bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transforming estimated breeding values from observed to probability scale: how to make categorical data analyses more efficient
Authors: Hidalgo Jorge , Misztal Ignacy , Tsuruta Shogo , Bermann Matias , Retallick Kelli , Garcia Andre , Bussiman Fernando , Lourenco Daniela 
Published: October 2024

Abstract
Threshold models are often used in genetic analysis of categorical data, such as calving ease. Solutions in the liability scale are easily transformed into probabilities; therefore, estimated breeding values are published as the probability of expressing the category of main interest and are the industry’s gold standard because they are easy to interpret and use for selection. However, because threshold models involve nonlinear equations and probability functions, implementing such a method is complex. Challenges include long computing time and convergence issues, intensified by including genomic data. Linear models are an alternative to overcome those challenges. Estimated breeding values computed using linear models are highly correlated (≥0.96) with those from threshold models; however, the lack of a transformation from the observed to the probability scale limits the use of linear models. The objective of this study was to propose transformations from observed to probability scale analogous to the transformation from liability to probability scale. We assessed computing time, peak memory use, correlations between estimated breeding values, and estimated genetic trends from linear and threshold models. With 11M animals in the pedigree and almost 965k genotyped animals, linear models were 5× faster to converge than threshold models (32 vs. 145 h), and peak memory use was the same (189 GB). The transformations proposed provided highly correlated probabilities from linear and threshold models. Correlations between direct (maternal) estimated breeding values from linear and threshold models and transformed to probabilities were ≥0.99 (0.97) for all animals in the pedigree, sires with/without progeny records, or animals with phenotypic records; therefore, estimated genetic trends were analogous, suggesting no loss of genetic progress in breeding programs that would adopt linear instead of threshold models. Furthermore, linear models reduced computing time by 5-fold compared to the threshold models; this enables weekly genetic evaluations and opens the possibility of using multi-trait models for categorical traits to improve selection effectiveness.
Children Born of Conflict-Related Sexual Violence as Direct Victims under International Criminal Law
Authors: Mionki Judy 
Published: October 2024

Abstract
This article explores specific cases of children born of conflict-related sexual violence (CRSV) to ascertain the precise nature of their harm making them a unique category of victims under international criminal law. It will identify and illustrate, inter alia, the nature, intent and impact of their victimhood, detailing precisely how to prosecute crimes against and affecting these children at the International Criminal Court (ICC). The research eschews the conventional approach of regarding these children as secondary victims by surfacing direct crimes under ICC jurisdiction and positioning them firmly within investigative, prosecutorial and judicial attention.
Surveillance of tick-borne pathogens present in ticks (Acari: Ixodidae) removed from companion animals in Louisiana, USA
Authors: Valdes Sabrina M , Simonson Sean , Scott-Waldron Christine , Balsamo Gary , Grasperge Britton J , Foil Lane D , Balasuriya Udeni , Macaluso Kevin R 
Published: October 2024

Abstract
Current knowledge of tick distribution and tick-borne pathogen presence across Louisiana is limited. Collaborating with veterinarians across the state, ticks removed from companion animals were recovered and assessed for the presence of zoonotic pathogens. A large number of ticks (n = 959) were removed from companion animals and subsequently screened using qPCR for Anaplasma phagocytophilum, Babesia microti, Borrelia burgdorferi, Bartonella henselae, Ehrlichia chaffeensis, and spotted fever group Rickettsia. Five different tick species, Ixodes scapularis (54.5%), Amblyomma americanum (18.4%), Amblyomma maculatum (12.5%), Dermacentor variabilis (11.2%), and Rhipicephalus sanguineus (0.3%) from different regions of Louisiana were collected from October 2018 to July 2019. There were 15 PCR-positive ticks for Rickettsia parkeri (1.6% prevalence), and four ticks were positive for Ehrlichia chaffeensis (0.4% prevalence). This survey identifies ticks and tick-borne pathogens associated with companion animals and areas for future active surveillance.
A unified model for the clustering of quasars and galaxies at z ≈ 6
Authors: Pizzati Elia , Hennawi Joseph F , Schaye Joop , Schaller Matthieu , Eilers Anna-Christina , Wang Feige , Frenk Carlos S , Elbers Willem , Helly John C , Mackenzie Ruari , Matthee Jorryt , Bordoloi Rongmon , Kashino Daichi , Naidu Rohan P , Yue Minghao 
Published: October 2024

