Miracle-dz/UniFAR-FTUs huggingface dataset:
Seroprevalence of Human T-Cell Lymphotropic Virus–1 in a Jamaican Antenatal Population and Assessment of Pooled Testing as a Cost Reduction Strategy for Implementation of Routine Antenatal Screening

ABSTRACT. Mother to child transmission (MTCT) of human T-cell lymphotropic virus (HTLV)–1 is associated with increased risk of adult T-cell leukemia and can be unrecognized without routine antenatal screening. We assessed the seroprevalence of HTLV-1/2 among pregnant women attending The University Hospital of the West Indies Antenatal Clinic, 2019, and validated a cost-effective strategy to screen antenatal clinic attendees for HTLV-1/2. Residual antenatal samples from 370 women were tested for HTLV-1/2 by chemiluminescence microparticle immunoassay (CMIA). Six samples were confirmed HTLV-1 positive by Western blot (none for HTLV-2) for a prevalence of 1.62%. Four mother–child pairs were able to be recruited for HTLV testing of children, with two children testing HTLV-1/2 positive. Medical records of HTLV-1–infected women revealed that all women breastfed, indicating an unrecognized risk for HTLV MTCT. To assess whether pooling of samples as a cost-reduction strategy could be introduced, we pooled all antenatal samples received between November and December 2021 into 12 pools of eight samples/pool. Two pools were CMIA positive, and de-pooling of samples identified two CMIA-positive samples (one per pool), both confirmed as HTLV-1 by Western blot. These results indicate that HTLV-1 remains prevalent in pregnant Jamaican women and that sample pooling can be a cost-effective strategy to limit MTCT in Jamaica.
Diet composition, adherence to calorie restriction, and cardiometabolic disease risk modification

Calorie restriction (CR) is a promising approach for attenuating the risk of age‐related disease. However, the role of diet composition on adherence to CR and the effects of CR on cardiometabolic markers of healthspan remains unknown. We used the Geometric Framework for Nutrition approach to examine the association between macronutrient composition and CR adherence during the 2‐year CALERIE trial. Adult participants without obesity were randomized to a 25% CR intervention or an ad libitum intake control. Correlations of cardiometabolic risk factors with macronutrient composition and standard dietary pattern indices [Alternate Mediterranean Diet Index (aMED), Dietary Inflammatory Index (DII), and Healthy Eating Index (HEI)] were also evaluated by Spearman's correlation at each time point. The mean age was 38.1 ± 7.2 years at baseline and the mean BMI was 25.1 ± 1.7. The study population was 70% female. The CR group, but not the control, consumed a higher percentage reported energy intake from protein and carbohydrate and lower fat at 12 months compared to baseline; comparable results were observed at 24 months. Protein in the background of higher carbohydrate intake was associated with greater adherence at 24 months. There was no correlation between macronutrient composition and cardiometabolic risk factors in the CR group. However, statistically significant correlations were observed for the DII and HEI. These findings suggest that individual self‐selected macronutrients have an interactive but not independent role in CR adherence. Additional research is required to examine the impact of varying macronutrient compositions on adherence to CR and resultant modification to cardiometabolic risk factors.
The expert clinical pharmacological advice program for tailoring on real-time antimicrobial therapies with emerging TDM candidates in special populations: how the ugly duckling turned into a swan

ABSTRACT Introduction The growing spread of infections caused by multidrug-resistant pathogens makes the need of tailoring antimicrobial therapies by means of a ‘patient-centered’ approach fundamental. In this scenario, therapeutic drug monitoring (TDM) of emerging antimicrobial candidates may be a valuable approach, but expert interpretation of TDM results should be granted for making them more clinically useful. The MD Clinical Pharmacologist may take over this task since this specialist may couple PK/PD expertise on drugs with a medical background and may provide expert interpretation of TDM results of antimicrobials for tailoring therapy on real-time in each single patient based on specific both drug/pathogen issues and patient issues. Areas covered This article aims to highlight the main key-points and organizational aspects for implementing a successful TDM-based expert clinical pharmacological advice (ECPA) program for tailoring antimicrobial therapies on real-time in different hospitalized patient special populations. Expert opinion TDM-based ECPA programs lead by the MD Clinical Pharmacologist may represent a way forward for maximizing clinical efficacy and for minimizing the risk of resistance developments and/or toxicity of antimicrobials. Stakeholders should be aware of the fact that this innovative approach may be cost-effective.
Late Miocene fish otoliths from the Colombacci Formation (Northern Apennines, Italy): implications for the Messinian ‘Lago‐mare’ event

