Miracle-dz/UniFAR-FTUs huggingface dataset:
“Keep your feet on the ground”: Simulated range of motion and hind foot posture of the Middle Jurassic sauropod Rhoetosaurus brownei and its implications for sauropod biology

The biomechanics of the sauropod dinosaur pes is poorly understood, particularly among the earliest members of the group. To date, reasonably complete and articulated pedes in Early Middle Jurassic sauropods are rare, limited to a handful of taxa. Of these, Rhoetosaurus brownei, from eastern Australia, is currently the only one from the Gondwanan Middle Jurassic that preserves an articulated pes. Using Rhoetosaurus brownei as a case exemplar, we assessed its paleobiomechanical capabilities and pedal posture. Physical and virtual manipulations of the pedal elements were undertaken to evaluate the range of motion between the pedal joints, under both bone‐to‐bone and cartilaginous scenarios. Using the results as constraints, virtual reconstructions of all possible pedal postures were generated. We show that Rhoetosaurus brownei was capable of significant digital mobility at the osteological metatarsophalangeal and distal interphalangeal joints. We assume these movements would have been restricted by soft tissue in life but that their presence would have helped in the support of the animal. Further insights based on anatomy and theoretical mechanical constraints restricted the skeletal postures to a range encompassing digitigrade to subunguligrade stances. The approach was extended to additional sauropodomorph pedes, and some validation was provided via the bone data of an African elephant pes. Based on the resulting pedal configurations, the in‐life plantar surface of the sauropod pes is inferred to extend caudally from the digits, with a soft tissue pad supporting the elevated metatarsus. The plantar pad is inferred to play a role in the reduction of biomechanical stresses, and to aid in support and locomotion. A pedal pad may have been a key biomechanical innovation in early sauropods, ultimately resulting in a functionally plantigrade pes, which may have arisen during the Early to Middle Jurassic. Further mechanical studies are ultimately required to permit validation of this long‐standing hypothesis.
Defining the RNA interactome by total RNA‐associated protein purification

UV crosslinking can be used to identify precise RNA targets for individual proteins, transcriptome-wide. We sought to develop a technique to generate reciprocal data, identifying precise sites of RNA-binding proteome-wide. The resulting technique, total RNA-associated protein purification (TRAPP), was applied to yeast (S. cerevisiae) and bacteria (E. coli). In all analyses, SILAC labelling was used to quantify protein recovery in the presence and absence of irradiation. For S. cerevisiae, we also compared crosslinking using 254 nm (UVC) irradiation (TRAPP) with 4-thiouracil (4tU) labelling combined with ~350 nm (UVA) irradiation (PAR-TRAPP). Recovery of proteins not anticipated to show RNA-binding activity was substantially higher in TRAPP compared to PAR-TRAPP. As an example of preferential TRAPP-crosslinking, we tested enolase (Eno1) and demonstrated its binding to tRNA loops in vivo. We speculate that many protein-RNA interactions have biophysical effects on localization and/or accessibility, by opposing or promoting phase separation for highly abundant protein. Homologous metabolic enzymes showed RNA crosslinking in S. cerevisiae and E. coli, indicating conservation of this property. TRAPP allows alterations in RNA interactions to be followed and we initially analyzed the effects of weak acid stress. This revealed specific alterations in RNA-protein interactions; for example, during late 60S ribosome subunit maturation. Precise sites of crosslinking at the level of individual amino acids (iTRAPP) were identified in 395 peptides from 155 unique proteins, following phospho-peptide enrichment combined with a bioinformatics pipeline (Xi). TRAPP is quick, simple and scalable, allowing rapid characterization of the RNA-bound proteome in many systems.
Promoters of Colistin Resistance in Acinetobacter baumannii Infections.

