bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decoding the diagnostic and therapeutic potential of microbiota using pan-body pan-disease microbiomics
Authors: Schmartz Georges P. , Rehner Jacqueline , Gund Madline P. , Keller Verena , Molano Leidy-Alejandra G. , Rupf Stefan , Hannig Matthias , Berger Tim , Flockerzi Elias , Seitz Berthold , Fleser Sara , Schmitt-Grohé Sabina , Kalefack Sandra , Zemlin Michael , Kunz Michael , Götzinger Felix , Gevaerd Caroline , Vogt Thomas , Reichrath Jörg , Diehl Lisa , Hecksteden Anne , Meyer Tim , Herr Christian , Gurevich Alexey , Krug Daniel , Hegemann Julian , Bozhueyuek Kenan , Gulder Tobias A. M. , Fu Chengzhang , Beemelmanns Christine , Schattenberg Jörn M. , Kalinina Olga V. , Becker Anouck , Unger Marcus , Ludwig Nicole , Seibert Martina , Stein Marie-Louise , Hanna Nikolas Loka , Martin Marie-Christin , Mahfoud Felix , Krawczyk Marcin , Becker Sören L. , Müller Rolf , Bals Robert , Keller Andreas 
Published: September 2024

AbstractThe human microbiome emerges as a promising reservoir for diagnostic markers and therapeutics. Since host-associated microbiomes at various body sites differ and diseases do not occur in isolation, a comprehensive analysis strategy highlighting the full potential of microbiomes should include diverse specimen types and various diseases. To ensure robust data quality and comparability across specimen types and diseases, we employ standardized protocols to generate sequencing data from 1931 prospectively collected specimens, including from saliva, plaque, skin, throat, eye, and stool, with an average sequencing depth of 5.3 gigabases. Collected from 515 patients, these samples yield an average of 3.7 metagenomes per patient. Our results suggest significant microbial variations across diseases and specimen types, including unexpected anatomical sites. We identify 583 unexplored species-level genome bins (SGBs) of which 189 are significantly disease-associated. Of note, the existence of microbial resistance genes in one specimen was indicative of the same resistance genes in other specimens of the same patient. Annotated and previously undescribed SGBs collectively harbor 28,315 potential biosynthetic gene clusters (BGCs), with 1050 significant correlations to diseases. Our combinatorial approach identifies distinct SGBs and BGCs, emphasizing the value of pan-body pan-disease microbiomics as a source for diagnostic and therapeutic strategies.
CEP192 localises mitotic Aurora-A activity by priming its interaction with TPX2
Authors: Holder James , Miles Jennifer A , Batchelor Matthew , Popple Harrison , Walko Martin , Yeung Wayland , Kannan Natarajan , Wilson Andrew J , Bayliss Richard , Gergely Fanni 
Published: September 2024

AbstractAurora-A is an essential cell-cycle kinase with critical roles in mitotic entry and spindle dynamics. These functions require binding partners such as CEP192 and TPX2, which modulate both kinase activity and localisation of Aurora-A. Here we investigate the structure and role of the centrosomal Aurora-A:CEP192 complex in the wider molecular network. We find that CEP192 wraps around Aurora-A, occupies the binding sites for mitotic spindle-associated partners, and thus competes with them. Comparison of two different Aurora-A conformations reveals how CEP192 modifies kinase activity through the site used for TPX2-mediated activation. Deleting the Aurora-A-binding interface in CEP192 prevents centrosomal accumulation of Aurora-A, curtails its activation-loop phosphorylation, and reduces spindle-bound TPX2:Aurora-A complexes, resulting in error-prone mitosis. Thus, by supplying the pool of phosphorylated Aurora-A necessary for TPX2 binding, CEP192:Aurora-A complexes regulate spindle function. We propose an evolutionarily conserved spatial hierarchy, which protects genome integrity through fine-tuning and correctly localising Aurora-A activity.
Neuro-Affirming Practices for Voice Care
Authors: Kapila Ruchi , Gaddy Caroline , Pilchman Ry 
Published: September 2024

Purpose:
The purpose of this article is to educate speech-language pathologists (SLPs) on the role of neuro-affirming care in voice and upper airway interventions. This publication provides an introduction and background for neuro-affirming care, rationale for its inclusion in the areas of voice and upper airway, current limitations in providing neuro-affirming care in traditional voice centers, and case scenarios to provide examples of neuro-affirming practices in voice interventions (Appendix B).

