bluuebunny/crossref_metadata_2025 huggingface dataset:
Quasi-in-situ observation of fatigue crack growth behavior of friction stir welded 2024-T4 joint
Authors: Yang Jun , Samiuddin Muhammad , Chen Xianmin , Chen Hao , Shen Zishi , Jin Feng
Published: May 2024

This study presents a quasi-in situ observation of the fatigue crack growth behavior in a friction stir welded 2024-T4 joint. The microstructure and fatigue properties of the joint were investigated using electron backscatter diffraction (EBSD) technique, scanning electron microscopy (SEM), and fatigue crack growth tests. The fatigue crack growth behavior of the joint was examined by conducting fatigue crack growth tests with different notch locations. The results show that the sample with the notch in the stir zone (SZ) exhibited the highest resistance to fatigue crack growth, followed by the notched samples of the Advancing side (AS) and Retreating side (RS) weldments. Microstructural observations showed a homogeneous microstructure with a fine grain size in SZ and it was observed that this fine-grained structure significantly enhanced the material’s resistance to fatigue crack growth. The experimental results were further analyzed using the Paris model to provide a quantitative understanding of the crack growth behavior. The study underlines the impact of microstructural characteristics and notch location on the fatigue performance of the weldment. Overall, the quasi-in situ observations and experimental findings contribute to a comprehensive understanding of the fatigue crack growth behavior in friction stir welded 2024-T4 joints.
Radiofrequency and Electrical Muscle Stimulation: A Synergistic Treatment That Achieves Lipolysis and Circumferential Waist Reduction in Noninvasive Body Contouring
Authors: Vranis Neil M , Ghavami Ashkan , Rohrich Rodney J , Theodorou Spero
Published: May 2024

Background

Surgeons and providers in aesthetic medicine seek noninvasive devices that can be utilized for safe, efficient, and effective body contouring. Patient demand has propelled the development of novel devices that can simultaneously improve skin laxity, adipolysis along with stimulation of muscle hypertrophy.

Objectives

To determine the efficacy of body contouring after 3 treatments using the noninvasive Transform (InMode, Lake Forest, CA) device.

Methods

A prospective, multicenter study was performed. Outcomes evaluated include: standardized caliper and ultrasound measurements of abdominal skin/soft-tissue thickness, waist circumference, histologic evaluation, patient comfort, and satisfaction assessments.

Results

Forty-four patients were successfully enrolled in the study and completed the series of 3 treatments which involved combined electrical muscle stimulation (EMS) and noninvasive bipolar radiofrequency (RF). Abdominal ultrasound measurements reveal a decrease in soft-tissue thickness (average 3.1 mm; P = .001), there was a significant decrease in caliper measurements of periumbilical skin thickness (P < .003), and the average reduction of abdominal circumference was 1.9 cm (P < .0001) 3 months after the treatment series. Histology confirmed subcutaneous adipolysis without damaging the dermal layer. Patients reported a high degree of satisfaction with the overall result (P = .003) and that each of the 3 treatments were progressively more comfortable (P < .005).

Conclusions

This study demonstrates that a series of simultaneous noninvasive RF with EMS treatments to the abdomen decreases subcutaneous soft-tissue thickness of the treated area. These comfortable treatments ultimately result in a high degree of patient satisfaction at 3 months.

Level of Evidence: 4
Visuospatial processing in early brain-based visual impairment is associated with differential recruitment of dorsal and ventral visual streams
Authors: Pamir Zahide , Manley Claire E , Bauer Corinna M , Bex Peter J , Dilks Daniel D , Merabet Lotfi B
Published: May 2024

Visuospatial processing impairments are prevalent in individuals with cerebral visual impairment (CVI) and are typically ascribed to “dorsal stream dysfunction” (DSD). However, the contribution of other cortical regions, including early visual cortex (EVC), frontal cortex, or the ventral visual stream, to such impairments remains unknown. Thus, here, we examined fMRI activity in these regions, while individuals with CVI (and neurotypicals) performed a visual search task within a dynamic naturalistic scene. First, behavioral performance was measured with eye tracking. Participants were instructed to search and follow a walking human target. CVI participants took significantly longer to find the target, and their eye gaze patterns were less accurate and less precise. Second, we used the same task in the MRI scanner. Along the dorsal stream, activation was reduced in CVI participants, consistent with the proposed DSD in CVI. Intriguingly, however, visual areas along the ventral stream showed the complete opposite pattern, with greater activation in CVI participants. In contrast, we found no differences in either EVC or frontal cortex between groups. These results suggest that the impaired visuospatial processing abilities in CVI are associated with differential recruitment of the dorsal and ventral visual streams, likely resulting from impaired selective attention.
The Zhongyong Dialectic: A Bridge into the Relational World
Authors: Qin Yaqing
Published: May 2024

Three tensions are said to exist in my relational theory, i.e. between ontology and behavior, between structure and process, and between substance and procedure. Underlying these tensions is a crucial question: How to identify the subject and object and understand the domination–subordination power relationship therein? These seeming inconsistencies appear if observed through a dualistic lens but may well disappear when viewed from the zhongyong dialectic, which, as an epistemological and methodological device, assumes no binary dichotomy in the first place. It believes in immanent relationality and dynamic transformability, holding that interaction based on difference rather than homogeneity generates healthy life and arguing that subject and object, structure and process, substance and procedure—all these categories constructed as dichotomous opposites are in fact mutually transformable as related parts of a whole. The evolution of global society, from international society of nation-states, to global society of humans, and to planetary society of all on earth (or beyond), clearly indicates the relational transformability across the ostensible subject–object divide. Power relations exist, but any unilateral exercise of power is ephemeral, for power over will not last, while power to will.
Algorithms For Cold-Start Game Recommendation Based On GNN Pre-training Model
Authors: Yang Hongjuan , Tian Gang , Xu Chengrui , Wang Rui
Published: May 2024