ABSTRACT
Recent observations from the EIGER JWST program have measured for the first time the quasar–galaxy cross-correlation function at $z\approx 6$. The autocorrelation function of faint $z\approx 6$ quasars was also recently estimated. These measurements provide key insights into the properties of quasars and galaxies at high redshift and their relation with the host dark matter haloes. In this work, we interpret these data building upon an empirical quasar population model that has been applied successfully to quasar clustering and demographic measurements at $z\approx 2\!-\!4$. We use a new, large-volume N-body simulation with more than a trillion particles, FLAMINGO-10k, to model quasars and galaxies simultaneously. We successfully reproduce observations of $z\approx 6$ quasars and galaxies (i.e. their clustering properties and luminosity functions), and infer key quantities such as their luminosity–halo mass relation, the mass function of their host haloes, and their duty cycle/occupation fraction. Our key findings are (i) quasars reside on average in $\approx 10^{12.5}\, {\rm M}_{\odot }$ haloes (corresponding to $\approx 5\sigma$ fluctuations in the initial conditions of the linear density field), but the distribution of host halo masses is quite broad; (ii) the duty cycle of (UV-bright) quasar activity is relatively low ($\approx 1~{{\ \rm per\ cent}}$); (iii) galaxies (that are bright in [O iii]) live in much smaller haloes ($\approx 10^{10.9}\, {\rm M}_{\odot }$) and have a larger duty cycle (occupation fraction) of $\approx 13~{{\ \rm per\ cent}}$. Finally, we focus on the inferred properties of quasars and present a homogeneous analysis of their evolution with redshift. The picture that emerges reveals a strong evolution of the host halo mass and duty cycle of quasars at $z\approx 2\!-\!6$, and calls for new investigations of the role of quasar activity across cosmic time.
What causes the ultraviolet extinction bump at the cosmic dawn?
Authors: Li Qi , Yang X J , Li Aigen 
Published: October 2024

ABSTRACT
The enigmatic ultraviolet (UV) extinction bump at 2175 $\, {\rm \mathring{\rm A}}$, the strongest spectroscopic absorption feature superimposed on the interstellar extinction curve, has recently been detected at the cosmic dawn by the JWST in JADES-GS-z6-0, a distant galaxy at redshift $z\approx 6.71$, corresponding to a cosmic age of just 800 million years after the big bang. Although small graphite grains have historically long been suggested as the carrier of the 2175 $\, {\rm \mathring{\rm A}}$ extinction bump and graphite grains are expected to have already been pervasive in the early Universe, in this work we demonstrate that small graphite grains are not responsible for the UV extinction bump seen at the cosmic dawn in JADES-GS-z6-0, as the extinction bump arising from small graphite grains is too broad and peaks at wavelengths that are too short to be consistent with what is seen in JADES-GS-z6-0.
Course and Predictors of Adult Spinal Sagittal Disorders
Authors: Mannström Heidi , Multanen Juhani , Ylinen Jari , Hautala Arto , Peuna Arttu , Karttunen Lauri , Pekkanen Liisa , Kyrölä Kati 
Published: October 2024

Study Design.
Prospective case series

Objective.
To study the natural course of adult spinal deformity (ASD) over a10-year period and the determinants associated with postural malalignments.

Summary of Background Data.
ASD comprises a heterogeneous spectrum of abnormalities of the thoracolumbar spine throughout adulthood. Radiographic deterioration of sagittal alignment is a combination of decreased lumbar lordosis (LL), PI-related retroversion of the pelvic tilt (PT), anteriorizing sagittal vertical axis (SVA) and increased T1 pelvic angle (TPA).

Methods.
The full spine radiographs were taken to measure the SRS-Schwab sagittal modifiers PI-LL, PT and SVA to measure the possible change in severity of deformity from the 204 volunteer participants (mean age 62.7 years, 61% female), which were 32% of the 637 consecutive patients with prolonged back pain who originally joined the study in 2012–2013. Each participant completed the Scoliosis Research Society 22r (SRS-22r) questionnaire.

Results.
The mean change in the SRS-Schwab score was 0.4 units (baseline 1.1 vs. follow-up 1.5, P < 0.001) implying deterioration of the spinal deformity. The SRS-Schwab score decreased (n=76, 37%), remained the same (n=102, 50%) or improved (n=26, 13%). Four predictive factors for a change of sagittal alignment were found, of which the poor score in the SRS-22r function domain (P=0.049) and severe pelvic tilt (PT greater than 30°, P=0.006) predicted the change.

Conclusion.
This study showed the variability in how sagittal alignment of the spine change during the 10-year follow-up period. The ASD patients with poor self-assessed functional ability and disturbed pelvic position were associated with the risk of deterioration in spinopelvic alignment. The diversity in the natural course of ASD and the known risk factors highlights the need for tailored advice when planning preventive treatment procedures for ASD patients.