Conclusions:
Given that neurodivergence often co-occurs with myriad conditions, it is likely SLPs across scope of practice, including voice and upper airway, will encounter neurodivergent individuals with voice and communication needs and will require greater awareness of neuro-affirming care to adequately serve these populations. Descriptions of neuro-affirming care principles, limitations and adaptations needed for neuro-affirming care in traditional voice settings, and case scenarios illustrating implementation of certain principles are provided. Future directions for neuro-affirming care in voice and upper airway should include neurodivergent researchers and clinicians in the investigation and implementation of these interventions.
YOLO‐RSFM: An efficient road small object detection method
Authors: Tang Pei , Ding Zhenyu , Lv Mao , Jiang Minnan , Xu Weikai 
Published: September 2024

AbstractTo tackle challenges in road multi‐object detection, such as object occlusion, small object detection, and multi‐scale object detection difficulties, a new YOLOv8n‐RSFM structure is proposed. The key improvement of this structure lies in the introduction of the transformer decoder head, which optimizes the matching between the ground truth and predicted boxes, thereby effectively addressing issues of object overlap and multi‐scale detection. Additionally, a small object detection layer is incorporated to retain crucial information beneficial for detecting small objects, significantly improving the detection accuracy for small targets. To enhance learning capacity and reduce redundant computations, the FasterNet backbone is employed to replace CSPDarknet53, thus accelerating the training process. Finally, the INNER‐MPDIoU loss function is introduced to replace the original algorithm's complete IoU to accelerate the convergence and obtain more accurate regression results. A series of experiments were conducted on different datasets. The experimental results show that the proposed model YOLOv8N‐RSFM outperforms the original model YOLOv8n in small target detection. On the VisDrone, TinyPerson, and VSCrowd datasets, the mean accuracy percentage improved by 7.9%, 12.3%, and 4.5%, respectively.
Running with the bulls
Authors: Winter Andrew J. , Benisty Myriam , Shuai Linling , Dûchene Gaspard , Cuello Nicolás , Anania Rossella , Cadiou Corentin , Joncour Isabelle 
Published: September 2024

Context. Stars and planets form in regions of enhanced stellar density, subjecting protoplanetary discs to gravitational perturbations from neighbouring stars. Observations in the Taurus star-forming region have uncovered evidence of at least three recent, star-disc encounters that have truncated discs (HV/DO Tau, RW Aurigae, and UX Tau), raising questions about the frequency of such events.
Aims. We aim to assess the probability of observing truncating star-disc encounters in Taurus.
Methods. We generated a physically motivated dynamical model including binaries and a spatial-kinematic substructure to follow the historical dynamical evolution of the Taurus star-forming region. We used this model to track star-disc encounters and the resulting outer disc truncation over the lifetime of Taurus.
Results. A quarter of discs are truncated below 30 au by dynamical encounters, but this truncation mostly occurs in binaries over the course of a few orbital periods, on a timescale ≲0.1 Myr. Nonetheless, some truncating encounters still occur up to the present age of Taurus. Strongly truncating encounters (ejecting ≳10 percent of the disc mass) occur at a rate ∼10 Myr−1, sufficient to explain the encounter between HV and DO Tau ∼0.1 Myr ago. If encounters that eject only ∼1 percent of the disc mass are responsible for RW Aurigae and UX Tau, then they are also expected with encounter rate Γenc ∼ 100–200 Myr−1. However, the observed sample of recent encounters is probably incomplete, since these examples occurred in systems that are not consistent with a random drawing from the mass function. One more observed example would statistically imply additional physics, such as replenishment of the outer disc material.
Conclusions. The marginal consistency of the frequency of observed recent star-disc encounters with theoretical expectations underlines the value of future large surveys searching for external structures associated with recent encounters. The outcome of such a survey offers a highly constraining, novel probe of protoplanetary disc physics.
Penile Reconstruction with Radial Forearm Free Flap—Present State of the Art
Authors: Jain Vasundhra , S. Shravan Rai K. , G. Srilekha Reddy , Guin Devajyoti , Gupta Shikha , Murarka Anil , Sharma Mohit 
Published: September 2024