In the absence of sufficient user behavior data, game recommendation systems face the cold-start problem. To address this issue, this paper proposes a solution based on the Graph Neural Network pre-training model to alleviate the cold-start problem. The proposed model directly reconstructs cold-start user/game embeddings using a meta-learning setup based on dataset training simulations and uses an adaptive neighbor sampler to improve user interaction relations and thereby to improve game recommendation performance. Experimental results demonstrate the effectiveness and practicality of the recommendation model proposed in this study. Moreover, the proposed model is embedded in the game recommendation system to visualize the recommendation results.
Structural properties of extended pseudo-fractal scale-free network with higher network efficiency
Authors: Liu Jia-Bao , Zhang Xue , Cao Jinde
Published: May 2024

Complex networks, as an important model for studying complex systems, have been gradually studied in various extension models. Firstly, the network is proved to be sparse by calculating the density of the extending pseudo-fractal network. Secondly, it is proved that the network nodes conform the power-law distribution by enumerate the degree sequence of nodes with power law index $ 2 \lt \gamma \leq 2.585 $ shows that the network has scale-free feature. Thirdly, it is also demonstrated that the average clustering coefficient $ \overline{C_{g}} $ can reach a theoretical lower limit value 0.8182 and the increase of extension coefficient m makes the $ \overline{C_{g}} $ higher than traditional fractal networks. Fourthly, we derive the analytical expression and limit expression of the average path length, and conclude that it has small-world effect. Meanwhile, it is shown that the average path length $ \overline{D_{g}} $ is logarithmically related to Ng growth relationship in Fg. Finally, it is concluded that this extended pseudo-fractal network becomes more effective under the effect of m.
DUVEL: an active-learning annotated biomedical corpus for the recognition of oligogenic combinations
Authors: Nachtegael Charlotte , De Stefani Jacopo , Cnudde Anthony , Lenaerts Tom
Published: May 2024

While biomedical relation extraction (bioRE) datasets have been instrumental in the development of methods to support biocuration of single variants from texts, no datasets are currently available for the extraction of digenic or even oligogenic variant relations, despite the reports in literature that epistatic effects between combinations of variants in different loci (or genes) are important to understand disease etiologies. This work presents the creation of a unique dataset of oligogenic variant combinations, geared to train tools to help in the curation of scientific literature. To overcome the hurdles associated with the number of unlabelled instances and the cost of expertise, active learning (AL) was used to optimize the annotation, thus getting assistance in finding the most informative subset of samples to label. By pre-annotating 85 full-text articles containing the relevant relations from the Oligogenic Diseases Database (OLIDA) with PubTator, text fragments featuring potential digenic variant combinations, i.e. gene–variant–gene–variant, were extracted. The resulting fragments of texts were annotated with ALAMBIC, an AL-based annotation platform. The resulting dataset, called DUVEL, is used to fine-tune four state-of-the-art biomedical language models: BiomedBERT, BiomedBERT-large, BioLinkBERT and BioM-BERT. More than 500 000 text fragments were considered for annotation, finally resulting in a dataset with 8442 fragments, 794 of them being positive instances, covering 95% of the original annotated articles. When applied to gene–variant pair detection, BiomedBERT-large achieves the highest F1 score (0.84) after fine-tuning, demonstrating significant improvement compared to the non-fine-tuned model, underlining the relevance of the DUVEL dataset. This study shows how AL may play an important role in the creation of bioRE dataset relevant for biomedical curation applications. DUVEL provides a unique biomedical corpus focusing on 4-ary relations between two genes and two variants. It is made freely available for research on GitHub and Hugging Face.

Database URL: https://huggingface.co/datasets/cnachteg/duvel or https://doi.org/10.57967/hf/1571
Relation of changes in ABC pathway compliance status to clinical outcomes in patients with atrial fibrillation: a report from the COOL-AF registry
Authors: Krittayaphong Rungroj , Chichareon Ply , Methavigul Komsing , Treewaree Sukrit , Lip Gregory Y H
Published: May 2024

Aims

The Atrial fibrillation Better Care (ABC) pathway provides a framework for holistic care management of atrial fibrillation (AF) patients. This study aimed to determine the impact of changes in compliance to ABC pathway management on clinical outcomes.

Methods and results

This is a prospective multicenter AF registry. Patients with non-valvular AF were enrolled and followed-up for 3 years. Baseline and follow-up compliance to the ABC pathway was assessed. The main outcomes were all-cause death, ischaemic stroke/systemic embolism, major bleeding, and heart failure. There studied 3096 patients (mean age 67.6 ± 11.1 years, 41.8% female). Patients were categorized into four groups: Group 1: ABC compliant at baseline and 1 year [n = 1022 (33.0%)]; Group 2: ABC non-compliant at baseline but compliant at 1 year [n = 307 (9.9%)]; Group 3: ABC compliant at baseline and non-compliant at 1 year [n = 312 (10.1%)]; and Group 4: ABC non-compliant at baseline and also at 1 year [n = 1455 (47.0%)]. The incidence rates [95% confidence intervals (CI)] of the composite outcome for Group 1–4 were 5.56 (4.54–6.74), 7.42 (5.35–10.03), 9.74 (7.31–12.70), and 11.57 (10.28–12.97), respectively. With Group 1 as a reference, Group 2–4 had hazard ratios (95% CI) of the composite outcome of 1.32 (0.92–1.89), 1.75 (1.26–2.43), and 2.07 (1.65–2.59), respectively.