Level of evidence.
3
Impact of Respiratory Syncytial Virus and Severe Acute Respiratory Syndrome Coronavirus 2 Coinfection on Clinical Severity and Outcomes Among Children Hospitalized With Lower Respiratory Tract Infections in Soweto, South Africa
Authors: Mrubata Kitso-Lesedi , Bailie Vicky , Solomon Fatima , Izu Alane , Ncube Musawenkosi , Nunes Marta C. , Dangor Ziyaad , Madhi Shabir A. , Moore David P. , Verwey Charl 
Published: October 2024

Background:
No data are available regarding the interplay and clinical manifestations of respiratory syncytial virus (RSV) and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) coinfection in African children. We compared clinical characteristics and outcomes between RSV-only, SARS-CoV-2–only and RSV/SARS-CoV-2 coinfection lower respiratory tract infections (LRTI) in hospitalized African children.

Methods:
Prospective surveillance of children (0–59 months) hospitalized with severe LRTI was undertaken between March 1, 2020, and March 31, 2023, in Johannesburg, South Africa. Nasopharyngeal swabs for respiratory viruses and clinical data were collected, and clinical characteristics and outcomes were described and compared. Respiratory index of severity in children (RISC) scores were calculated for HIV-uninfected children, and covariates associated with high RISC scores (≥5) were evaluated.

Results:
Seven thousand four hundred fifty-six children [6.1 months (interquartile range, 14.4–18.6); 57.7% male] were enrolled, 1372 (18.4%) testing RSV+/SARS-CoV-2– (RSV only), 223 (3.0%) RSV−/SARS-CoV-2+ (SARS-CoV-2–only) and 28 (0.4%) RSV+/SARS-CoV-2+ (RSV/SARS-CoV-2 coinfection). Children with RSV only and RSV/SARS-CoV-2 coinfection were more likely to present with bronchiolitis than those with SARS-CoV-2–only (673/1372 and 15/28 vs. 46/223; P < 0.001). Children with RSV/SARS-CoV-2 coinfection had more severe disease than those with RSV or SARS-CoV-2–only, as well as a higher RISC score than SARS-CoV-2–only. Weight-for-age Z scores [adjusted risk ratio (aRR): 0.92], room air saturations (aRR: 0.988) and RSV+ status (aRR: 1.40) were independently associated with severe disease.

Conclusions:
Although both RSV and SARS-CoV-2 LRTI occurred commonly, coinfection did not. Children with RSV/SARS-CoV-2 coinfection had a higher prevalence of severe LRTI than those with RSV or SARS-CoV-2–only. These findings reinforce the urgent need for safe and effective RSV and SARS-CoV-2 vaccines, especially in children in low- and middle-income countries, where the burden of disease is the highest and the access to medical resources the lowest.
Treatment of Macrolide-resistant Mycoplasma pneumoniae Pneumonia in Children: A Meta-analysis of Macrolides Versus Tetracyclines
Authors: Bolormaa Erdenetuya , Park Ji Young , Choe Young June , Kang Cho Ryok , Choe Seung Ah , Mylonakis Eleftherios 
Published: October 2024

Background:
The global prevalence of macrolide-resistant Mycoplasma pneumoniae (MRMP) pneumonia infections, particularly in children, is on the rise. It is imperative to assess the clinical efficacies of alternative antibiotics such as tetracyclines to ensure effective treatment, mitigate antibiotic resistance, enhance clinical outcomes, and minimize the spread of resistant strains among MRMP-infected children. The objective of this study was to compare the therapeutic efficacies of macrolides and tetracyclines in treating MRMP pneumonia in children.

Methods:
We systematically searched the literature to identify comparative studies that examined the clinical outcomes of macrolide and tetracycline antibiotics in children with MRMP pneumonia. We conducted a meta-analysis of the mean duration of fever, hospital stay duration, therapeutic efficacies, and time to defervescence to compare macrolides and tetracyclines.

Results:
Eleven studies involving 1143 patients compared the clinical efficacies of macrolides and tetracyclines in children with MRMP pneumonia. The studies were conducted in China, Japan, and Korea, and the outcomes of febrile days, hospital stay duration, therapeutic efficacy, and time to defervescence were analyzed. The macrolides studied were azithromycin and clarithromycin, whereas the tetracyclines included minocycline and doxycycline. The pooled estimate of 5 studies showed that the mean duration of febrile days and hospital stay was longer in the macrolides group than tetracycline group [weighted mean difference = 1.64 days, 95% confidence interval (CI): 0.68–2.59, weighted mean difference = 1.22 days, 95% CI: 0.82–1.62, respectively]. The therapeutic efficacy was significantly lower in the macrolide group than in the tetracycline group (odds ratio: 0.33, 95% CI: 0.20–0.57).