A fish otolith assemblage from the Messinian ‘Lago‐mare’ deposits of the Colombacci Formation cropping out in the Montecalvo in Foglia Syncline, Marche, central Italy, is described. The assemblage displays a low diversity and consists of seven taxa belonging to three families: the Gobiidae, Myctophidae and Sciaenidae. Sciaenid otoliths are the most abundant elements representing 88% of the entire assemblage. The palaeoecological analysis reveals a coastal shallow marine environment strongly influenced by continental outflow. The low diversity and high abundance of the euryecious sciaenids are indicative of a very simplified food web, which probably represented an ecological response to the fluctuating environmental parameters and available food resources. The fish remains documented here provide an unambiguous evidence that normal marine conditions were present in the Mediterranean, at least in the upper part of the ‘Lago‐mare’ event, and unquestionably demonstrate that the marine refilling preceded the Mio‐Pliocene boundary. These findings clearly demonstrate that fishes, because of their mobility and migratory behaviour, represent a useful tool for the large‐scale interpretation of the environmental conditions of the Messinian Mediterranean water body. The necessity of a new scenario of palaeoenvironmental evolution for the post‐evaporitic Messinian of the Mediterranean is also discussed. Copyright © 2006 John Wiley & Sons, Ltd.
Genetic variants linked to the phenotypic outcome of invasive disease and carriage of Neisseria meningitidis

Neisseria meningitidis can be a human commensal in the upper respiratory tract but is also capable of causing invasive diseases such as meningococcal meningitis and septicaemia. No specific genetic markers have been detected to distinguish carriage from disease isolates. The aim here was to find genetic traits that could be linked to phenotypic outcomes associated with carriage versus invasive N. meningitidis disease through a bacterial genome-wide association study (GWAS). In this study, invasive N. meningitidis isolates collected in Sweden (n=103) and carriage isolates collected at Örebro University, Sweden (n=213) 2018–2019 were analysed. The GWAS analysis, treeWAS, was applied to single-nucleotide polymorphisms (SNPs), genes and k-mers. One gene and one non-synonymous SNP were associated with invasive disease and seven genes and one non-synonymous SNP were associated with carriage isolates. The gene associated with invasive disease encodes a phage transposase (NEIS1048), and the associated invasive SNP glmU S373C encodes the enzyme N-acetylglucosamine 1-phosphate (GlcNAC 1-P) uridyltransferase. Of the genes associated with carriage isolates, a gene variant of porB encoding PorB class 3, the genes pilE/pilS and tspB have known functions. The SNP associated with carriage was fkbp D33N, encoding a FK506-binding protein (FKBP). K-mers from PilS, tbpB and tspB were found to be associated with carriage, while k-mers from mtrD and tbpA were associated with invasiveness. In the genes fkbp, glmU, PilC and pilE, k-mers were found that were associated with both carriage and invasive isolates, indicating that specific variations within these genes could play a role in invasiveness. The data presented here highlight genetic traits that are significantly associated with invasive or carriage N. meningitidis across the species population. These traits could prove essential to our understanding of the pathogenicity of N. meningitidis and could help to identify future vaccine targets.
CAMBRIAN NARAOIIDS (ARTHROPODA): MORPHOLOGY, ONTOGENY, SYSTEMATICS, AND EVOLUTIONARY RELATIONSHIPS