Conclusion

Re-evaluation of compliance status of the ABC pathway management is needed to optimize integrated care management and improve clinical outcomes. AF patients who were ABC pathway compliant at baseline and also at follow-up had the best clinical outcomes.
Heterogeneity of European farmers’ risk preferences: an individual participant data meta-analysis
Authors: Garcia Viviana , McCallum Chloe , Finger Robert
Published: May 2024

We present a new approach to establish an empirical overview of farmers’ risk preferences and the characteristics associated with these preferences. We rely on an Individual Participant Data Meta-analysis whereby we identify studies eliciting risk preferences through self-assessments and Holt and Laury lotteries, and construct and analyse a unique dataset of 5,157 farmers from 19 studies in 13 European countries. Our results reveal significant heterogeneity in risk preferences across elicitation methods, within and across studies, risk domains and farm and farmer characteristics. European farmers are on average risk-averse when risk preferences are elicited by lotteries, and on average risk-neutral when elicited by self-assessments. Beyond differences in the average risk aversion, there are distributional differences pointing to a limited convergence between elicitation methods and a larger explanatory power of farm and farmer characteristics to determine risk preferences elicited with self-assessments compared to lotteries.
Enrichment and characterization of human-associated mucin-degrading microbial consortia by sequential passage
Authors: Fricker Ashwana D , Yao Tianming , Lindemann Stephen R , Flores Gilberto E
Published: May 2024

Mucin is a glycoprotein secreted throughout the mammalian gastrointestinal tract that can support endogenous microorganisms in the absence of complex polysaccharides. While several mucin-degrading bacteria have been identified, the interindividual differences in microbial communities capable of metabolizing this complex polymer are not well described. To determine whether community assembly on mucin is deterministic across individuals or whether taxonomically distinct but functionally similar mucin-degrading communities are selected across fecal inocula, we used a 10-day in vitro sequential batch culture fermentation from three human donors with mucin as the sole carbon source. For each donor, 16S rRNA gene amplicon sequencing was used to characterize microbial community succession, and the short-chain fatty acid profile was determined from the final community. All three communities reached a steady-state by day 7 in which the community composition stabilized. Taxonomic comparisons amongst communities revealed that one of the final communities had Desulfovibrio, another had Akkermansia, and all three shared other members, such as Bacteroides. Metabolic output differences were most notable for one of the donor’s communities, with significantly less production of acetate and propionate than the other two communities. These findings demonstrate the feasibility of developing stable mucin-degrading communities with shared and unique taxa. Furthermore, the mechanisms and efficiencies of mucin degradation across individuals are important for understanding how this community-level process impacts human health.
MIKC type MADS-box transcription factor LcSVP2 is involved in dormancy regulation of the terminal buds in evergreen perennial litchi (Litchi chinensis Sonn.)
Authors: Ma Meng-Meng , Zhang Hui-Fen , Tian Qi , Wang Hui-Cong , Zhang Fang-Yi , Tian Xue , Zeng Ren-Fang , Huang Xu-Ming
Published: May 2024

SHORT VEGETATIVE PHASE (SVP), a member of the MADS-box transcription factor family, has been reported to regulate bud dormancy in deciduous perennial plants. Previously, three LcSVPs (LcSVP1, LcSVP2 and LcSVP3) were identified from litchi genome, and LcSVP2 was highly expressed in the terminal buds of litchi during growth cessation or dormancy stages and down-regulated during growth stages. In this study, the role of LcSVP2 in governing litchi bud dormancy was examined. LcSVP2 was highly expressed in the shoots, especially in the terminal buds at growth cessation stage, whereas low expression was showed in roots, female flowers and seeds. LcSVP2 was found to be located in the nucleus and have transcription inhibitory activity. Overexpression of LcSVP2 in Arabidopsis thaliana resulted in a later flowering phenotype compared to the wild-type control. Silencing LcSVP2 in growing litchi terminal buds delayed re-entry of dormancy, resulting in significantly lower dormancy rate. The treatment also significantly up-regulated litchi FLOWERING LOCUS T2 (LcFT2). Further study indicates that LcSVP2 interacts with an AP2-type transcription factor, SMALL ORGAN SIZE1 (LcSMOS1). Silencing LcSMOS1 promoted budbreak and delayed bud dormancy. Abscisic acid (200 mg/L), which enforced bud dormancy, induced a short-term increase in the expression of LcSVP2 and LcSMOS1. Our study reveals that LcSVP2 may play a crucial role, likely together with LcSMOS1, in dormancy onset of the terminal bud and may also serve as a flowering repressor in evergreen perennial litchi.
Reviewing the constitution-making process in Kenya: The failure of the 2005 constituent process
Authors: Arias Sonsoles
Published: May 2024

