bluuebunny/crossref_metadata_2025_split huggingface dataset:
A covariant formulation for cosmological radiative transfer of the 21-cm line
Authors: Chan Jennifer Y H , Han Qin , Wu Kinwah , McEwen Jason D 
Published: April 2024

ABSTRACT
The 21-cm hyperfine line of neutral hydrogen is a useful tool to probe the conditions of the Universe during the Dark Ages, Cosmic Dawn, and the Epoch of Reionization. In most of the current calculations, the 21-cm line signals at given frequencies are computed, using an integrated line-of-sight line opacity, with the correction for cosmological expansion. These calculations have not fully captured the line and continuum interactions in the radiative transfer, in response to evolution of the radiation field and the variations of thermal and dynamic properties of the line-of-sight medium. We construct a covariant formulation for the radiative transfer of the 21-cm line and derive the cosmological 21-cm line radiative transfer (C21LRT) equation. The formulation properly accounts for local emission and absorption processes and the interaction between the line and continuum when the radiation propagates across the expanding Universe to the present observer. Our C21LRT calculations show that methods simply summing the line optical depth could lead to error of 5 per cent in the 21-cm signals for redshift z ∼ 12–35 and of $\gt 10~{{\ \rm per\ cent}}$ for redshift z ≲ 8. Proper covariant radiative transfer is therefore necessary for producing correct theoretical templates for extracting information of the structural evolution of the Universe through the Epoch of Reionization from the 21-cm tomographic data.
The Number and Pattern of Viral Genomic Reassortments are not Necessarily Identifiable from Segment Trees
Authors: Lin Qianying , Goldberg Emma E , Leitner Thomas , Molina-París Carmen , King Aaron A , Romero-Severson Ethan O 
Published: April 2024

Abstract
Reassortment is an evolutionary process common in viruses with segmented genomes. These viruses can swap whole genomic segments during cellular co-infection, giving rise to novel progeny formed from the mixture of parental segments. Since large-scale genome rearrangements have the potential to generate new phenotypes, reassortment is important to both evolutionary biology and public health research. However, statistical inference of the pattern of reassortment events from phylogenetic data is exceptionally difficult, potentially involving inference of general graphs in which individual segment trees are embedded. In this paper, we argue that, in general, the number and pattern of reassortment events are not identifiable from segment trees alone, even with theoretically ideal data. We call this fact the fundamental problem of reassortment, which we illustrate using the concept of the “first-infection tree,” a potentially counterfactual genealogy that would have been observed in the segment trees had no reassortment occurred. Further, we illustrate four additional problems that can arise logically in the inference of reassortment events and show, using simulated data, that these problems are not rare and can potentially distort our observation of reassortment even in small data sets. Finally, we discuss how existing methods can be augmented or adapted to account for not only the fundamental problem of reassortment, but also the four additional situations that can complicate the inference of reassortment.
Comprehensive profiling of L1 retrotransposons in mouse
Authors: Zhang Xuanming , Celic Ivana , Mitchell Hannah , Stuckert Sam , Vedula Lalitha , Han Jeffrey S 
Published: April 2024

Abstract
L1 elements are retrotransposons currently active in mammals. Although L1s are typically silenced in most normal tissues, elevated L1 expression is associated with a variety of conditions, including cancer, aging, infertility and neurological disease. These associations have raised interest in the mapping of human endogenous de novo L1 insertions, and a variety of methods have been developed for this purpose. Adapting these methods to mouse genomes would allow us to monitor endogenous in vivo L1 activity in controlled, experimental conditions using mouse disease models. Here, we use a modified version of transposon insertion profiling, called nanoTIPseq, to selectively enrich young mouse L1s. By linking this amplification step with nanopore sequencing, we identified &gt;95% annotated L1s from C57BL/6 genomic DNA using only 200 000 sequencing reads. In the process, we discovered 82 unannotated L1 insertions from a single C57BL/6 genome. Most of these unannotated L1s were near repetitive sequence and were not found with short-read TIPseq. We used nanoTIPseq on individual mouse breast cancer cells and were able to identify the annotated and unannotated L1s, as well as new insertions specific to individual cells, providing proof of principle for using nanoTIPseq to interrogate retrotransposition activity at the single-cell level in vivo.
RNase E searches for cleavage sites in RNA by linear diffusion: direct evidence from single-molecule FRET
Authors: Banerjee Tithi , Rothenberg Eli , Belasco Joel G 
Published: April 2024