Abstract Naraoiids, defined as lightly sclerotized arthropods with a dimidiate tergum of two sclerites separated by a single transverse articulation, have been found in the Cambrian and Silurian. During the Cambrian they had a wide distribution coinciding with trilobite realms. This pattern may be related to the breakup of a Neoproterozoic supercontinent, probably Pannotia, which implies that naraoiids originated before the Cambrian “explosion. ” Based on new observations on the original material from the Burgess Shale (Middle Cambrian, British Columbia), Naraoia halia is reconsidered as a valid species. The validity is further confirmed by a new record of the occurrence of this species in the Chengjiang Lagerstätte (Lower Cambrian, China). In addition, some structures of N. compacta of the Burgess Shale have been reinterpreted. Two more naraoiid species are redescribed in detail from the Chengjiang Lagerstätte on the basis of more than 1,000 well-preserved specimens. Naraoia spinosa shows dimorphism and Misszhouia longicaudata exhibits geographical variation in the overall shape of the dorsal exoskeleton. Naraoiids may have a protaspis-like larva, but the previously assigned protaspis has proven to be a separate taxon, Primicaris. In dorsal view, naraoiids resemble a giant “degree 0” meraspis (i.e., without thorax), and could have originated from different heterochronic processes, neoteny or hypermorphosis. Naraoiids are generally accepted as vagrant benthos. A predatory/scavenging life mode is supported by functional morphology and recent analogues. A healed injury in M. longicaudata suggests that they could be the prey of larger predators, most likely anomalocaridids. We suggest that differences in exopod composition might represent evolutionary changes through the Early–Middle Cambrian. The monophyly of the Naraoiidae is not firmly established. Similarity to liwiids, supposed to be the close relatives of naraoiids, is limited to overall shape. We exclude naraoiids from the Trilobita, though there do exist a number of similarities between them.
Comparative study in estrogen-depleted mice identifies skeletal and osteocyte transcriptomic responses to abaloparatide and teriparatide

Osteocytes express parathyroid hormone (PTH)/PTH-related protein (PTHrP) receptors and respond to the PTHrP analog abaloparatide (ABL) and to the PTH 1-34 fragment teriparatide (TPTD), which are used to treat osteoporosis. Several studies indicate overlapping but distinct skeletal responses to ABL or TPTD, but their effects on cortical bone may differ. Little is known about their differential effects on osteocytes. We compared cortical osteocyte and skeletal responses to ABL and TPTD in sham-operated and ovariectomized mice. Administered 7 weeks after ovariectomy for 4 weeks at a dose of 40 μg/kg/d, TPTD and ABL had similar effects on trabecular bone, but ABL showed stronger effects in cortical bone. In cortical osteocytes, both treatments decreased lacunar area, reflecting altered peri-lacunar remodeling favoring matrix accumulation. Osteocyte RNA-Seq revealed that several genes and pathways were altered by ovariectomy and affected similarly by TPTD and ABL. Notwithstanding, several signaling pathways were uniquely regulated by ABL. Thus, in mice, TPTD and ABL induced a positive osteocyte peri-lacunar remodeling balance, but ABL induced stronger cortical responses and affected the osteocyte transcriptome differently. We concluded that ABL affected the cortical osteocyte transcriptome in a manner subtly different from TPTD, resulting in more beneficial remodeling/modeling changes and homeostasis of the cortex.
Multi-Scale Spatio-Temporal Fusion With Adaptive Brain Topology Learning for fMRI Based Neural Decoding

Neural decoding aims to extract information from neurons' activities to reveal how the brain functions. Due to the inherent spatial and temporal characteristics of brain signals, spatio-temporal computing has become a hot topic for neural decoding. However, the extant spatio-temporal decoding methods usually use static brain topology, ignoring the dynamic patterns of the interaction between brain regions. Further, they do not identify the hierarchical organization of brain topology, leading to only superficial insight into brain spatio-temporal interactions. Therefore, here we propose a novel framework, the Multi-Scale Spatio-Temporal framework with Adaptive Brain Topology Learning (MSST-ABTL), for neural decoding. It includes two new capabilities to enhance spatio-temporal decoding: i) ABTL module, which learns dynamic brain topology while updating specific patterns of brain regions, ii) MSST module, which captures the association of spatial pattern and temporal evolution, and further enhances the interpretability of the learned dynamic topology from multi-scale perspective. We evaluated the framework on the public Human Connectome Project (HCP) dataset (resting-state and task-related fMRI data). The extensive experiments show that the proposed MSST-ABTL outperforms state-of-the-art methods on four evaluation metrics, and also can renew the neuroscientific discoveries in the brain's hierarchical patterns.
Learning Skill Training Schedules From Domain Experts for a Multi-Patient Multi-Robot Rehabilitation Gym

