Miracle-dz/UniFAR-FTUs huggingface dataset:
Gravity inversion constrained by OBS receiver function reveals crustal structure in Ryukyu Trench

The Ryukyu Trench is located in the northern Philippine Sea. The subduction of the Philippine Sea Plate to the Eurasia Plate along the Ryukyu Trench in the NNW direction leads to extremely complex tectonic processes such as subduction, collision, accretion, and back-arc expansion. It is of great significance to obtain the crustal structure of the Ryukyu Trench for understanding the crustal deformation characteristics, subduction direction and the scale of the Philippine Sea Plate. The ocean bottom seismometer (OBS) could provide important information on the deep structure of the oceanic area, and the wide coverage of gravity anomaly can provide more constraints for the regional crustal structure. In this study, we put the time-delay term of the sedimentary layer into the H-κ stacking formula, which eliminates the influence of the sedimentary layer in traditional H-κ stacking. Based on the accurate crustal thickness at OBS locations, a gravity inversion method is proposed to solve the problem of non-uniqueness in gravity data and limited distribution of OBSs. By using this method, we obtain a crustal structure with higher resolution than Crust1.0 model in Ryukyu Trench. The results show that the crustal thickness in the Ryukyu Trench region thickens along the NNW subduction direction, revealing that the Philippine Plate’s subduction direction towards the Eurasian Plate is in the NNW direction.
Friction Modeling With Tensor Product Transformation

The Tensor Product (TP) model transformation is a recently proposed technique for transforming given Linear Parameter-Varying (LPV) state-space models into polytopic model form, namely, to parameter-varying convex combination of Linear Time Invariant (LTI) systems. The main advantage of the TP model transformation is that it is executable in a straightforward way and the Linear Matrix Inequality (LMI) based control design frameworks can immediately be applied to the resulting polytopic models to yield controllers with tractable and guaranteed performance. The main contribution of this paper is that it represents the friction of a DC servo drive in TP model form, where LMI based controller for friction compensation can be automatically designed.
Finisher lamb growth and rumen fermentation responses to the plane of nutrition and naturally occurring coccidiosis

The objective of the present study was to investigate the interaction of plane of nutrition and naturally occurring coccidiosis on finisher lamb growth performance, FAMACHA score, and rumen volatile fatty acid profile. The study included 30 Suffolk, Dorset or Suffolk x Dorset lambs and were divided into 2 groups based on their initial body weight and assigned to 2 feeding groups differing in dietary energy intake to create lambs representing divergent growth curves due to differing nutritional management. Lambs with naturally occurring coccidiosis and healthy lambs were present in both feeding groups making a 2 × 2 factorial arrangement of treatments, (a) high plane of nutrition (HPN) lambs with no clinical coccidiosis diagnosis (HPNH), (b) HPN lambs with clinical coccidiosis (HPNC), (c) low plane of nutrition (LPN) lambs with no clinical coccidiosis diagnosis (LPNH), (d) LPN lambs with clinical coccidiosis (LPNC). Body weight and FAMACHA scores were recorded once every 2 weeks. On d 65 of feeding, lambs were slaughtered, and rumen fluid samples were collected and analyzed for volatile fatty acid concentrations. All response variables were analyzed statistically using a linear mixed effects model with fixed effects for plane of nutrition, health status, and a random effect for initial body weight nested within the pen. The total and average weight gain were not associated with planes of nutrition, health status, or the interaction. Health status had an impact on FAMACHA© score (P = 0.047) and concentration of isobutyrate (P = 0.037) and tended to affect total VFA (P = 0.085) and acetate (P = 0.071) concentrations. The interaction between the plane of nutrition and the health status tended to affect butyrate concentration (P = 0.058). These data support the conclusion that coccidiosis infection impacted on rumen fermentation in a manner independent of the plane of nutrition; however, the translation of these rumen level impacts did not translate to the production responses.
Genomic analysis of the population structure of Paenibacillus larvae in New Zealand