Abstract
The ability of obstacles in cellular transcripts to protect downstream but not upstream sites en masse from attack by RNase E has prompted the hypothesis that this mRNA-degrading endonuclease may scan 5′-monophosphorylated RNA linearly for cleavage sites, starting at the 5′ end. However, despite its proposed regulatory importance, the migration of RNase E on RNA has never been directly observed. We have now used single-molecule FRET to monitor the dynamics of this homotetrameric enzyme on RNA. Our findings reveal that RNase E slides along unpaired regions of RNA without consuming a molecular source of energy such as ATP and that its forward progress can be impeded when it encounters a large structural discontinuity. This movement, which is bidirectional, occurs in discrete steps of variable length and requires an RNA ligand much longer than needed to occupy a single RNase E subunit. These results indicate that RNase E scans for cleavage sites by one-dimensional diffusion and suggest a possible molecular mechanism.
Massively parallel identification of sequence motifs triggering ribosome-associated mRNA quality control
Authors: Chen Katharine Y , Park Heungwon , Subramaniam Arvind Rasi 
Published: April 2024

Abstract
Decay of mRNAs can be triggered by ribosome slowdown at stretches of rare codons or positively charged amino acids. However, the full diversity of sequences that trigger co-translational mRNA decay is poorly understood. To comprehensively identify sequence motifs that trigger mRNA decay, we use a massively parallel reporter assay to measure the effect of all possible combinations of codon pairs on mRNA levels in S. cerevisiae. In addition to known mRNA-destabilizing sequences, we identify several dipeptide repeats whose translation reduces mRNA levels. These include combinations of positively charged and bulky residues, as well as proline-glycine and proline-aspartate dipeptide repeats. Genetic deletion of the ribosome collision sensor Hel2 rescues the mRNA effects of these motifs, suggesting that they trigger ribosome slowdown and activate the ribosome-associated quality control (RQC) pathway. Deep mutational scanning of an mRNA-destabilizing dipeptide repeat reveals a complex interplay between the charge, bulkiness, and location of amino acid residues in conferring mRNA instability. Finally, we show that the mRNA effects of codon pairs are predictive of the effects of endogenous sequences. Our work highlights the complexity of sequence motifs driving co-translational mRNA decay in eukaryotes, and presents a high throughput approach to dissect their requirements at the codon level.
High-density generation of spatial transcriptomics with STAGE
Authors: Li Shang , Gai Kuo , Dong Kangning , Zhang Yiyang , Zhang Shihua 
Published: April 2024

Abstract
Spatial transcriptome technologies have enabled the measurement of gene expression while maintaining spatial location information for deciphering the spatial heterogeneity of biological tissues. However, they were heavily limited by the sparse spatial resolution and low data quality. To this end, we develop a spatial location-supervised auto-encoder generator STAGE for generating high-density spatial transcriptomics (ST). STAGE takes advantage of the customized supervised auto-encoder to learn continuous patterns of gene expression in space and generate high-resolution expressions for given spatial coordinates. STAGE can improve the low quality of spatial transcriptome data and smooth the generated manifold of gene expression through the de-noising function on the latent codes of the auto-encoder. Applications to four ST datasets, STAGE has shown better recovery performance for down-sampled data than existing methods, revealed significant tissue structure specificity, and enabled robust identification of spatially informative genes and patterns. In addition, STAGE can be extended to three-dimensional (3D) stacked ST data for generating gene expression at any position between consecutive sections for shaping high-density 3D ST configuration.
Awake pediatric brain-MRI: a fast multi-sequence scan augmented with motion compensated single-shot 2D acquisitions
Authors: van Niekerk Adam , Svoboda Jan , Aspelin Åsa , Sprenger Tim , Rydén Henric , Norbeck Ola , Avventi Enrico , Johansson Katarina , Rygaard Natalie , Lindberg Peter , Wickström Ronny , Delgado Anna Falk , Skare Stefan 
Published: April 2024

Abstract

Background
Magnetic resonance imaging (MRI) is susceptible to motion artifacts, a particular challenge in pediatric imaging. External motion tracking devices and navigator techniques have been previously explored, but challenges persist necessitating sedation.

Purpose
To establish a new awake brain-MRI exam tolerated by children with diagnostic quality images.