Abstract
Background Patients with congenital or acquired penile defects face significant psychological trauma. Various methods for penile reconstruction have been described of which the free radial artery forearm flap using the tube-within-tube design is found to be the most commonly used. We have assimilated the best practices described at different times in our bid to standardize the technique and have strived to make it reproducible. The reconstructed phalluses with this method can withstand the test of time, allowing the patients to lead a normal life.
Materials and Methods We conducted a retrospective review of the past 16 years and collected data for all radial forearm free flap phalloplasties. We have modified the design originally described by Biemer. The urethra is kept 1 cm longer than the shaft and the proximal 5 mm of the prospective urethra is not sutured to allow for spatulation of the urethral anastomosis.
Results A total of nine patients were included out of which six patients had congenital malformations, two had traumatic injuries, and one had penile carcinoma. Six out of the nine patients had implants placed which were wrapped in fascia lata graft. One of these patients experienced displacement of the implant which needed to be repositioned. Three patients faced postoperative complications. All patients had tactile and erogenous sensation at the tip of the glans at the end of 1 year and all patients could micturate while standing. One patient's esthetic and functional outcome was compromised. One of the married patients has fathered a child through normal sexual intercourse.
Conclusion Radial forearm phalloplasty done by this technique allows us to achieve consistently stable functional and esthetic outcomes. We firmly believe that this standardized protocol for penile reconstruction could be of great benefit to patients as well as to the treating reconstructive surgeon in their quest to achieve a completely rehabilitated patient.
A new ground electronic state potential energy surface of HeLiH+: Analytical representation and investigation of the dynamics of He + LiH+ (v = 0, j = 0) → LiHe+ + H reaction
Authors: Rawat Ajay Mohan Singh , Alamgir Mohammed , Goswami Sugata , Mahapatra Susanta 
Published: September 2024

An improved global potential energy surface (PES) for the electronic ground state of the HeLiH+ system is reported. The data points are calculated at the full configuration-interaction level of theory and extrapolated to the complete basis set limit. The fitting procedure implements a combination of neural network and Aguado–Paniagua functional forms to fit the ab initio data points. The fitted surface reproduces the ab initio data points accurately in short as well as long ranges and has an overall root mean square error of 1.76 × 10−3 eV (14.21 cm−1) in energy space &lt;10 and 9.28 × 10−4 eV (7.48 cm−1) upto 2 eV. The optimized global minimum is also accurately reproduced using the fitted surface. To establish the accuracy of the new PES, dynamics investigation of the He + LiH+(v = 0, j = 0) → LiHe+ + H reaction is performed using the Coriolis coupled quantum mechanical and quasi-classical trajectory methods. The results, such as integral cross sections and rate constants, show the effect of the opening of the collision-induced dissociation (CID) channel at low collision energy and are significantly different from the earlier study of Tacconi et al. [Phys. Chem. Chem. Phys. 14, 637–645 (2012)]. These discrepancies appear to be a result of the treatment of the CID channel in the dynamics calculations, which is excluded from the reactive channel in the current work.
Dried distiller’s grains in the diets of feedlot lambs: implications for production, carcass characteristics and rumen morphometrics
Authors: dos Santos Isabela J. , G. Dias Junior Paulo C. , S. Vicente Ana C. , G. de Assis Rhaissa , Carlis Matheus S. P. , Biava Janaina S. , Alvarenga Tharcilla I. R. C. , Comelli Jamile H. , Pires Alexandre V. , Relling Alejandro E. , Ferreira Evandro M. 
Published: September 2024