New Zealand is a remote country in the South Pacific Ocean. The isolation and relatively late arrival of humans into New Zealand has meant there is a recorded history of the introduction of domestic species. Honey bees (Apis mellifera) were introduced to New Zealand in 1839, and the disease American foulbrood was subsequently found in the 1870s. Paenibacillus larvae, the causative agent of American foulbrood, has been genome sequenced in other countries. We sequenced the genomes of P. larvae obtained from 164 New Zealand apiaries where American foulbrood was identified in symptomatic hives during visual inspection. Multi-locus sequencing typing (MLST) revealed the dominant sequence type to be ST18, with this clonal cluster accounting for 90.2% of isolates. Only two other sequence types (with variants) were identified, ST5 and ST23. ST23 was only observed in the Otago area, whereas ST5 was limited to two geographically non-contiguous areas. The sequence types are all from the enterobacterial repetitive intergenic consensus I (ERIC I) genogroup. The ST18 and ST5 from New Zealand and international P. larvae all clustered by sequence type. Based on core genome MLST and SNP analysis, localized regional clusters were observed within New Zealand, but some closely related genomes were also geographically dispersed, presumably due to hive movements by beekeepers.
Prognostic value of neutrophil to lymphocyte ratio in gastric cancer patients receiving immune checkpoint inhibitors: a systematic review and meta-analysis

Background The neutrophil to lymphocyte ratio (NLR) is a cost-effective and easily identifiable inflammatory biomarker that has been shown to be closely associated with tumor prognosis and predict survival in patients with multiple malignancies. However, the predictive value of NLR in patients with gastric cancer (GC) treated with immune checkpoint inhibitors (ICIs) has not been fully explored. Therefore, we conducted a meta-analysis to explore the potential of NLR as a predictor of survival in this population. Methods We systematically searched the PubMed, Cochrane Library, and EMBASE databases from inception to the present for observational researches on NLR and its relationship with progression or survival in GC patients receiving ICIs. To assess the prognostic significance of NLR on overall survival (OS) or progression-free survival (PFS), we used fixed or random-effect models to derive and combine hazard ratios (HRs) with 95% confidence intervals (CIs). We also examined the relationship between NLR and treatment efficacy by calculating relative risks (RRs) with 95% CIs for objective response rate (ORR) and disease control rate (DCR) in patients with GC receiving ICIs. Results Nine studies of 806 patients were eligible. OS and PFS data were obtained from 9 and 5 studies, respectively. In nine studies, NLR was associated with poor survival, the pooled HR was 1.98 (95% CI 1.67- 2.35, p < 0.001), indicating a significant association between high NLR and worse OS. We conducted subgroup analyses based on study characteristics to confirm the robustness of our findings. A relationship between NLR and PFS were reported in five studies with a HR of 1.49 (95% CI 0.99- 2.23, p = 0.056), which was not significantly associated. Pooling four studies that examined the correlation between NLR and ORR/DCR in GC patients, we observed a significant correlation between NLR and ORR (RR = 0.51, p = 0.003), but no significant correlation between NLR and DCR (RR = 0.48, p = 0.111). Conclusion In summary, this meta-analysis indicates that increased NLR is significantly linked to worse OS in patients with GC receiving ICIs. In addition, lowering NLR can improve ORR. Thus, NLR can serve as a predictor for prognosis and treatment response in GC patients treated with ICIs. Nevertheless, further high-quality prospective studies are required to verify our findings in the future.
Factors associated with antimicrobial resistant enterococci in Canadian beef cattle: A scoping review