Materials and Methods
Participants were prospectively recruited and investigated using an in-house developed multi-sequence scan called NeuroMix that produces T1-weighted, T2-weighted, T2*-weighted, T2-FLAIR, and diffusion-weighted images in under 3 minutes. Additionally, a self-created motion tracking device was attached to participants' foreheads to perform prospective motion correction (PMC) on 2D single-shot sequences that produce higher resolution images of the same contrasts as NeuroMix.
Three neuroradiologists scored the completed series for artifacts. The effects of age group (&lt;5 vs ≥5 years) and sequence type (NeuroMix vs PMC) were evaluated with a Chi2-test.

Results
Of the 64 participants recruited (mean age 6.7 years [2.7 standard deviation]) 58 completed their examination. Head motion recorded during PMC sequences revealed prevalent superior-inferior displacements [25% (67/293) exceeding 13.2 mm], and chin-up/down rotations [25% (67/293) exceeding 13.7°]. Sequence redundancy through NeuroMix and PMC scans resulted in 93% (54/58) of completed examinations having all series essential for producing an MRI-report rated as artifact-free, and therefore a report of high confidence in 84% (54/64) of participants. 22% (13/58) of completed exam reports could have been written using NeuroMix alone, the remaining required PMC- T2-weighted or T2-FLAIR sequences.

Conclusion
This protocol reliably provided diagnostic quality images and reports with high radiologist confidence and could reduce the use of procedure sedation in children.
Longitudinal study of patients with anti-SAE antibody-positive dermatomyositis: a multicenter cohort study in China
Authors: Zhang Yingfang , Liu Lei , Duan Xinwang , Pi Hui , Jiang Lili , Li Jiang , Wang Guochun , Shu Xiaoming 
Published: April 2024

Abstract

Objectives
To describe the longitudinal study and long-term prognosis of a multicentre large inception cohort of patients with anti-SAE positive DM.

Methods
We retrospectively recruited patients with anti-SAE+DM in four tertiary referral centres from China between March 2005 and December 2022. Long-term survival analysis was performed on the enrolled patients. The Myositis Damage Index and Cutaneous Disease Area and Severity Index were used to evaluate the degree of different organ damage and the extent of skin rashes. Longitudinal CT patterns were analysed. Phenotypes were characterized using unsupervised cluster analysis.

Results
All-cause death occurred in 10.5% (4/38) of all patients, in which three patients succumbed to malignancies at 13, 18 and 36 months. Most patients had favourable long-term outcomes, 35.3% of them were in drug-free remission. Skin rashes showed significant improvement evaluated by Cutaneous Disease Area and Severity Index with time. However, damage to different systems was observed in 70.6% of the surviving patients using the Myositis Damage Index, which mainly consisted of skin damage, accounting for 47.1%. Nine patients with anti-SAE+DM-associated interstitial lung disease underwent repeat CT showed marked radiological improvement at 6 months or being stable after 12 months. In further, different characteristics and outcomes were also showed in three clusters identified by unsupervised analysis.

Conclusions
Anti-SAE+DM is characterized with a lower mortality rate and the development of malignancies being the primary cause of death. Patients who survived showed notable cutaneous damage, while the interstitial lung disease tends to stabilize. Clusters identified with unsupervised analysis could assist physicians in identifying a higher risk of mortality.
Temporal trends in mortality in patients with systemic lupus erythematosus: a Danish population-based matched cohort study
Authors: Kristensen Salome , Duch Kirsten , Soussi Bolette Gylden , de Saint-Aubain Constance Jensina , Laugesen Monika , Dreyer Lene 
Published: April 2024

Abstract

Objective
Excess mortality has been demonstrated in patients with SLE compared with the general population. We aimed to investigate the 5-year and 10-year all-cause mortality in patients with SLE compared with the general population in recent decades.

Methods
This was a Danish nationwide population-based exposure-matched cohort study. Incident cases of SLE diagnosed between 1996 and 2015 were identified using administrative health registries and followed until 2020, allowing for 5 and 10 years of follow-up. Patients with SLE were matched 1:5 on age and sex with individuals from the Danish general population. Time-to-event analyses were performed using the pseudo-observation approach.