Kenya began its democratic era after its declaration of independence and the adoption of its first constitution in 1963. However, this supreme norm of the country would undergo countless reforms by the political elites from the very beginning, mostly to satisfy the partisan demands of the political leaders of the moment. These reforms succeeded in transforming the initially democratic model into an authoritarian, one-party system. After two decades of corruption and abuses of power, political changes in the country, and a wave of democratization after the fall of the Berlin Wall fueled the popular clamor for constitutional change. This article analyses the development of the constitution-making process, which began with the first constitutional amendments introduced to the constitution of the independence, as well as the main factors that led to the rejection of a new draft constitution in the ratification referendum held on November 21, 2005. A key element contributing to the failure of the whole process is the strong influence of political forces in the process, all using partisan methods to achieve perceived political advantages.
Bridging distance: Transnational and local family ties in refugees’ social support networks
Authors: Heidinger Ellen
Published: May 2024

This study examines the familial ties in the social support network of refugees in Germany. It investigates whether distance to family plays a role in the provision of emotional and informational support and how this relationship is moderated by social network services (SNS). Using data from the IAB-BAMF-SOEP Survey of Refugees (N = 5237), the paper provides evidence for a family-centred network. Increasing distance to family is generally negatively associated with receiving support. However, the strength of support from the partner and sibling is less affected by distance than support from parents. Findings indicate that emotional support can generally be conveyed across greater distances, while informational support, often entailing location-bound aid, is not as easily transmittable. This study contributes to the understanding of refugee networks as transnational families with intergenerational differences in support. It also refines the depiction of support dynamics as being multifaceted and potentially limited due to fragmented contacts.
Clusternets: a deep learning approach to probe clustering dark energy
Authors: Chegeni Amirmohammad , Hassani Farbod , Vafaei Sadr Alireza , Khosravi Nima , Kunz Martin
Published: May 2024

Machine learning (ML) algorithms are becoming popular in cosmology for extracting valuable information from cosmological data. In this paper, we evaluate the performance of a convolutional neural network (CNN) trained on matter density snapshots to distinguish clustering dark energy (DE) from the cosmological constant scenario and to detect the speed of sound (cs) associated with clustering DE. We compare the CNN results with those from a Random Forest (RF) algorithm trained on power spectra. Varying the DE equation of state parameter wDE within the range of −0.7 to −0.99 while keeping $c_s^2 = 1$, we find that the CNN approach results in a significant improvement in accuracy over the RF algorithm. The improvement in classification accuracy can be as high as 40 per cent depending on the physical scales involved. We also investigate the ML algorithms’ ability to detect the impact of the speed of sound by choosing $c_s^2$ from the set {1, 10−2, 10−4, 10−7} while maintaining a constant wDE for three different cases: wDE ∈ {−0.7, −0.8, −0.9}. Our results suggest that distinguishing between various values of $c_s^2$ and the case where $c_s^2=1$ is challenging, particularly at small scales and when wDE ≈ −1. However, as we consider larger scales, the accuracy of $c_s^2$ detection improves. Notably, the CNN algorithm consistently outperforms the RF algorithm, leading to an approximate 20 per cent enhancement in $c_s^2$ detection accuracy in some cases.
Discovery of free precession in the magnetar SGR 1806−20 with the ASCA Gas Imaging Spectrometer
Authors: Makishima Kazuo , Uchida Nagomi , Enoto Teruaki
Published: May 2024

Four X-ray datasets of the soft gamma repeater SGR 1806−20, taken with the Gas Imaging Spectrometer (GIS) onboad ASCA, were analyzed. Three of them were acquired over 1993 October 9–20, the last one in 1995 October. Epoch-folding analysis of the 2.8–12 keV signals confirmed the ∼7.6 s pulses in these data, which Kouveliotou et al. (1998, Nature, 393, 235) reported as one of the earliest pulse detections from this object. In the 1995 observation, 3–12 keV pulses were phase modulated with a period of T = 16.4 ± 0.4 ks, and an amplitude of ∼1 s. This makes a fourth example of the behavior observed from magnetars. As in the previous three sources, the pulse-phase modulation of SGR 1806−20 disappeared at ≲2.5 keV, where the soft X-ray component dominates. In the 1993 datasets, this periodic modulation was reconfirmed, and successfully phase-connected coherently across the 11 d interval. As a result, the modulation period was refined to T = 16.435 ± 0.024 ks. The implied high stability of the phenomenon strengthens its interpretation in terms of free precession of the neutron star, which is deformed to an asphericity of ∼10−4, presumably by the stress of toroidal magnetic fields reaching ∼1016 G. Toroidal fields of this level can be common among magnetars.
Polyphenols-based intelligent oral barrier membranes for periodontal bone defect reconstruction
Authors: Chen Enni , Wang Tianyou , Sun Zhiyuan , Gu Zhipeng , Xiao Shimeng , Ding Yi
Published: May 2024