OBJECTIVES We aimed to describe the mechanisms of colistin resistance in Acinetobacter baumannii. MATERIALS AND METHODS Twenty-nine patients diagnosed with colistin-resistant A. baumannii infection were included to the study. The mutations in pmrCAB, lpxA, lpxC, and lpxD genes, expression of pmrCAB, carbapenemases, and mcr-1 positivity were studied. RESULTS Twenty-seven (93%) of the patients received IV colistin therapy during their stay, and the case fatality rate was 45%. All mutations in pmrC and pmrB were found to be accompanied with a mutation in lpxD. The most common mutations were I42V and L150F in pmrC (65%), E117K in lpxD (65%), and A138T in pmrB (58.6%). The colistin minimum inhibitory concentrations (MICs) of the isolates having any of these four mutations were higher than the isolates with no mutations (p < 0.001). The two most common mutations in pmrC (I42V and L150F) were found to be associated with higher expressions of pmrA and pmrC and higher colistin MIC values (p = 0.010 and 0.031). All isolates were blaOXA-23 positive. CONCLUSION Coexistence of the lpxD mutation along with mutations in pmrCAB indicates synergistic function of these genes in development of colistin resistance in A. baumannii.
A Path Model Analysis of the Causal Relationship between Self-care Agency and Healthy Behavior in Community-dwelling Older People from the GAINA Study.

Background Self-care agency is an important determinant of self-care behavior. The purpose of this study was to identify the causal relationship between self-care agency and healthy behavior, and to construct a conceptual model of healthy behavior among older people living in a rural community. Methods This study was conducted as a cross-sectional survey at the Hino, a town in western Tottori Prefecture, Japan. Participants who were enrolled in the Good Ageing and Intervention against Nursing Care and Activity Decline (GAINA) study from 2014 to 2018 (467 new participants) were initially investigated. Of 398 participants aged ≥ 65 years, 5 were excluded due to missing data, and thus 393 were analyzed. Nurse researchers conducted face-to-face interviews with participants to check the accuracy of data obtained from a self-administered questionnaire, which included demographic information, physical condition (comorbidities, knee pain, low back pain, and locomotive syndrome), healthy behavior, and self-care agency. Correlations among variables were investigated by Pearson's correlation coefficient analysis, and path analysis was performed to assess causal relationships. Results A total of 393 persons (160 men and 233 women) were investigated, ranging in age from 65 to 92 years, with a mean age of 75.1 years (SD: 6.9 years). Path analysis revealed poor fit of a model in which pain and locomotive syndrome were factors inhibiting healthy behavior. When the model included only self-care agency, the indices of model fit were almost satisfactory (Goodness-of-fit index = 0.967, Adjusted goodness-of-fit index = 0.900, Comparative fit index = 0.951, and Root mean square error of approximation = 0.088), and the coefficient of determination (R2) was 0.38. The self-care agency items with the greatest influence on healthy behavior were the ability to "grasp the techniques/tips needed to maintain health," and the ability to "persist with healthy behavior. " Conclusion Self-care agency can promote healthy behavior among community-dwelling older people. Regardless of physical problems such as pain and locomotive syndrome, older people have the potential to adopt positive healthy behavior if they acquire self-care agency.
Downregulation of long noncoding RNA LINC00683 associated with unfavorable prognosis in prostate cancer based on TCGA

Prostate cancer (PCa) is the third most common reason of cancer‐related deaths in men. Accumulating evidence has shown that dysregulation of long noncoding RNAs (lncRNAs) is closely related to cancer initiation and development. Although large numbers of lncRNAs have been discovered, knowledge regarding their function and physiological/pathological significance remains limited. In this study, we aimed to reveal functional lncRNAs and identify prognosis‐related RNAs in PCa by analyzing data from The Cancer Genome Atlas (TCGA). To achieve this, an lncRNA‐mRNA coexpression network was constructed by weighted correlation network analysis. Additionally, a subnetwork was extracted from this weighted correlation network, and seven lncRNAs were identified as core nodes. Further Kaplan‐Meier survival analysis showed that three lncRNAs (LINC00683, LINC00857, and FENDRR) were significantly downregulated in PCa samples, and there was a strong positive correlation with patient survival. Importantly, LINC00683 has not been fully reported as related with PCa. Additionally, gene set enrichment analysis indicated that LINC00683 might be involved in cancer‐related pathways such as the Wnt pathway. Based on the findings of this study, lncRNA LINC00683 is likely to provide a new diagnostic biomarker and therapeutic target for future PCa treatments.
A Randomized Placebo-controlled Trial of an Oral Preparation of High Molecular Weight Fucoidan in Patients with Type 2 Diabetes with Evaluation of Taste Sensitivity.