A robotic gym with multiple rehabilitation robots allows multiple patients to exercise simultaneously under the supervision of a single therapist. The multi-patient training outcome can potentially be improved by dynamically assigning patients to robots based on monitored patient data. In this paper, we present an approach to learn dynamic patient-robot assignment from a domain expert via supervised learning. The dynamic assignment algorithm uses a neural network model to predict assignment priorities between patients. This neural network was trained using a synthetic dataset created in a simulated rehabilitation gym to imitate a domain expert’s assignment behavior. The approach is evaluated in three simulated scenarios with different complexities and different expert behaviors meant to achieve different training objectives. Evaluation results show that our assignment algorithm imitates the expert’s behavior with mean accuracies ranging from 75.4% to 84.5% across scenarios and significantly outperforms three baseline assignment methods with respect to mean skill gain. Our approach solves simplified patient training scheduling problems without complete knowledge about the patient skill acquisition dynamics and leverages human knowledge to learn automated assignment policies.
Parent‐child agreement on children's psychopathology and the impact of parental depression

Abstract Background Parental depression increases children's risk of mental illness and may simultaneously impair the detection of children's symptoms. Here we investigate the nature of parent‐child agreement of children's psychopathology in children of parents with current (cMD) versus remitted (rMD) major depression. Methods Baseline data from 100 parent‐child dyads including healthy children aged 8–17 (M = 11.89, SD = 2.83) and their parents with a history of depression were analysed. The presence of sub‐clinical psychopathology (yes/no) in children was assessed using semi‐structured diagnostic interviews with child and parent (K‐DIPS). Self‐ (YSR) and parent‐report (CBCL) questionnaires were used to measure the severity of symptoms. Parent‐child agreement was calculated using Chi‐square tests and Cohen's kappa respectively. We compared whether agreement differed between children of parents with cMD (n = 52) versus rMD (n = 48). Results In the interviews parents more frequently reported sub‐clinical child psychopathology than the children themselves (χ 2 1,100 = 4.63, p < 0.001, d = 0.59). This pattern characterised parents with cMD (χ 2 1,52 = 7.99, p = 0.005; κ = 0.582) but not rMD (χ 2 1,48 = 000, p = 0.686; κ = −0.010), a difference which was statistically significant (z = 3.14, p < 0.001, d = 0.66). Conclusion Since agreement between parents and children about the severity of children's symptoms was particularly poor in families where parents were currently depressed, parental mental illness should be taken into account when assessing youth psychopathology.
Culture-independent analyses of carrion beetle (Coleoptera: Silphidae) secretion bacterial communities

ABSTRACT In the central plains of North America, the beetle family Silphidae comprised two subfamilies, Silphinae and Nicrophorinae, differentiated by reproductive behaviors. Silphinae, known as carrion beetles, feed on carrion and fly larvae and produce free-living larvae that receive no parental care. Adult Nicrophorinae, known as burying beetles, prepare a vertebrate carcass into a brood ball and provide biparental care to their offspring. Preparation of a brood ball involves coating the carcass in antimicrobial oral and anal secretions. These secretions contain a community of microbes, referred to as the secretion microbiome, which inhibit carcass microbe succession, preventing normal decomposition. Here, the secretion microbiomes of five species of Nicrophorinae and two species of Silphinae, both sampled from Oklahoma, with additional Nicrophorinae from Nebraska, were characterized using culture-independent analyses to understand and decipher factors shaping diversity and community structure. We identify the core secretion microbiome across Silphidae and show that, while the host subfamily, secretion type, and collection locality had no significant effect on the bacterial community alpha diversity, these factors significantly influenced bacterial community structure. Global and local tests of phylogenetic associations identified 14 genera with phylogenetic signals to the host subfamily and species. Description of the bacterial communities present in silphid secretions furthers our understanding of how these beetles interact with microbes for carcass nutrient processing. Future culture-dependent studies from silphid secretions may identify novel antimicrobials and nontoxic compounds that can act as meat preservatives or sources for antimicrobials. IMPORTANCE The manuscript explores the secretion bacterial community of carrion and burying beetles of the central plains of North America. A core secretion microbiome of 11 genera is identified. The host subfamily, secretion type, and collection locality significantly affects the secretion microbiome. Future culture-dependent studies from silphid secretions may identify novel antimicrobials and nontoxic compounds that can act as meat preservatives or sources for antimicrobials. The manuscript explores the secretion bacterial community of carrion and burying beetles of the central plains of North America. A core secretion microbiome of 11 genera is identified. The host subfamily, secretion type, and collection locality significantly affects the secretion microbiome. Future culture-dependent studies from silphid secretions may identify novel antimicrobials and nontoxic compounds that can act as meat preservatives or sources for antimicrobials.
Silicic Magma Formation in Overthickened Crust: Melting of Charnockite and Leucogranite at 15, 20 and 25 kbar