Periodontitis-induced periodontal bone defects significantly impact patients’ daily lives. The guided tissue regeneration and guided bone regeneration techniques, which are based on barrier membranes, have brought hope for the regeneration of periodontal bone defects. However, traditional barrier membranes lack antimicrobial properties and cannot effectively regulate the complex oxidative stress microenvironment in periodontal bone defect areas, leading to unsatisfactory outcomes in promoting periodontal bone regeneration. To address these issues, our study selected the collagen barrier membrane as the substrate material and synthesized a novel barrier membrane (PO/4-BPBA/Mino@COL, PBMC) with an intelligent antimicrobial coating through a simple layer-by-layer assembly method, incorporating reactive oxygen species (ROS)-scavenging components, commercial dual-functional linkers and antimicrobial building blocks. Experimental results indicated that PBMC exhibited good degradability, hydrophilicity and ROS-responsiveness, allowing for the slow and controlled release of antimicrobial drugs. The outstanding antibacterial, antioxidant and biocompatibility properties of PBMC contributed to resistance to periodontal pathogen infection and regulation of the oxidative balance, while enhancing the migration and osteogenic differentiation of human periodontal ligament stem cells. Finally, using a rat periodontal bone defect model, the therapeutic effect of PBMC in promoting periodontal bone regeneration under infection conditions was confirmed. In summary, the novel barrier membranes designed in this study have significant potential for clinical application and provide a reference for the design of future periodontal regenerative functional materials.
Influence of epinephrine reactivity to stress on meat quality in goats
Authors: Shaik Arshad , Batchu Phaneendra , Naldurtiker Aditya , Gurrapu Priyanka , Kouakou Brou , Terrill Thomas H , Kannan Govind
Published: May 2024

The magnitude of physiological responses to a stressor can vary among individual goats within a herd; however, whether these differences can differentially affect meat quality is not known. This study was conducted to determine the influence of the magnitude of epinephrine response (ER) to acute stress on muscle metabolome and meat quality in goats. Male Spanish goats (6 mo old) were transported for 180 min. (N = 75 goats; 25 goats/d) to impose stress. Blood samples were obtained after transport for analysis of physiological responses. Goats were slaughtered using humane procedures and samples were collected for muscle metabolomics and meat quality analyses. The data obtained from blood and muscle/meat analysis were then categorized based on epinephrine concentrations into low (LE), medium (ME), and high (HE) ER groups (n = 12/ER group). The physiological and meat quality variables were analyzed as a Completely Randomized Design in SAS, and metabolomics data were analyzed using R software. Plasma glucose concentrations were significantly high in the HE group, low in the LE group, and intermediate in the ME group (P < 0.05). However, leukocyte counts and cortisol, norepinephrine, blood urea nitrogen, and creatine concentrations were not different among the ER groups. Muscle (Longissimus dorsi) glycogen concentrations (15 min postmortem) were significantly higher (P < 0.05) in the ME and LE groups than in the HE group. However, postmortem Longissimus muscle pH and temperature (15 min and 24 h), 24 h calpastatin and desmin levels, and rib chop color (L*, a*, and b*), cooking loss, and Warner-Bratzler shear force values were unaffected by ER. Targeted metabolomics analysis of Longissimus muscle (15 min) revealed that diacyl phosphatidylcholines (C38:0; 40:6) and sphingomyelin (C20:2) were significantly different (P < 0.05) among the ER groups, with the concentrations of these metabolites being consistently high in the LE group. These differential muscle metabolite concentrations suggest that ER can influence biochemical pathways associated with cell membrane integrity and signaling. ER had a significant effect on dopamine concentrations, with the levels increasing with increasing levels of ER. The results indicate that differences in epinephrine reactivity can influence selected physiological responses and muscle metabolites; however, it does not significantly influence meat quality attributes.
The diverse liver viromes of Australian geckos and skinks are dominated by hepaciviruses and picornaviruses and reflect host taxonomy and habitat
Authors:  Mahar Jackie E ,  Wille Michelle ,  Harvey Erin ,  Moritz Craig C ,  Holmes Edward C
Published: May 2024

Lizards have diverse ecologies and evolutionary histories, and represent a promising group to explore how hosts shape virome structure and virus evolution. Yet, little is known about the viromes of these animals. In Australia, squamates (lizards and snakes) comprise the most diverse order of vertebrates, and Australia hosts the highest diversity of lizards globally, with the greatest breadth of habitat use. We used meta-transcriptomic sequencing to determine the virome of nine co-distributed, tropical lizard species from three taxonomic families in Australia and analyzed these data to identify host traits associated with viral abundance and diversity. We show that lizards carry a large diversity of viruses, identifying more than thirty novel, highly divergent vertebrate-associated viruses. These viruses were from nine viral families, including several that contain well known pathogens, such as the Flaviviridae, Picornaviridae, Bornaviridae, Iridoviridae, and Rhabdoviridae. Members of the Flaviviridae were particularly abundant across species sampled here, largely belonging to the genus Hepacivirus: fourteen novel hepaciviruses were identified, broadening the known diversity of this group and better defining its evolution by uncovering new reptilian clades. The evolutionary histories of the viruses studied here frequently aligned with the biogeographic and phylogenetic histories of the hosts, indicating that exogenous viruses may help infer host evolutionary history if sampling is strategic and sampling density high enough. Notably, analysis of alpha and beta diversity revealed that virome composition and richness in the animals sampled here was shaped by host taxonomy and habitat. In sum, we identified a diverse range of reptile viruses that broadly contributes to our understanding of virus-host ecology and evolution.
Expression of HER2 in urothelial carcinoma and its significance
Authors: Chang Yao , Zhao Delong , Wang Zicheng , Zhu Kejia , Guo Andong , Cao Jishuang , Wu Chenrui , Ding Sentai
Published: May 2024

Objectives

We explored the expression levels and clinical significance of human epidermal growth factor receptor 2 (HER2) in urothelial carcinoma (UC) tissues.