Background Fucoidan is derived from seaweed widely used in Japanese cuisine, but little is known about its influence on glucose metabolism. To obtain information about the physiological effects of fucoidan on glucose metabolism, the digestive system, and the gustatory system controlling taste sensation in patients with type 2 diabetes, we conducted a randomized, double-blind, placebo-controlled study. Methods Thirty patients with type 2 diabetes on diet therapy were recruited from an outpatient clinic (22 men and 8 women aged 59.10 ± 13.24 years, body mass index: 25.18 ± 3.88, hemoglobin A1c: 7.04 ± 1.24%). They were divided into 2 groups and underwent 2 interventions with a 4-week interval. One group received fucoidan for 12 weeks (a daily 60 mL test beverage containing 1,620 mg of fucoidan) and then placebo (60 mL) for the subsequent 12-week period, while the order was reversed in the other group. Evaluation was performed just before and after each intervention. Taste sensitivity was measured for 5 basic tastes by the filter paper disk method and food intake was evaluated with a validated diet questionnaire. Results No adverse events occurred during the study period. Despite no change of the diet, stool frequency increased during fucoidan intake (from 7.78 ± 4.64/week in Week 1 to 9.15 ± 5.03/week in Week 5, P < 0.001), and it increased more in lean subjects. In 11 subjects whose stool frequency exceeded the mean value, the thresholds for sweet, salty, bitter and umami tastes were significantly reduced (enhancement of sensitivity) after fucoidan intake. In 14 subjects with normal HOMA-IR (homeostatic model assessment of insulin resistance, < 2.5), hemoglobin A1c decreased after fucoidan intake (from 6.73 ± 1.00 to 6.59 ± 1.00%, P < 0.05), as did the fasting plasma level of GLP-1 (glucagon-like peptide-1, from 6.42 ± 3.52 to 4.93 ± 1.88 pmol/L, P < 0.05). Conclusion Sustained fucoidan intake led to alterations of gastrointestinal function, including increased stool frequency and enhanced taste sensitivity, which could contribute to better control of diabetes.
Novel multi‐component vaccine approaches for Burkholderia pseudomallei

Burkholderia pseudomallei is the causative agent of melioidosis. Historically believed to be a relatively rare human disease in tropical countries, a recent study estimated that, worldwide, there are approximately 165 000 human melioidosis cases per year, more than half of whom die. The bacterium is inherently resistant to many antibiotics and treatment of the disease is often protracted and ineffective. There is no licensed vaccine against melioidosis, but a vaccine is predicted to be of value if used in high‐risk populations. There has been progress over the last decade in the pursuit of an effective vaccine against melioidosis. Animal models of disease including mouse and non‐human primates have been developed, and these models show that antibody responses play a key role in protection against melioidosis. Surprisingly, although B. pseudomallei is an intracellular pathogen there is limited evidence that CD8+ T cells play a role in protection. It is evident that a multi‐component vaccine, incorporating one or more protective antigens, will probably be essential for protection because of the pathogen's sophisticated virulence mechanisms as well as strain heterogeneity. Multi‐component vaccines in development include glycoconjugates, multivalent subunit preparations, outer membrane vesicles and other nano/microparticle platforms and live‐attenuated or inactivated bacteria. A consistent finding with vaccine candidates tested in mice is the ability to induce sterilizing immunity at low challenge doses and extended time to death at higher challenge doses. Further research to identify ways of eliciting more potent immune responses might provide a path for licensing an effective vaccine.
Prevention of Adjacent Segmental Disease after Fusion in Degenerative Spinal Disorder: Correlation between Segmental Lumbar Lordosis Ratio and Pelvic Incidence–Lumbar Lordosis Mismatch for a Minimum 5-Year Follow-up