Context The demand and production of renewable fuels are boosting the production of biofuels. Agricultural industries have been playing a role in the increase of ethanol production from corn and, consequently, their by-products. Dried distiller’s grain (DDG) is a by-product of corn ethanol and can be used as a source of protein and energy in the diet of feedlot lambs. Aims The objectives of this experiment were to evaluate the effects of including DDG in high-concentrate diets on performance, rumen morpho-histology, and carcass characteristics in feedlot lambs. Methods Forty-five Santa Inês × Dorper male lambs with an initial body weight of 21 ± 3.2 kg (mean ± s.d.) and 82 ± 12 days old (mean ± s.d.) were distributed in a randomised complete-block design (nine blocks and five treatments). The experimental diets contained 900 g/kg of concentrate and 100 g/kg of coastcross hay, and DDG was used in replacement of soybean meal and corn. Lambs were fed one of the following five diets for 112 days: control without DDG (0DDG), or diet with 150 (150DDG), 300 (300DDG), 450 (450DDG) and 600 (600DDG) g/kg DM of DDG. Key results The inclusion of DDG from 150 up to 600 g/kg DM in the diet of the lambs linearly decreased (P < 0.01) dry-matter intake (DMI), net energy of maintenance intake, net energy of gain, average daily gain, final body weight and feed efficiency (P < 0.01). The inclusion of DDG linearly decreased (P ≤ 0.04) hot carcass weight, cold carcass weight, hot carcass yield and cold carcass yield. For ruminal morpho-histology, there was a linear decrease in the area of papillae and absorptive surface area (P < 0.01) Conclusions An increase in the DDG level from 150 to 600 g/kg DM in the diet of lambs negatively affected feedlot performance, with detrimental effects on carcass traits and the development of rumen papillae. The lambs showed low acceptance of DDG, even at the lowest level of dietary inclusion (150g/kg DM) as DMI was impaired. Implications DDG should be used with caution in diets for finishing lambs. Dietary inclusion of DDG up to 150 g/kg DM is recommended. Higher inclusions levels may significantly affect performance and carcass weight and yield.
State and trend of surface soil organic carbon stocks and associated nutrients in Tongatapu, Kingdom of Tonga
Authors: Stockmann U. , Farrell M. , Carter T. , Krawitz S. , Wong V. N. L. , Minoneti V. , Finau D. , Sharma A. , Barringer J. , Manu V. T. , Karunaratne S. , Macdonald B. C. T. 
Published: September 2024

Context The status and temporal trend in soil organic carbon (SOC) stocks are unknown in Tongatapu, the main island and agriculture hub of the Kingdom of Tonga. This is a critical shortcoming in relation to agricultural sustainability and food security. Aim Evaluate the soil organic carbon stocks within Tongatapu’s main soil series relative to historic data. Methods Historical studies were used to establish a SOC baseline for different soil series on Tongatapu. These sites were revisited and sampled in 2018 and the SOC content of the soil samples was determined using a dry combustion analytical method. Changes in the soil nitrogen (N), phosphorus (P), and sulfur (S) nutrient pools were estimated using stoichiometry. Key results There was a decline in SOC stocks over the last 20–30 years. The mineralisation of soil organic matter, as represented by the decline in SOC stocks, has likely also reduced the pool of N, P, and S. Soils with the greatest SOC stocks (>50 t C ha−1) declined at the highest rates relative to soils with SOC stocks of 20–30 t C ha−1. Conclusion Agricultural practices that are employed on Tongatapu have caused the decline of SOC stocks and are threatening sustainable agriculture production. Implications This study shows that new farming and soil management practices should be employed that build SOC and broader soil functions.
Comparison of arm cavity optical losses for the two wavelengths of the Einstein telescope gravitational wave detector
Authors: Le Jean Maxime , Degallaix Jerome , Hofman David , Pinard Laurent , Forest Danièle , Granata Massimo , Michel Christophe , Steinlechner Jessica , Amra Claude , Lequime Michel , Zerrad Myriam 
Published: September 2024

Abstract
A new generation of gravitational wave detectors is currently being designed with the likely use of a different laser wavelength compared to current instruments. The estimation of the optical losses for this new wavelength is particularly relevant to derive the detector sensitivity and also to anticipate the optical performances of future instruments. In this article, we measured the absorption and angle-resolved scattering of several mirror samples in order to compare optical losses at a wavelength of 1064 and 1550 nm. In addition, we have carried out simulations of the Einstein Telescope arm cavities at 1064 and 1550 nm taking into account losses due to surface low-spatial frequency flatness. Our results suggest that optical losses as measured at 1064 nm are about twice as large as those at 1550 nm as predicted with a simple model.
Paddle-wheels, friction, and moving-boundary work
Authors: Crespi Andrea 
Published: September 2024

Abstract
Moving-boundary work, also called pressure-volume work or expansion work, is perhaps the main form of work discussed in introductory courses about thermodynamics. Here, we take a particular definition of this kind of thermodynamic work. On this basis, we show with simple reasoning that significant phenomena involving dissipation of mechanical energy, often mentioned as well in those courses but with a vague formalization, can be traced back right to moving-boundary processes. We refer in particular to the conversion of external work into internal energy in paddle-wheel experiments such as the one conducted by J. P. Joule in 1850, and to other processes involving friction.
Absorption of electromagnetic waves by cylindrical surface plasmon resonance
Authors: Zhou Mingjie , Tan Haiyun , Zhuge Lanjian , Wu Xuemei 
Published: September 2024