Materials and methods

Patient data were reviewed, and 111 paraffin specimens of UC obtained from the Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, from 2020 to 2021 were collected. Immunohistochemistry was used to detect HER2 protein expression in all UC tumor tissues.χ2and Fisher exact tests were used to analyze the relationship between HER2 protein expression and clinicopathological data (sex, age, histopathological diagnosis, invasiveness, histopathological grade, maximum tumor diameter, muscle invasion, regional lymph node metastasis, and clinical stage).

Results

In this study, 92 cases (82.88%) showed HER2 protein expression, and there was a statistically significant difference in the distribution of HER2 positivity (immunohistochemistry 2+ and 3+) according to the pathological grades of UC (p= .021). Human epidermal growth factor receptor 2 positivity was not associated with sex, age, histopathological diagnosis, invasiveness, maximum tumor diameter, muscle invasion, regional lymph node metastasis, or clinical stage (allp< .05).

Conclusions

HER2 protein is highly expressed in UC, and its expression may be closely related to the high pathological grade of UC.
Pulmonary Epithelial Myoepithelial Carcinoma on 18F-FDG PET/CT
Authors: Huang Shuhui , Dai Hongyuan , Huang Rui
Published: May 2024

Pulmonary epithelial myoepithelial carcinoma is very rare. We reported the imaging finding of pulmonary epithelial myoepithelial carcinoma of bronchus in a 61-year-old man on 18F-FDG PET/CT. An irregular mass with an SUVmax of 6.36 growing along right upper lobe bronchus and multiple pulmonary nodules around the mass were found on 18F-FDG PET/CT. Postoperative pathology demonstrated the diagnosis of epithelial myoepithelial carcinoma.
A chromosome-level genome assembly of the cabbage aphidBrevicoryne brassicae
Authors: Wu Jun , Li Guomeng , Lin Zhimou , Zhang Yangzi , Yu Wenyun , Hu Rong , Zhan Shuai , Chen Yazhou
Published: May 2024

The cabbage aphid,Brevicoryne brassicae, is a major pest on Brassicaceae plants, and causes significant yield losses annually. However, lacking genomic resources hinders the progress in understanding this pest at the level of molecular biology. Here, a high-quality, chromosomal-level genome was assembled forB. brassicaebased on PacBio HIFI long-read sequencing and Hi-C data. The final assembled size was 429.99 Mb with a scaffold N50 of 93.31 Mb. Importantly, 96.2% of the assembled sequences were anchored to eight chromosomes. The genome recovered 98.50% of BUSCO genes and 92.30% of CEGMA genes, supporting the high level of completeness. By combining high-coverage transcriptome data, a total of 22,671 protein-coding genes and 3,594 lncRNA genes were annotated. Preliminary comparative genomic analyses were focused on genes related to host colonisation, such as chemosensory- and detoxification-related genes, as well as those encoding putative protein effectors and cross-kingdom lncRNAYa. In summary, our study presents a contiguous and complete genome forB. brassicaethat will benefit our understanding of the biology of it and other aphids.
More extinction driven by Red Queen in smaller habitats
Authors: Liu Xiao , Zhang Quan-Guo
Published: May 2024

Populations in antagonistic coevolutionary interactions may “run or die”, and their fates are determined by their evolutionary potential. The asymmetry of evolutionary speed between coevolving partners, e.g., resulting from genetic constraints, can be mitigated in larger populations. We hypothesize more frequent extinction driven by antagonistic coevolution when habitat size declines. In bacterium-virus systems, viruses (the consumers) typically suffer an evolutionary disadvantage due to constraints of genetic variation; and this pattern may apply to host-parasite interactions in general. Here in our experiment with the bacteriumPseudomonas fluorescensSBW25 and its lytic phage virus SBW25Φ2, the likelihood of viral extinction was greater in smaller habitats. Among viral populations that did persist, those from small habitats showed lower infectivity and their coevolving bacterial populations had greater densities. Therefore, the impact of habitat size reduction on biodiversity could be exacerbated by coevolutionary processes. Our results also lead to a number of suggestions for biocontrol practices, particularly for evolutionary training of phages.
ctQCimproves biological inferences from single cell and spatial transcriptomics data
Authors: Lakshmanan Vairavan , Kahraman Merve , Macalinao Dominique Camat , Gunn Nicole , Venkatesh Prasanna Nori , Meihuan Chang , Fu Cherylin , Qiang Leow Wei , Tan Iain Beehuat , Prabhakar Shyam
Published: May 2024

Quality control (QC) is the first critical step in single cell and spatial data analysis pipelines. QC is particularly important when analysing data from primary human samples, since genuine biological signals can be obscured by debris, perforated cells, cell doublets and ambient RNA released into the “soup” by cell lysis. Consequently, several QC methods for single cell data, employ fixed or data-driven quality thresholds. While these approaches efficiently remove empty droplets, they often retain low-quality cells. Here, we propose cell type-specific QC (ctQC), a stringent, data-driven QC approach that adapts to cell type differences and discards soup and debris. Evaluating single cell RNA-seq data from colorectal tumors, human spleen, and peripheral blood mononuclear cells, we demonstrate thatctQCoutperforms existing methods by improving cell type separation in downstream clustering, suppressing cell stress signatures, revealing patient-specific cell states, eliminating artefactual clusters and reducing ambient RNA artifacts. When applied to sequencing-based spatial RNA profiling data (Slide-seq),ctQCimproved spatial coherence of cell clusters and consistency with anatomical structures. These results demonstrate that strict, data-driven, cell-type-specific QC is applicable to diverse sample types and substantially improves the quality and reliability of biological inferences from single cell and spatial RNA profiles.
Targeting a shared neoepitope derived from non-canonical translation of c-MYConcogene in cancer cells
Authors: Baulu E. , Bolon A. , Etchegaray E. , Raimundo F. , Merienne A. , Martin J. , Grandsire J. , Richard T. , Tonon L. , Dubois C. , Estornes Y. , Boulos R. , Tabone O. , Bonaventura P. , Page A. , Gardet C. , Alcazer V. , Hughes S. , Gillet B. , Gervois N. , Labarrière N. , Wang Q. , Valladeau-Guilemond J. , Chuvin N. , Marcel V. , Diaz J- J. , Depil S.
Published: May 2024