Study Design Retrospective study. Purpose Associations among risk factors related to adjacent segmental disease (ASD) remain unclear. We evaluated the risk factors and segmental lordosis ratio to prevent ASD developing after lumbar spinal fusion. Overview of Literature Risk factors related to ASD development are age, sex, obesity, pre-existing degeneration, number of fusion segments, and decreased postoperative lumbar lordosis (LL). However, the associations among these factors are still unclear and should be clearly identified. Methods We retrospectively reviewed data on 274 patients who underwent lumbar spinal fusion of three segments or below for lumbar degenerative disease from January 2010 to December 2012, with over 5 years of follow-up. Patients with preoperative sagittal vertical axis (SVA) >5 cm were excluded due to sagittal imbalance. A total of 37 patients with ASD and 40 control patients (CTRL) were randomly selected in a similar distribution of matching variables: age, sex, and preoperative degenerative changes. Sex, age, number of fusion segments, radiologic measurements, L4–5–S1/L1–S1 LL ratio, and spinopelvic parameters (pelvic incidence [PI], pelvic tilt [PT], sacral slope [SS], and SVA) were analyzed. Logistic regression was used to analyze the correlation between PI–LL mismatch and L4–5–S1 segmental lordosis rate. Results No significant difference was found between ASDs and CTRL groups regarding age, sex, number of fusion segments, fusion method, and preoperative and postoperative spinopelvic parameters (PI, SS, PT, and LL). However, regarding the L4–5–S1/L1–S1 lordosis ratio, 50% (p=0.045), 60% (p=0.031), 70% (p=0.042), 80% (p=0.023), and 90% (p=0.023) were statistically significant; <20% (p=0.478), 30% (p=0.223), and 40% (p=0.089) were not statistically significant. In the postoperative PI–LL <10 group, ASD occurred less frequently than in the PI–LL >10 group, and the difference was statistically significant (p=0.048). Conclusions Patients with a postoperative L4–5–S1/L1–S1 lordosis ratio >50% had less occurrence of ASD. Correcting LL according to PI and physiologic segmental lordosis ratio is important in preventing ASD.
Fine‐needle cytology of intraglandular parotid lymph node: A useful procedure in the management of salivary gland nodules

Enlarged intra‐parotid lymph nodes (pLNs) may be misdiagnosed at ultrasound (US) being rare entities and because of their similarities to parotid nodules. Fine‐needle cytology (FNC) is used in the preoperative diagnosis of parotid nodules, and may be used on pLNs to assess their nature and the underlying pathological processes.
Gender variation in symptomatic peripheral arterial occlusive disease among type-2 diabetic patients

Purpose: Little is known about the existence of potential gender disparities in peripheral arterial occlusive disease. To our knowledge, this is the first study to analyze differences attributed to gender in type-2 diabetic patients with symptomatic peripheral arterial occlusive disease, with regard to clinical presentations, risk factors and anatomical distributions of atherosclerosis. Patients and methods: This study was conducted at King Abdullah University Hospital, Jordan. Medical records of all diabetic (type-2) patients who presented with symptomatic peripheral arterial occlusive disease in the period from January 2012 and November 2017 were reviewed, data were collected retrospectively. In all, 364 patients (282 males and 82 females) were involved. Criteria for diagnosis include the following Ankle-Brachial Index ⩽ 0.9 and intermittent claudication or critical limb ischemia. Risk factors for atherosclerosis (age, smoking and hypertension) and computed tomography-angiogram findings were analyzed using Statistical Package for the Social Sciences. p < 0.05 was considered statistically significant. Results: The mean age was higher in females than males (67.61 vs 62.61 years; p = 0.001). Females had greater prevalence of uncontrolled diabetes compared to males (HbA1c 9.07 in females vs 8.51 in males; p = 0.03). High density lipoprotein was higher in females than males (1.02 vs 0.935; p = 0.009). Females presented more with critical limb ischemia than intermittent claudication in comparison with males (p = 0.017). Involvement of superficial femoral artery, deep femoral artery and peroneal artery in hemodynamic relevant atherosclerotic lesion was significantly higher in females than males (p < 0.05). However, involvement of common iliac artery with hemodynamic relevant atherosclerotic lesion was significantly higher in males than females (p = 0.003). Conclusions: Clinical presentation, risk factors and anatomical distributions of atherosclerosis among type-2 diabetic patients with symptomatic peripheral arterial occlusive disease are different between males and females. When compared to males, female patients presented more with critical limb ischemia than intermittent claudication. Females showed higher age at presentation, poor control of diabetes mellitus and higher level of high density lipoprotein. Involvement of superficial femoral artery, deep femoral artery and peroneal artery in hemodynamic relevant atherosclerotic lesion were significantly higher in females than males. In contrast, common iliac artery involvement with hemodynamic relevant atherosclerotic lesion was significantly higher in males than females.
Interactions between soil heterogeneity and freezing: Implications for grassland plant diversity and relative species abundances