Abstract
The absorption characteristics of cylindrical surface plasmon resonance (CSPR) have been studied. We demonstrated that a single plasma column with CSPRs can achieve high absorptivity at the plasmon frequency. We also studied the effects of plasma density and collision frequency on the absorptivity. As both of them increase, the corresponding absorptivity tends to increase first and then decrease, but with different reasons. Such manifestation is explained by analyzing transmission and reflection spectra in both cases, as well as magnetic field distribution patterns at the frequency of plasmon. On the one hand, the increase in plasma density leads to the enhancement of plasmons, improving transmittance; On the other hand, the increase in collision frequency leads to a weakening of plasmons and an increase in reflectivity. Finally, we investigated the absorption characteristics of plasmons in the plasma photonic crystals (PPCs) structure and overcame the absorption attenuation caused by the increase in plasma density by increasing the number of plasma columns. Meanwhile, the absorption generated by surface plasmon resonance is not affected by the lattice constant of PPCs. The research has shown that efficient absorption can be achieved using CSPR, resulting in extremely high absorptivity when using fewer plasma columns. Finally, we verified the absorption ability of CSPRs through experiments.
Enhancing the yellow-LED performance with improvised pre-stress alleviation layer: a theoretical and numerical analysis
Authors: Singh Chandra Prakash , Ghosh Kankat 
Published: September 2024

Abstract
The decline in quantum efficiency observed in yellow-LEDs emitting wavelength around ∼575 nm, commonly known as the ‘green-yellow gap’, is predominantly influenced by the fact that high In-content In

x

Ga1−x
N/GaN (x = 30%) yellow-multiple quantum wells (yellow-MQWs) are typically grown on GaN template. This configuration leads to substantial compressive stress, contributing to the structural defects and the significant quantum confined stark effect. To address this challenge, our strategy involves achieving superior lattice constant alignment within the yellow-MQWs by growing a pre-stress alleviation layer (PSAL) prior to the growth of yellow-MQWs. Our comprehensive theoretical study, coupled with numerical simulations, aimed to explore the impact of two distinct practical and commercially viable PSAL approaches: pre-quantum well, comprising short periods of InYGa1−Y
N/GaN and pre-thin layer, incorporating a thin layer of In
Z
Ga1−Z
N. Following a thorough analysis of these approaches, we propose an innovative improved optimized structure that demonstrates the highest internal quantum efficiency of 74.2%, minimal efficiency droop of 14.7% at 20 A cm−2, and a 20 nm favourable red-shift in electroluminescence characteristic with narrower full-width-half-maximum of 28 nm without any adverse effect on the pure yellow-color emission at 20 A cm−2. This advancement holds promise for providing better crystal quality and addressing the green-yellow gap issue in yellow-LED technology.
UV and blue light cut-off filters using phosphorus doped carbon quantum dots extracted from raw egg yolk
Authors: Hegazy M M , Ayad M M , Ghali M 
Published: September 2024

Abstract
Using raw egg yolk and phosphoric acid, a simple hydrothermal treatment for synthesizing carbon quantum dots (CQDs) has been developed for the manufacture of UV and blue light-blocking filters. Several samples with different doping ratios of phosphoric acid were prepared. Namely: reference (REF.), 25%, 50%, 75% and 100%. The synthesized CQDs were embedded in polyvinyl alcohol (PVA) to produce blocking-light films with desired optical properties. Six films were prepared, one of which was PVA alone, and the other five samples were the prepared CQDs, with different phosphorus doping levels, mixed with PVA in a 1:1 ratio. We aimed to test the ability of these films to block ultraviolet rays and blue light. The experimental results revealed that the prepared films were able to block the blue light, emitted from a 450 nm blue LED, with blocking ratios of 7%, 17.5%, 27%, 30%, 37% and 70% for the films: PVA alone, REF., 25%, 50%, 75% and 100%, respectively. Moreover, it was found that these phosphorus-doped CQDs films can prevent destructive UV light with substantial value reaching 86%. These results suggest that carbon dots, derived from raw egg yolk, can be effectively applied to block harmful UV and blue lights.