Introduction Antimicrobial resistance (AMR) is a global health concern, occurring when bacteria evolve to render antimicrobials no longer effective. Antimicrobials have important roles in beef production; however, the potential to introduce AMR to people through beef products is a concern. This scoping review identifies factors associated with changes in the prevalence of antimicrobial-resistant Enterococcus spp. applicable to the Canadian farm-to-fork beef continuum. Methods Five databases (MEDLINE, BIOSIS, Web of Science, Embase, and CAB Abstracts) were searched for articles published from January 1984 to March 2022, using a priori inclusion criteria. Peer-reviewed articles were included if they met all the following criteria: written in English, applicable to the Canadian beef production context, primary research, in vivo research, describing an intervention or exposure, and specific to Enterococcus spp. Results Out of 804 screened articles, 26 were selected for inclusion. The included articles discussed 37 factors potentially associated with AMR in enterococci, with multiple articles discussing at least two of the same factors. Factors discussed included antimicrobial administration (n = 16), raised without antimicrobials (n = 6), metal supplementation (n = 4), probiotics supplementation (n = 3), pen environment (n = 2), essential oil supplementation (n = 1), grass feeding (n = 1), therapeutic versus subtherapeutic antimicrobial use (n = 1), feeding wet distiller grains with solubles (n = 1), nutritional supplementation (n = 1) and processing plant type (n = 1). Results were included irrespective of their quality of evidence. Discussion Comparability issues arising throughout the review process were related to data aggregation, hierarchical structures, study design, and inconsistent data reporting. Findings from articles were often temporally specific in that resistance was associated with AMR outcomes at sampling times closer to exposure compared to studies that sampled at longer intervals after exposure. Resistance was often nuanced to unique gene and phenotypic resistance patterns that varied with species of enterococci. Intrinsic resistance and interpretation of minimum inhibitory concentration varied greatly among enterococcal species, highlighting the importance of caution when comparing articles and generalizing findings. Systematic Review Registration [http://hdl.handle. net/1880/113592]
The mushroom body development and learning ability of adult honeybees are influenced by cold exposure during their early pupal stage

The honeybees are the most important pollinator in the production of crops and fresh produce. Temperature affects the survival of honeybees, and determines the quality of their development, which is of great significance for beekeeping production. Yet, little was known about how does low temperature stress during development stage cause bee death and any sub-lethal effect on subsequent. Early pupal stage is the most sensitive stage to low temperature in pupal stage. In this study, early pupal broods were exposed to 20°C for 12, 16, 24, and 48 h, followed by incubation at 35°C until emergence. We found that 48 h of low temperature duration cause 70% of individual bees to die. Although the mortality at 12 and 16 h seems not very high, the association learning ability of the surviving individuals was greatly affected. The brain slices of honeybees showed that low temperature treatment could cause the brain development of honeybees to almost stop. Gene expression profiles between low temperature treatment groups (T24, T48) and the control revealed that 1,267 and 1,174 genes were differentially expressed respectively. Functional enrichment analysis of differentially expressed genes showed that the differential expression of Map3k9, Dhrs4, and Sod-2 genes on MAPK and peroxisome signaling pathway caused oxidative damage to the honeybee head. On the FoxO signal pathway, InsR and FoxO were upregulated, and JNK, Akt, and Bsk were downregulated; and on the insect hormone synthesis signal pathway, Phm and Spo genes were downregulated. Therefore, we speculate that low temperature stress affects hormone regulation. It was detected that the pathways related to the nervous system were Cholinergic synapse, Dopaminergic synapse, GABAergic synapse, Glutamatergic synapse, Serotonergic synapse, Neurotrophin signaling pathway, and Synaptic vesicle cycle. This implies that the synaptic development of honeybees is quite possibly greatly affected by low temperature stress. Understanding how low temperature stress affects the physiology of bee brain development and how it affects bee behavior provide a theoretical foundation for a deeper comprehension of the temperature adaptation mechanism that underlies the “stenothermic” development of social insects, and help to improve honeybee management strategies to ensure the healthy of colony.
CO1 barcodes resolve an asymmetric biphyletic clade for Diabrotica undecimpunctata subspecies and provide nucleotide variants for differentiation from related lineages using real-time PCR