Cancer cells rely on alternative modes of translation for protein synthesis, promoting internal ribosome entry site (IRES)-dependent translation of mRNA encoding pro-oncogenic factors. Furthermore, ribosomes translate mRNA with lower fidelity in tumor cells. We proposed that these translational modifications in cancer produce shared tumor-specific epitopes derived from IRES-containing oncogenes. To identify such neoepitopes, we developed anin silico-based method that we applied toc-MYC. We showed that the non-canonical translation ofc-MYCmRNA in cancer cells, involving a (+1) ribosomal frameshift, generates a shared neoepitope which induces high-avidity T cells able to kill tumor cellsin vitroandin vivowhile sparing normal cells. Our data provide preclinical rationale for developing immunotherapies targeting thisc-MYC-derived neoepitope and validate a new type of shared translation-associated neoantigens.
Fast and exact gap-affine partial order alignment with POASTA
Authors: van Dijk Lucas R. , Manson Abigail L. , Earl Ashlee M. , Garimella Kiran V , Abeel Thomas
Published: May 2024

Motivation

Partial order alignment is a widely used method for computing multiple sequence alignments, with applications in genome assembly and pangenomics, among many others. Current algorithms to compute the optimal, gap-affine partial order alignment do not scale well to larger graphs and sequences. While heuristic approaches exist, they do not guarantee optimal alignment and sacrifice alignment accuracy.

Results

We present POASTA, a new optimal algorithm for partial order alignment that exploits long stretches of matching sequence between the graph and a query. We benchmarked POASTA against the state-of-the-art on several diverse bacterial gene datasets and demonstrated an average speed-up of 4.1x and up to 9.8x, using less memory. POASTA’s memory scaling characteristics enabled the construction of much larger POA graphs than previously possible, as demonstrated by megabase-length alignments of 342Mycobacterium tuberculosissequences.

Availability and implementation

POASTA is available on Github athttps://github.com/broadinstitute/poasta.
Stromal mediated DNA damage promotes high grade serous ovarian cancer initiation
Authors: Garcia Geyon L. , Orellana Taylor , Gorecki Grace , Frisbie Leonard G. , Baruwal Roja , Goldfield Ester , Beddows Ian , MacFawn Ian P. , Britt Ananya K. , Hale Macy M. , Shen Hui , Buckanovich Ronald , Finkel Toren , Drapkin Ronny , Soong T. Rinda , Bruno Tullia C. , Atiya Huda I. , Coffman Lan
Published: May 2024

The fundamental steps in high-grade serous ovarian cancer (HGSOC) initiation are unclear, thus providing critical barriers to the development of prevention or early detection strategies for this deadly disease. Increasing evidence demonstrates most HGSOC starts in the fallopian tube epithelium (FTE). Current models propose HGSOC initiates when FTE cells acquire increasing numbers of mutations allowing cells to evolve into serous tubal intraepithelial carcinoma (STIC) precursors and then to full blown cancer. Here we report that epigenetically altered mesenchymal stem cells (termed high risk MSC-hrMSCs) can be detected prior to the formation of ovarian cancer precursor lesions. These hrMSCs drive DNA damage in the form of DNA double strand breaks in FTE cells while also promoting the survival of FTE cells in the face of DNA damage. Indicating the hrMSC may actually drive cancer initiation, we find hrMSCs induce full malignant transformation of otherwise healthy, primary FTE resulting in metastatic cancerin vivo. Further supporting a role for hrMSCs in cancer initiation in humans, we demonstrate that hrMSCs are highly enriched in BRCA1/2 mutation carriers and increase with age. Combined these findings indicate that hrMSCs may incite ovarian cancer initiation. These findings have important implications for ovarian cancer detection and prevention.
Enzymes enabling the biosynthesis of various C20polyunsaturated fatty acids in a sea urchinHemicentrotus pulcherrimus
Authors: Peng Yingying , Haga Yutaka , Kabeya Naoki
Published: May 2024