Conclusions:
The clinical efficacy of tetracycline treatment was superior to that of macrolide treatment in children with MRMP pneumonia. However, further research is required to validate these findings and inform evidence-based clinical practice guidelines.
Biomechanical corneal effects of LASIK Xtra compared with conventional FS-LASIK in high myopic eyes
Authors: Kaiser Klemens Paul , Biller Marvin Lucas , Jandewerth Tyll , Davidova Petra , Hemkeppler Eva , Lwowski Christoph , Böhm Myriam , Kohnen Thomas 
Published: October 2024

Purpose:
To investigate the in vivo corneal biomechanical response to FS-LASIK combined with accelerated corneal crosslinking (LASIK Xtra) compared with conventional FS-LASIK (convLASIK) in highly myopic eyes.

Setting:
Department of Ophthalmology, Goethe-University, Frankfurt am Main, Germany.

Design:
Prospective, randomized fellow eye-controlled clinical trial.

Methods:
Patients who received treatment with LASIK Xtra (30mW/cm2, 90 seconds with continuous UV-A) in 1 eye and convLASIK in the other eye were enrolled. Both eyes were subjected preoperatively and 12 months postoperatively to a Corvis ST examination. The stiffness parameter at first applanation (SP-A1), integrated inverse radius (IIR), deformation amplitude (DA), deformation amplitude 2 mm away from apex, and the apical deformation (DARatio2mm) were evaluated.

Results:
The study included 38 high myopic eyes (−7.34 ± 1.02 diopters) of 19 patients. The results of the corneal biomechanical measurement showed a significant reduction in overall corneal stiffness with a significant decrease in postoperative SP-A1 and increase in IIR, DA, and DARatio2mm (P < .001). In a direct comparison, there was no evidence of an increase in corneal stiffness in the LASIK Xtra group compared with the convLASIK group 12 months postoperatively. No statistically significant difference was detected in any of the 4 biomechanical parameters (P > .05).

Conclusions:
The corneal biomechanical response to convLASIK and LASIK Xtra did not vary significantly. With a similar corneal thickness loss, there was no significant difference in the 4 biomechanical metrics between the convLASIK and LASIK Xtra groups. Thus, LASIK Xtra appeared not to have a protective corneal stiffening effect compared with convLASIK 12 months postoperatively.
GPR35 agonists inhibit TRPA1-mediated colonic nociception through suppression of substance P release
Authors: Gupta Rohit A. , Higham James P. , Pearce Abigail , Urriola-Muñoz Paulina , Barker Katie H. , Paine Luke , Ghooraroo Joshua , Raine Tim , Hockley James R. F. , Rahman Taufiq , St John Smith Ewan , Brown Alastair J. H. , Ladds Graham , Suzuki Rie , Bulmer David C. 
Published: October 2024

Abstract
The development of nonopioid analgesics for the treatment of abdominal pain is a pressing clinical problem. To address this, we examined the expression of Gi/o-coupled receptors, which typically inhibit nociceptor activation, in colonic sensory neurons. This led to the identification of the orphan receptor GPR35 as a visceral analgesic drug target because of its marked coexpression with transient receptor potential ankyrin 1 (TRPA1), a mediator of noxious mechanotransduction in the bowel. Building on in silico docking simulations, we confirmed that the mast cell stabiliser, cromolyn (CS), and phosphodiesterase inhibitor, zaprinast, are agonists at mouse GPR35, promoting the activation of different Gi/o subunits. Pretreatment with either CS or zaprinast significantly attenuated TRPA1-mediated colonic nociceptor activation and prevented TRPA1-mediated mechanosensitisation. These effects were lost in tissue from GPR35−/− mice and were shown to be mediated by inhibition of TRPA1-evoked substance P (SP) release. This observation highlights the pronociceptive effect of SP and its contribution to TRPA1-mediated colonic nociceptor activation and sensitisation. Consistent with this mechanism of action, we confirmed that TRPA1-mediated colonic contractions evoked by SP release were abolished by CS pretreatment in a GPR35-dependent manner. Our data demonstrate that GPR35 agonists prevent the activation and sensitisation of colonic nociceptors through the inhibition of TRPA1-mediated SP release. These findings highlight the potential of GPR35 agonists to deliver nonopioid analgesia for the treatment of abdominal pain.
Analgesia and peripheral c-fiber modulation by selective Nav1.8 inhibition in rhesus
Authors: Vardigan Joshua D. , Pall Parul S. , McDevitt Dillon S. , Huang ChienJung , Clements Michelle K. , Li Yuxing , Kraus Richard L. , Breslin Michael J. , Bungard Christopher J. , Nemenov Mikhail I. , Klukinov Mikhail , Burgey Chritopher S. , Layton Mark E. , Stachel Shawn J. , Lange Henry S. , Savitz Alan T. , Santarelli Vincent P. , Henze Darrell A. , Uslaner Jason M. 
Published: October 2024

