Galactic plane
Authors: Sengar R , Bailes M , Balakrishnan V , Barr E D , Bhat N D R , Burgay M , Bernadich M C I , Cameron A D , Champion D J , Chen W , Flynn C M L , Jameson A , Johnston S , Keith M J , Kramer M , Morello V , Ng C , Possenti A , Stevenson S , Shannon R M , van Straten W , Wongphechauxsorn J 
Published: December 2024

ABSTRACT
We conducted a GPU-accelerated reprocessing of $\sim 87~{{\ \rm per\ cent}}$ of the archival data from the High Time Resolution Universe South Low Latitude (HTRU-S LowLat) pulsar survey by implementing a pulsar search pipeline that was previously used to reprocess the Parkes Multibeam Pulsar Survey (PMPS). We coherently searched the full 72-min observations of the survey with an acceleration search range up to $|50|\, \rm m\, s^{-2}$, which is most sensitive to binary pulsars experiencing nearly constant acceleration during 72 min of their orbital period. Here we report the discovery of 71 pulsars, including six millisecond pulsars, of which five are in binary systems, and seven pulsars with very high dispersion measures (DM $\gt 800 \, \rm pc \, cm^{-3}$). These pulsar discoveries largely arose by folding candidates to a much lower spectral signal-to-noise ratio than in previous surveys and by exploiting the coherence of folding over the incoherent summing of the Fourier components to discover new pulsars as well as candidate classification techniques. We show that these pulsars could be fainter and on average more distant as compared with both the previously reported 100 HTRU-S LowLat pulsars and the background pulsar population in the survey region. We have assessed the effectiveness of our search method and the overall pulsar yield of the survey. We show that through this reprocessing we have achieved the expected survey goals, including the predicted number of pulsars in the survey region, and discuss the major causes why these pulsars were missed in previous processing of the survey.
A comparative study of galaxy evolution with four different active galactic nucleus torus models and two different host geometries
Authors: Papadopoulos Michail , Papadopoulou Lesta Vicky , Michos Ioannis , Farrah Duncan , Efstathiou Andreas 
Published: December 2024

ABSTRACT
Estimating physical quantities such as the star formation rate, stellar mass, and active galactic nucleus (AGN) fraction of galaxies is a key step in understanding galaxy formation and evolution. In order to estimate the uncertainties in the predicted values for these quantities, in this paper we explore the impact of adopting four different AGN torus models in fitting the multiwavelength spectral energy distributions (SED) of galaxies. We also explore the impact of adopting two different geometries for the host, a spheroidal geometry, more appropriate for late-stage mergers, and a disc geometry, more appropriate for galaxies forming stars with secular processes. We use optical to submillimetre photometry from the Herschel Extragalactic Legacy Project (HELP) and utilize a Markov chain Monte Carlo SED-fitting code. We use exclusively radiative transfer models for the AGN torus as well as for the starburst and host galaxy. We concentrate on a sample of 200 galaxies at $z\approx 2$, selected in the ELAIS-N1 field. All galaxies have a detection at 250 $\mu \mathrm{ m}$ which ensures the presence of a starburst. We find that the stellar mass and star formation rate of the galaxies can be robustly estimated by the SED fitting but the AGN fraction depends very much on the adopted torus model. We also find that the vast majority of the galaxies in our sample are better fitted by a spheroidal geometry and lie above the main sequence. Our method predicts systematically higher SFR and lower stellar mass than the popular energy balance method cigale.
The nature of low-luminosity AGNs discovered by JWST based on clustering analysis: progenitors of low-z quasars?
Authors: Arita Junya , Kashikawa Nobunari , Onoue Masafusa , Yoshioka Takehiro , Takeda Yoshihiro , Hoshi Hiroki , Shimizu Shunta 
Published: December 2024