50–60 vol. %, accompanied by settling of residualof crustal source rocks at depths >50 km; (2) production of syenite crystals, would lead to a magma of restricted compositional rangemagma by partial melting of quartzofeldspathic rocks at pressures with a heavy rare earth element depleted pattern. Overall, the granitic>15 kbar. Melting experiments at 15, 20 and 25 kbar were melt composition obtained in the experiments diVers from that ofperformed on Archaean biotite-bearing charnockite of opx-bearing A-type granite. However, at degrees of melting below
Detoxification of reactive oxygen species by the hyaluronic acid capsule of group A Streptococcus

ABSTRACT The pro-inflammatory cytokine IL-6 regulates antimicrobial responses that are broadly crucial in the defense against infection. Our prior work shows that IL-6 promotes the killing of the M4 serotype group A Streptococcus (GAS) but does not impact the globally disseminated M1T1 serotype associated with invasive infections. Using in vitro and in vivo infection models, we show that IL-6 induces phagocyte reactive oxygen species (ROS) that are responsible for the differential susceptibility of M4 and M1T1 GAS to IL-6-mediated defenses. Clinical isolates naturally deficient in capsule, or M1T1 strains deficient in capsule production, are sensitive to this ROS killing. The GAS capsule is made of hyaluronic acid, an antioxidant that detoxifies ROS and can protect acapsular M4 GAS when added exogenously. During in vitro interactions with macrophages and neutrophils, acapsular GAS can also be rescued with the antioxidant N-acetylcysteine, suggesting this is a major virulence contribution of the capsule. In an intradermal infection model with gp91phox -/- (chronic granulomatous disease [CGD]) mice, phagocyte ROS production had a modest effect on bacterial proliferation and the cytokine response but significantly limited the size of the bacterial lesion in the skin. These data suggest that the capsule broadly provides enhanced resistance to phagocyte ROS but is not essential for invasive infection. Since capsule-deficient strains are observed across several GAS serotypes and are competent for transmission and both mild and invasive infections, additional host or microbe factors may contribute to ROS detoxification during GAS infections.
Selection of Standards for Sonographic Fetal Femur Length by Use of z-scores

Abstract Objectives This study aimed to evaluate which of four established norms should be used for sonographic assessment of fetal femur length (FL). Study Design Cross-sectional study using pooled data from four maternal–fetal medicine practices. Inclusion criteria were singleton fetus, gestational age (GA) 22 0/7 to 39 6/7 weeks, biometry measured, and fetal cardiac activity present. Four norms of FL were studied: Hadlock et al, the INTERGROWTH-21 st Project (IG-21 st ), the World Health Organization Fetal Growth Curves (WHO), and the National Institutes of Child Health and Human Development Fetal Growth Studies, unified standard (NICHD-U). The fit of our FL measurements to each norm was assessed by these criteria: mean z-score close to 0, standard deviation (SD) of z close to 1, Kolmogorov–Smirnov D-statistic close to zero, Youden J-statistic close to 1, approximately 5% of exams <5th percentile, and approximately 5% of exams >95th percentile. Results In 26,177 ultrasound exams, our FL measurements had the best fit to the WHO standard (mean z-score 0.15, SD of z 1.02, D-statistic <0.01, J-statistic 0.95, 3.4% of exams <5th percentile, 7.0% of exams >95th percentile). The mean of the IG-21 st standard was smaller than the other norms and smaller than our measurements, resulting in underdiagnosis of short FL. The mean of the Hadlock reference was larger than the other norms and larger than our measurements, resulting in overdiagnosis of short FL. The SD of the NICHD-U standard was larger than the other norms and larger than our observations, resulting in underdiagnosis of both short and long FL. Restricting the analysis to a subgroup of 7,144 low-risk patients without risk factors for large- or small-for- GA produced similar results. Conclusion Of the norms studied, the WHO standard is likely best for diagnosis of abnormal FL. Key Points There are >30 norms for fetal FL. It is unknown which norm should be used. Our data fit the World Health Organization standard better than the other norms.