Abstract
Voltage-gated sodium (Nav) channels present untapped therapeutic value for better and safer pain medications. The Nav1.8 channel isoform is of particular interest because of its location on peripheral pain fibers and demonstrated role in rodent preclinical pain and neurophysiological assays. To-date, no inhibitors of this channel have been approved as drugs for treating painful conditions in human, possibly because of challenges in developing a sufficiently selective drug-like molecule with necessary potency not only in human but also across preclinical species critical to the preclinical development path of drug discovery. In addition, the relevance of rodent pain assays to the human condition is under increasing scrutiny as a number of mechanisms (or at the very least molecules) that are active in rodents have not translated to humans, and direct impact on pain fibers has not been confirmed in vivo. In this report, we have leveraged numerous physiological end points in nonhuman primates to evaluate the analgesic and pharmacodynamic activity of a novel, potent, and selective Nav1.8 inhibitor compound, MSD199. These pharmacodynamic biomarkers provide important confirmation of the in vivo impact of Nav1.8 inhibition on peripheral pain fibers in primates and have high translational potential to the clinical setting. These findings may thus greatly improve success of translational drug discovery efforts toward better and safer pain medications, as well as the understanding of primate biology of Nav1.8 inhibition broadly.
Sex-specific role of RNA-binding protein, pAUF1, on prolonged hypersensitivity after repetitive ischemia with reperfusion injury
Authors: Quijas Meranda M. , Queme Luis F. , Woodke Samantha T. , Weyler Alex A. , Buesing Dana , Butterfield Ally , Joshi Diya P. , Mitxelena-Balerdi Irati , Ulrich-Lai Yvonne M. , Jankowski Michael P. 
Published: October 2024

Abstract
Repetitive ischemia with reperfusion (I/R) injury is a common cause of myalgia. Ischemia with reperfusion injuries occur in many conditions that differentially affect males and females including complex regional pain syndrome and fibromyalgia. Our preclinical studies have indicated that primary afferent sensitization and behavioral hypersensitivity caused by I/R injury may be due to sex-specific gene expression in the dorsal root ganglia (DRG) and distinct upregulation of growth factors and cytokines in the affected muscles. To determine how these unique gene expression programs may be established in a sex-dependent manner in a model that more closely mimics clinical scenarios, we used a developed prolonged ischemic myalgia model in mice whereby animals experience repeated I/R injuries and compared behavioral results with unbiased and targeted screening strategies in male and female DRG. Several distinct proteins were found to be differentially expressed in male and female DRG, including phosphorylated AU-rich element RNA-binding protein (pAUF1), which is known to regulate gene expression. Nerve-specific siRNA-mediated knockdown of AUF1 inhibited prolonged hypersensitivity in females only, whereas overexpression of AUF1 in male DRG neurons increased pain-like responses. AUF1 knockdown was able to specifically inhibit repeated I/R-induced gene expression in females potentially downstream of prolactin receptor signaling. Data suggest RNA-binding proteins such as pAUF1 may underlie the sex-specific effects on DRG gene expression that modulates behavioral hypersensitivity after repeated I/R injury through prolactin signaling. This study may aid in finding distinct receptor differences related to the evolution of acute to chronic ischemic muscle pain development between sexes.
Signals in Health Inequity
Authors: Fiori Kevin P. , Levano Samantha R. , Colman Silvie , Oliveira Jason , Haughton Jessica , Lemberg Miya , Chambers Earle C. , Telzak Andrew , Spurrell-Huss Elizabeth , Sirois Adam , Stark Allison , Racine Andrew 
Published: October 2024

Previous research has demonstrated that social determinants of health are drivers of medical utilization, cost, and health outcomes. In this study, we compared the mean annual total cost to deliver health services per patient by health-related social need (HRSN) status and total HRSNs using linear regression and ANOVA, respectively. Patients with ≥1 HRSN (n = 8409) yielded $1772 higher annual costs compared to patients without HRSNs (n = 34 775) (P < .0001). Compared to patients without HRSNs, delivering care to patients with 1 HRSN (n = 4222) cost $1689 (P < .0001) more and to patients with ≥2 HRSN (n = 4187) cost $1856 (P < .0001) more per year.