Plant stress resulting from soil freezing is expected to increase in northern temperate regions over the next century due to reductions in snow cover caused by climate change. Within plant communities, soil spatial heterogeneity can potentially buffer the effects of plant freezing stress by increasing the availability of soil microsites that function as microrefugia. Moreover, increased species richness resulting from soil heterogeneity can increase the likelihood of stress‐tolerant species being present in a community. We used a field experiment to examine interactions between soil heterogeneity and increased freezing intensity (achieved via snow removal) on plant abundance and diversity in a grassland. Patches of topsoil were mixed with either sand or woodchips to create heterogeneous and homogeneous treatments, and plant community responses to snow removal were assessed over three growing seasons. Soil heterogeneity interacted significantly with snow removal, but it either buffered or exacerbated the snow removal response depending on the specific substrate (sand vs. woodchips) and plant functional group. In turn, snow removal influenced plant responses to soil heterogeneity; for example, adventive forb cover responded to increased heterogeneity under ambient snow cover, but this effect diminished with snow removal. Our results reveal that soil heterogeneity can play an important role in determining plant responses to changes in soil freezing stress resulting from global climate change. While the deliberate creation of soil microsites in ecological restoration projects as a land management practice could increase the frequency of microrefugia that mitigate plant community responses to increased freezing stress, the design of these microsites must be optimized, given that soil heterogeneity also has the potential to exacerbate freezing stress responses.
Association of HIV Preexposure Prophylaxis With Incidence of Sexually Transmitted Infections Among Individuals at High Risk of HIV Infection

Importance Emerging evidence suggests that risk of bacterial sexually transmitted infections (STIs) increases among gay and bisexual men following initiation of HIV preexposure prophylaxis (PrEP). Objective To describe STI incidence and behavioral risk factors among a cohort of predominantly gay and bisexual men who use PrEP, and to explore changes in STI incidence following PrEP commencement. Design, Setting, and Participants The Pre-exposure Prophylaxis Expanded (PrEPX) Study, a multisite, open-label intervention study, was nested within the Australian Collaboration for Coordinated Enhanced Sentinel Surveillance (ACCESS) clinic network. A total of 4275 participants were enrolled (July 26, 2016–April 1, 2018) in Victoria, Australia. Of these, 2981 enrolled at 5 ACCESS clinics (3 primary care, 1 sexual health, and 1 community-based HIV rapid testing service), had at least 1 follow-up visit, and were monitored until April 30, 2018. Exposures Upon enrollment, participants received daily oral tenofovir disoproxil fumurate and emtricitabine for HIV PrEP, quarterly HIV and STI testing, and clinical monitoring. Main Outcomes and Measures The primary outcome was incidence of chlamydia, gonorrhea, or syphilis. Incidence rates and hazard ratios describing behavioral risk factors of STI diagnosis were calculated. Incidence rate ratios (IRRs), adjusted for change in testing frequency, described changes in STI incidence from 1-year preenrollment to study follow-up among participants with preenrollment testing data (n = 1378). Results Among the 2981 individuals (median age, 34 years [interquartile range, 28-42]), 98.5% identified as gay or bisexual males, 29% used PrEP prior to enrollment, 89 (3%) withdrew and were censored at date of withdrawal, leaving 2892 (97.0%) enrolled at final follow-up. During a mean follow-up of 1.1 years (3185.0 person-years), 2928 STIs were diagnosed among 1427 (48%) participants (1434 chlamydia, 1242 gonorrhea, 252 syphilis). STI incidence was 91.9 per 100 person-years, with 736 participants (25%) accounting for 2237 (76%) of all STIs. Among 2058 participants with complete data for multivariable analysis, younger age, greater partner number, and group sex were associated with greater STI risk, but condom use was not. Among 1378 participants with preenrollment testing data, STI incidence increased from 69.5 per 100 person-years prior to enrollment to 98.4 per 100 person-years during follow-up (IRR, 1.41 [95% CI, 1.29-1.56]). After adjusting for testing frequency, the increase in incidence from 1 year preenrollment to follow-up was significant for any STI (adjusted IRR, 1.12 [95% CI, 1.02-1.23]) and for chlamydia (adjusted IRR, 1.17 [95% CI, 1.04-1.33]). Conclusions and Relevance Among gay and bisexual men using PrEP, STIs were highly concentrated among a subset, and receipt of PrEP after study enrollment was associated with an increased incidence of STIs compared with preenrollment. These findings highlight the importance of frequent STI testing among gay and bisexual men using PrEP.