Sea urchins, integral to marine ecosystems and valued as a delicacy in Asia and Europe, contain physiologically important long-chain (>C20) polyunsaturated fatty acids (PUFA) in their gonads, including arachidonic acid (ARA, 20:4n-6), eicosapentaenoic acid (EPA, 20:5n-3), and unusual non-methylene interrupted fatty acids (NMI-FA) such as 20:2Δ5,11. Although these fatty acids may partially be derived from their diet, such as macroalgae, the present study onHemicentrotus pulcherrimushas uncovered multiple genes encoding enzymes involved in LC-PUFA biosynthesis. Specifically, three fatty acid desaturases (FadsA, FadsC1 and FadsC2) and thirteen elongation of very-long chain fatty acids proteins (Elovl-like, Elovl1/7-like, Elovl2/5-like, Elovl4-like, Elovl8-like, Elovl6-like A to H) were identified in their genome and transcriptomes. Functional analysis showed that FadsA and FadsC2 function as a Δ5 desaturase and a Δ8 desaturase, respectively, enabling the conversion of 18:2n-6 and 18:3n-3 into ARA and EPA, respectively, along with Elovl, particularly Elovl6-like C. Elovl6-like C demonstrates elongase activity towards both C18PUFA and monounsaturated fatty acids (MUFA). Consequently, FadsA and Elovl6-like C enable to synthesise several NMI-FA, including 20:2Δ5,11and 20:3Δ5,11,14, from C18precursors. This indicates thatH. pulcherrimuscan endogenously synthesise a wide variety of C20PUFA and NMI-FA, highlighting active biosynthesis pathways within sea urchins.
PCBS: an R package for fast and accurate analysis of bisulfite sequencing data
Authors: Lande Kathryn , Williams April E.
Published: May 2024

Motivation

Whole-genome bisulfite sequencing is a powerful tool for analyzing chromatin methylation genome-wide, but analysis of whole-genome bisulfite data is hampered by slow, inaccurate, and inflexible pipelines.

Results

We developed PCBS, a computationally efficient R package for Whole Genome Bisulfite Sequencing analysis that demonstrates remarkable accuracy and flexibility compared to current tools. PCBS identifies differentially methylated loci and differentially methylated regions and offers novel functionality that allows for more targeted methylation analyses. PCBS uses minimal computational resources; a complete pipeline in mouse can run on a local RStudio instance in a matter of minutes.

Availability and Implementation

PCBS is an R package available under a GNU GPLv3 license at:https://github.com/katlande/PCBSand from CRAN:

https://CRAN.R-project.org/package=PCBS. Instructions for use are available at:https://katlande.github.io/PCBS/.

Supplementary Information

“Supplementary data are available on BioRXiv.”
Family supplemented patient monitoring after surgery (SMARTER): process evaluation of a complex intervention in Uganda
Authors: Hewitt-Smith Adam , Bulamba Fred , Nanimambi Juliana , Adong Lucy Ruth , Emacu Bernard , Kabaleta Mary , Khanyalano Justine , Hussein Maiga Ayub , Mugume Charles , Nakibuule Joanitah , Nandyose Loretta , Sejja Martin , Weere Winfred , Pearse Rupert M. , Stephens Timothy
Published: May 2024

Background

Improving outcomes after surgery in Africa is a priority. The SMARTER Pilot Trial was a step-wedge cluster-randomised trial of family member supplemented vital signs monitoring after surgery. A concurrent process evaluation provides contextual understanding of intervention delivery.

Methods

Mixed methods approach with qualitative data sources including field notes from a research team diary and focus group discussions. Deductive analysis used the consolidated framework for implementation research. Quantitative data evaluating the efficacy of family members recognising abnormal vital signs and reporting them to nursing staff were collected following a prespecified intervention review held after two months.

Findings

Focus group discussions were conducted with 16 nurses and research assistants. Field notes included 88 episodes documented throughout the trial in a research team diary. Quantitative data were collected in the final 397 patients following ethics amendments. Intervention facilitators included: relative advantage, inner context factors including tension for change and relative priority, and individual characteristics centred around knowledge and beliefs. Available resources, culture, and compatibility were identified as important barriers, with a smaller negative influence from self-efficacy and intervention complexity. Family members recognised 91.3% (42/46) of abnormal sets of vital signs and communicated 100% (42/42) of these to a member of the nursing or medical team. The team responded 90.5% (38/42) of the time.

Interpretation

Family members were able to supplement nurse led monitoring of patients after surgery. This complex intervention was affected by context specific positive and negative influences. Scaling this intervention requires careful consideration of local context during planning.

Trial registration

SMARTER Pilot Trial registered onclinicaltrials.gov-NCT04341558
Optimal algorithms for controlling infectious diseases in real time using noisy infection data
Authors: Beregi Sandor , Parag Kris V.
Published: May 2024

Deciding when to enforce or relax non-pharmaceutical interventions (NPIs) based on real-time outbreak surveillance data is a central challenge in infectious disease epidemiology. Reporting delays and infection under-ascertainment, which characterise practical surveillance data, can misinform decision-making, prompting mistimed NPIs that fail to control spread or permitting deleterious epidemic peaks that overload healthcare capacities. To mitigate these risks, recent studies propose more data-insensitive strategies that trigger NPIs at predetermined times or infection thresholds. However, these strategies often increase NPI durations, amplifying their substantial costs to livelihood and life-quality. We develop a novel model-predictive control algorithm that optimises NPI decisions by jointly minimising their cumulative, future risks and costs over stochastic epidemic projections. Our algorithm is among the earliest to realistically incorporate uncertainties underlying both the generation and surveillance of infections. We find, except under extremely delayed reporting, that our projective approach outperforms data-insensitive strategies and show that earlier decisions strikingly improve real-time control with reduced NPI costs. Moreover, we expose how surveillance quality, disease growth and NPI frequency intrinsically limit our ability to flatten epidemic peaks or dampen endemic oscillations and why this potentially makes Ebola virus more controllable than SARS-CoV-2. Our algorithm provides a general framework for guiding optimal NPI decisions ahead-of-time and identifying the key factors limiting practical epidemic control.