Results
In total, 1351 incident cases of SLE and 6755 matched controls were identified. The crude risk difference (RD) for 5-year mortality decreased over the study period, from 10.3% (95% CI 6.5–14.1%) to 4.6% (95% CI 1.4–7.8%) for patients with SLE compared with controls. The relative risk (RR) for 5-year mortality decreased similarly in the same period. Adjustment for comorbidities revealed lower RD and RR for mortality in patients with SLE compared with controls, but the decreasing trend remained. The crude and adjusted RD and RR for 10-year mortality did not change over the calendar period. The 10-year RR was highest in young patients with SLE (&lt;50 years of age).

Conclusion
The 5-year mortality risk decreased over time for both patients with SLE and matched controls. However, excess 5-year mortality for patients with SLE in the most recent calendar period and excess mortality late in their disease course remained. Continued focus on preventing disease progression and comorbidity is required.
Minimum Wage Policy and Poverty in Indonesia
Authors: Merdikawati Nurina , Izzati Ridho Al 
Published: April 2024

Abstract
This paper investigates whether minimum wage policy played any significant role in poverty reduction in Java Island, Indonesia, between 2002 and 2014. Its identification strategy exploits variation in minimum wages over time within pairs of geographically proximate districts. The study finds that the minimum wage has a distributional impact on wage workers just below the 20th percentile up to those in the middle of the wage distribution, with no overall loss of employment. However, the minimum wage policy has no distributional impact on per capita household expenditure, and a limited effect on changes in poverty status.
The Effects of Perineural Dexamethasone on Rebound Pain After Nerve Block in Patients with Unicompartmental Knee Arthroplasty A Randomized Controlled Trial
Authors: Li Qingbao , Nie Hanxiao , Wang Zifan , Li Shihong , Wang Yibin , Chen Naiqi , Wang Wei , Xu Fei , Zhang Deli 
Published: April 2024

Objectives:
A single nerve block provides excellent analgesia in a short time, but rebound pain after the nerve block disappears has attracted researchers’ attention. The aim of this study is to evaluate the effect of perineural dexamethasone on rebound pain after sciatic nerve block and femoral nerve block in patients undergoing unicompartmental knee arthroplasty (UKA).

Methods:
In a double-blinded fashion, We recruited 72 patients undergoing UKA, each of whom received sciatic and femoral nerve block. Patients were randomly assigned to two groups (n=36): X (ropivacaine only) and D (ropivacaine combined with dexamethasone). The primary outcome was the incidence of rebound pain. The secondary outcomes were rebound pain score, the duration of rebound pain, the duration of nerve block, pain score, sufentanil consumption and rescue analgesic, patient-controlled intravenous analgesia, distance walked, sleep quality score, C-reactive protein levels, and adverse effects.

Results:
Compared with group X, the incidence of rebound pain in group D was higher, the rebound pain score was higher and the duration of nerve block was prolonged (P<0.05). At 12, 16, and 20 hours postoperatively, the pain scores at rest in group D was lower. At 32 and 36 hours postoperatively, the pain scores at rest in group D was higher (P<0.05). Moreover, patients in group D had lower levels of C-reactive protein after surgery (P<0.05).

Discussion:
Addition of dexmedetomidine to ropivacaine for UKA effectively prolonged the duration of nerve block and decreased c-reactive protein levels, but increased the incidence of rebound pain and rebound pain score, and had no beneficial effects on the postoperative analgesia.
Bacterial Contamination Control with Sodium Hypochlorite and Jet Lavage Irrigation in a Severe Stage 4 Pelvic Pressure Injury: A Case Report
Authors: Stiehl James B. 
Published: April 2024

ABSTRACT
This case report reviews the effect of combining a 250-cc bottle of standard antimicrobial, buffered sodium hypochlorite with a surgical method, low-pressure jet lavage irrigation in the outpatient setting to control difficult wound contamination. A 73-year-old man had been in treatment for over 8 years, undergoing at least 18 surgical wound debridement procedures for an extensive undermined pelvic pressure injury involving the sacrum, ischium, and greater trochanter. Cultures and polymerase chain reaction diagnostics revealed a multibacterial presence. Autofluorescent imaging (AFI) was used in 21 examinations performed after a 72-hour delay over a long weekend. The AFI contamination exceeded log 4 colony-forming units/g of tissue in all pretreatment examinations and was reduced to less than log 2 colony-forming units in 6 of 21 examinations, with the remaining 15 showing an estimated 80% or higher removal of the bacterial porphyrin “red” appearance. A total of 54 AFI examinations were performed using the combination treatment, and no adverse reactions were encountered. Treatment paradigms can be improved with a multifactorial approach.
Effect of Heated Saline Solution on Pain Intensity, Wound Bed Temperature, and Comfort during Chronic Wound Dressing Changes: Crossover Randomized Clinical Trial
Authors: Galdino-Júnior Hélio , Martins de Oliveira Segundo Emilson , Gomes Malaquias Suelen , Vinaud Marina Clare , Pereira Lilian Varanda , Guimarães Rafael Alves , Bachion Maria Márcia 
Published: April 2024