Diabrotica undecimpunctata is a multivoltine polyphagous beetle species that has long been documented as a significant agricultural pest throughout its native range in North America. This beetle can vector bacterial and viral plant pathogens that result in major losses to crops such as cucumber and soybean. Many countries outside the Americas treat D. undecimpunctata as a species of quarantine importance, while in the USA only the subspecies D. u. duodecimnotata is subject to quarantine, to prevent introduction from Mexico. Identification of D. undecimpunctata on the basis of morphology alone can be complicated given the use of conflicting characters in the description of some subspecific taxa. To better understand relationships among D. undecimpunctata subspecies and other related species, we sequenced mitochondrial cytochrome oxidase 1 (CO1) and nuclear internal transcribed spacer 2 (ITS2) DNA from individuals in different subspecific taxa and across different parts of the species range using museum samples and interceptions. When our data were combined with publicly available Diabrotica data, no pattern of divergence consistent with the currently recognized subspecific designations was found. In addition, we compared phylogenetic patterns in CO1 data from the congener D. virgifera to demonstrate the utility of mitochondrial data in resolving subspecies. From the CO1 data, a diagnostic real-time PCR assay was developed that could successfully identify all haplotypes within the large D. undecimpunctata clade for use in surveys and identification at ports of entry. These findings underscore the need to resolve molecular and morphological datasets into cogent, lineage-based groupings. Such efforts will provide an evolutionary context for the study of agriculturally important attributes of Diabrotica such as host preferences, xenobiotic metabolism, and natural and anthropogenic patterns of dispersal.
Efficacy of mindfulness- and acceptance-based cognitive-behavioral therapies for bodily distress in adults: a meta-analysis

Objective Bodily distress, i.e., somatoform disorders and associated functional somatic syndromes, is highly prevalent, often persistent and highly disabling. It has been proposed that “third wave” therapies may be beneficial variants of cognitive behavioral treatments. However, evidence on their efficacy is scarce. This meta-analysis examines the efficacy of “third wave” psychotherapies (mindfulness-based cognitive therapy [MBCT], mindfulness-based stress reduction [MBSR], and acceptance and commitment therapy [ACT]) in adults with bodily distress. Method We included randomized controlled trials (RCTs) treating adults with bodily distress using MBCT, MBSR, and ACT compared to inactive and non-specific control groups. A random effects model was used. The primary outcome was somatic symptom severity. Secondary outcomes were degrees of depression and of anxiety, health anxiety, perceived health status, mindfulness, psychological inflexibility, and pain acceptance. Results Sixteen RCTs with 1,288 participants were included in the analysis (k = 4 MBCT, k = 7 MBSR, k = 5 ACT; k = 7 fibromyalgia, k = 5 irritable bowel syndrome, k = 1 chronic fatigue syndrome, k = 2 bodily distress, k = 1 medically unexplained symptoms). However, not all studies provided data for each of the relevant outcomes. The analyses revealed that “third wave“ therapies were more effective than control conditions in reducing somatic symptom severity (k = 15, n = 1,100, g = −0.51, 95%CI −0.69; −0.32). Heterogeneity was moderate (I2 = 52.8%, 95%CI 15.1 to 73.8). Effects for secondary outcomes were small to moderate with varying degrees of heterogeneity. We did not find differences between the different therapy approaches (mindfulness- vs. acceptance-based therapies); neither therapy dosis (i.e., total duration of therapy sessions) nor number of sessions were significant moderators of efficacy. Conclusions The therapies addressing mindfulness and acceptance proved to be more effective than control conditions. Hence, they are promising treatment approaches for bodily distress. However, there is still need for research on which patient groups may benefit from these psychological approaches. Systematic review registration https://osf.io/g7hby, identifier: 10.17605/OSF.IO/4RZGC.
Central adiposity as a predictor of mortality in older adults: Identification of cutoffs using generalized additive models

Background Obesity is associated with premature mortality in adults; however, this association has been inconsistent in the older adult population. In addition, there is a lack of specific cutoff points for indicators of negative health outcomes in older adults. Methods: This is a prospective study with 796 non-institutionalized older adults. Data on sociodemographic characteristics, lifestyle, food consumption, and nutritional status were obtained at baseline. Generalized additive models were used to identify cutoff points for the waist circumference (WC) and waist-to-height ratio (WHtR) and Cox proportional hazards models to assess the independent association between adiposity and mortality. Results Over the 9 years of follow-up, 197 deaths (24.7%) occurred, of which 51.8% were men, with a mean age of 76.1 ± 9.0 years. Older adults at higher risk of death had WHtR of <0.52 or ≥0.63 and WC of <83 cm or ≥101 cm. An increased risk of death was observed in older adults with high WC (HR: 2.03 95% CI: 1.20–3.41) and high WHtR (HR: 1.51 95% CI: 1.01–2.26) in the adjusted models, and an increase in WC was a risk factor for higher CVD mortality (HR: 2.09, 95% CI: 1.12–3.88) in the adjusted models. Conclusion Adiposity was associated with an increased risk of death in older adults. In view of these results and considering the lack of cutoff points for anthropometric indices in Brazilian older adults, further studies are needed to confirm the WC and WHtR cutoff values found in this study.
Fungal community remediate quartz tailings soil under plant combined with urban sludge treatments