ABSTRACT
JWST has discovered many faint AGNs at high-z by detecting their broad Balmer lines. However, their high number density, lack of X-ray emission, and overly high black hole masses with respect to their host stellar masses suggest that they are a distinct population from general type-1 quasars. Here, we present clustering analysis of 27 low-luminosity broad-line AGNs found by JWST (JWST AGNs) at $5\lt z\lt 6$ based on cross-correlation analysis with 679 photometrically-selected galaxies to characterize their host dark matter halo (DMH) masses. From the angular and projected cross-correlation functions, we find that their typical DMH mass is $\log (M_{\mathrm{halo}}/h^{-1}\, \mathrm{M_\odot }) = 11.46_{-0.25}^{+0.19},$ and $11.53_{-0.20}^{+0.15}$, respectively. This result implies that the host DMHs of these AGNs are ${\sim} 1$ dex smaller than those of luminous quasars. The DMHs of the JWST AGNs at $5\lt z\lt 6$ are predicted to grow to $10^{12-13}\, h^{-1}\, \mathrm{M_\odot }$ at $z\lesssim 3$, which is comparable to that of a more luminous quasar at the same epoch. Applying the empirical stellar-to-halo mass ratio to the measured DMH mass, we evaluate their host stellar mass as $\log (M_*/\mathrm{M_\odot })=9.48_{-0.41}^{+0.31},$ and $9.60_{-0.33}^{+0.24}$, which are higher than some of those estimated by the SED fitting. We also evaluate their duty cycle as $f_{\mathrm{duty}}=0.37_{-0.15}^{+0.19}$ per cent, corresponding to ${\sim} 4\times 10^6$ yr as the lifetime of the JWST AGNs. While we cannot exclude the possibility that the JWST AGNs are simply low-mass type-1 quasars, these results suggest that the JWST AGNs are a different population from type-1 quasars and the progenitors of quasars at $z\lesssim 3$.
Co-evolution and Gene Transfers Drive Speciation Patterns in Host-Associated Bacteria
Authors: Stott Caroline , Diop Awa , Raymann Kasie , Bobay Louis-Marie 
Published: December 2024

Abstract
Microbial communities that maintain symbiotic relationships with animals evolve by adapting to the specific environmental niche provided by their host, yet understanding their patterns of speciation remains challenging. Whether bacterial speciation occurs primarily through allopatric or sympatric processes remains an open question. In addition, patterns of DNA transfers, which are pervasive in bacteria, are more constrained in a closed host-gut system. Eusocial bees have co-evolved with their specialized microbiota for over 85 million years, constituting a simple and valuable system to study the complex dynamics of host-associated microbial interactions. Here, we studied the patterns of speciation and evolution of seven specialized gut bacteria from three clades of eusocial bee species: western honey bees, eastern honey bees, and bumblebees. We conducted genomic analyses to infer species delineation relative to the patterns of homologous recombination (HR), and horizontal gene transfer (HGT). The studied bacteria presented various modes of evolution and speciation relative to their hosts, but some trends were consistent across all of them. We observed a clear interruption of HR between bacteria inhabiting different bee hosts, which is consistent with a mechanism of allopatric speciation, but we also identified interruptions of HR within hosts, suggesting recent or ongoing sympatric speciation. In contrast to HR, we observed that HGT events were not constrained by species borders. Overall, our findings show that in host-associated bacterial populations, patterns of HR and HGT have different impacts on speciation patterns, which are driven by both allopatric and sympatric speciation processes.
Less, but More: New Insights From Appendicularians on Chordate Fgf Evolution and the Divergence of Tunicate Lifestyles
Authors: Sánchez-Serna Gaspar , Badia-Ramentol Jordi , Bujosa Paula , Ferrández-Roldán Alfonso , Torres-Águila Nuria P , Fabregà-Torrus Marc , Wibisana Johannes N , Mansfield Michael J , Plessy Charles , Luscombe Nicholas M , Albalat Ricard , Cañestro Cristian 
Published: December 2024

Abstract
The impact of gene loss on the diversification of taxa and the emergence of evolutionary innovations remains poorly understood. Here, our investigation on the evolution of the Fibroblast Growth Factors (FGFs) in appendicularian tunicates as a case study reveals a scenario of “less, but more” characterized by massive losses of all Fgf gene subfamilies, except for the Fgf9/16/20 and Fgf11/12/13/14, which in turn underwent two bursts of duplications. Through phylogenetic analysis, synteny conservation, and gene and protein structure, we reconstruct the history of appendicularian Fgf genes, highlighting their paracrine and intracellular functions. An exhaustive analysis of developmental Fgf expression in Oikopleura dioica allows us to identify four associated evolutionary patterns characterizing the “less, but more” conceptual framework: conservation of ancestral functions; function shuffling between paralogs linked to gene losses; innovation of new functions after the duplication bursts; and function extinctions linked to gene losses. Our findings allow us to formulate novel hypotheses about the impact of Fgf losses and duplications on the transition from an ancestral ascidian-like biphasic lifestyle to the fully free-living appendicularians. These hypotheses include massive co-options of Fgfs for the development of the oikoblast and the tail fin; recruitment of Fgf11/12/13/14s into the evolution of a new mouth, and their role modulating neuronal excitability; the evolutionary innovation of an anterior tail FGF signaling source upon the loss of retinoic acid signaling; and the potential link between the loss of Fgf7/10/22 and Fgf8/17/18 and the loss of drastic metamorphosis and tail absorption in appendicularians, in contrast to ascidians.