ABSTRACT

Objective
To evaluate the use of heated saline solution during wound cleaning on the intensity of pain related to the procedure, the temperature of the wound bed, and the comfort of patients with chronic wounds. Further, to investigate patient preference in relation to the temperature of the solution used for cleaning.

Methods
Crossover, single-blind, clinical trial with 32 people with chronic wounds. Providers cleaned the wounds with room temperature and heated saline solution. Participants were randomized into group 1 A/B (heated solution first, room temperature second) or group 2 B/A (room temperature solution first, heated solution second), with a 10-minute washout period. Investigators evaluated pain intensity, wound bed temperature, and patient-reported comfort and preference.

Results
The heated solution was preferred (P = .04) and more often referred to as comfortable (P = .04) by the participants. There was no difference in pain intensity before and after cleaning with room temperature (2.03; P = .155) and heated saline (2.25; P = .44). The heated solution increased the temperature of the wound bed by 0.5 °C.

Conclusions
Although heating saline solution could be an important comfort measure during dressing changes, quantitatively, the temperature of the solution did not significantly change the temperature of the wound bed nor the intensity of pain patients experienced.
Randomized Double-blind Cost-effectiveness Comparison of Two 10% Urea Creams in Patients with Diabetic Foot Syndrome
Authors: Tejeda Ramírez Sol , Tardáguila-García Aroa , López-Moral Mateo , Sanz-Corbalán Irene , García-Madrid Marta , Lázaro-Martínez José Luis 
Published: April 2024

ABSTRACT

OBJECTIVE
To evaluate the cost-effectiveness of two 10% urea creams in patients with diabetic foot syndrome.

METHODS
This was a prospective, longitudinal, single-center, randomized, double-blind, prospective clinical trial that evaluated the skin quality of 20 feet belonging to 10 patients with diabetic foot syndrome after the application of two 10% urea creams purchased from pharmacies and supermarkets.

RESULTS
At follow-up, 19 (95%) of the participants’ feet showed improved skin quality, irrespective of the cream applied. On visual inspection, participants had a decreased presence of xerosis, hyperkeratosis, and preulcerative signs such as subkeratotic bruising and areas of redness on the dorsum of the toes. At the 3-month follow-up, nine (90%) of the participants stated that they had continued to apply the cream as a method of self-management to prevent complications.

CONCLUSIONS
Creams containing 10% urea purchased in supermarkets improve foot skin quality in patients with diabetic foot syndrome, regardless of their cost. Based on these findings, the authors recommend creams containing 10% urea as a self-management tool for patients with diabetic foot syndrome.
Comparison of Histopathological Findings in Psoriasis According to the Lesion Location From Biopsy
Authors: Kayaçetin Serra , Öcalan Devrim Tuba , Gül Ülker 
Published: April 2024

Abstract:
The aim of this study was to investigate whether the histopathological findings of psoriasis varied by the biopsied lesion location. Age, gender, age at disease onset, lesion locations, presence or absence of a preliminary diagnosis of psoriasis, and histopathological findings of 307 patients were recorded. The sections prepared from the patients' paraffin blocks were reexamined microscopically, the severity of the observed findings was graded, and various histopathological features were recorded. The female-to-male ratio was 1.2 to 1. Family history for psoriasis was positive in 30% of patients. A clinically preliminary diagnosis of psoriasis was present in 232 patients. The most common histopathological features included hyperkeratosis, parakeratosis, Munro/Kogoj microabscesses, suprapapillary thinning–hypogranulosis, and vascular dilation–capillary proliferation. Hyperkeratosis was least common in the trunk. A linear and moderately strong correlation was found between the histopathological findings of inflammation, capillary proliferation, and suprapapillary thinning. For the first time, the clinical and demographic features of psoriasis are evaluated and the severity of the histopathological findings is compared by the biopsied lesion location in a large number of patients.