Introduction Tailings can cause extensive damage to soil structure and microbial community. Phytoremediation is an effective strategy for remedied tailings soil due to its environmentally friendly and low-cost advantage. Fungi play a crucial role in nutrient cycling, stress resistance, stabilizing soil structure, and promoting plant growth. However, the fungal community variation in phytoremediation remains largely unexplored. Methods We analyzed soil fungal community based on high-throughput sequencing during three plant species combined with urban sludge to remediate quartz tailings soil. Results The results indicated that the fungal diversity was significantly increased with plant diversity, and the highest fungal diversity was in the three plant species combination treatments. Moreover, the fungal diversity was significantly decreased with the addition of urban sludge compared with plant treatments, while the abundance of potential beneficial fungi such as Cutaneotrichosporon, Apiotrichum, and Alternaria were increased. Notably, the fungal community composition in different plant species combination treatments were significant difference at the genus level. The addition of urban sludge increased pH, available phosphorus (AP), and available nitrogen (AN) content that were the main drivers for fungal community composition. Furthermore, the fungal networks of the plant treatments had more nodes and edges, higher connectedness, and lower modularity than plant combined with urban sludge treatments. Conclusion Our results showed that three plant species combined with urban sludge treatments improved fungal community and soil properties. Our results provide insights for quartz tailings soil remediation using plant-fungi- urban sludge.
Prevalence of mental disorders, psychosocial distress, and perceived need for psychosocial support in cancer patients and their relatives stratified by biopsychosocial factors: rationale, study design, and methods of a prospective multi-center observational cohort study (LUPE study)

Background Despite remarkable progress, cancer remains a life-threatening disease for millions of people worldwide, also resulting in significant psychosocial limitations. High-quality, comprehensive cancer care requires patient and family involvement and the provision of needs-based, targeted psychosocial services. Although progress has been made in understanding the occurrence of mental comorbidity and psychosocial distress in cancer patients, comparatively little is known about the course of psychological comorbidity and psychosocial distress in early survivorship among patients and their families. We therefore aim to estimate the prevalence of mental disorders according to the DSM-5, psychosocial distress, perceived needs for psychosocial support and utilization of psychosocial support offers in newly diagnosed cancer patients and their relatives, taking into account potential contributing biopsychosocial factors for the occurrence of psychological comorbidity. Methods/design This study follows a prospective multi-center observational cohort design across four measurement time points: within 2 months after cancer diagnosis (t1), and in the follow-up period at 6 months (t2), at 12 months (t3), and at 18 months (t4) after t1. Patients older than 18 years who have a confirmed initial diagnosis of a malignant solid tumor and are scheduled for cancer treatment at one of the participating cancer centers are eligible for study participation. Relatives of eligible patients are also eligible for study participation if they are older than 18 years. Patients are interviewed using the Structured Clinical Interview for DSM-5 Disorders (SCID-5-CV). In addition, patients and relatives receive a set of validated questionnaires at each measurement time point, covering comorbid conditions and functional performance, perceived psychological distress and quality of life, partnership aspects and social relationships, supportive care needs and use of psychosocial support services, health literacy, and health behavior and meaning in life. Discussion This prospective multi-center observational cohort study has a major focus on increasing quality of care and quality of life in cancer survivors through providing rigorous longitudinal data for the development and implementation of target group-specific psychosocial support services. Trial registration NCT04620564, date of registration 9/11/2020; DKG OnkoZert: Registrier-No.: ST-U134, date of registration 5/11/2021.