Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeny and Paleobiogeography of Hegetotheriidae (Mammalia, Notoungulata)

ABSTRACT Hegetotheriidae are one of the most derived families of the Order Notoungulata. It is composed of two subfamilies: Hegetotheriinae, which resolves as paraphyletic in most recent phylogenies, and Pachyrukhinae, which historically is considered monophyletic. The family is recognized from late Oligocene to Pliocene and is well diversified from its earliest records. Most papers on the family are systematic studies and, to a lesser degree, investigate its phylogenetic relationships, but paleobiogeographic approaches are rare. A phylogenetic analysis was carried out using TNT, based on a previous matrix that was augmented with additional taxa and characters. Previous results are supported, viz., the paraphyly of Hegetotherium Ameghino and Paedotherium Burmeister, and the monophyly of Pachyrukhinae, but new conclusions arise, such as the paraphyly of Hemihegetotherium Rovereto and the monophyly of Prohegetotherium Ameghino and Hegetotheriinae. In this work, a paleobiogeographic analysis on hegetotheriids is carried out by means of the Bayesian method using the RASP program, with the aim of estimating the possible ancestral area and vicariance, dispersal, and extinction events. This analysis shows that Hegetotheriidae and both subfamilies originated in central Patagonia (southeast of Chubut and northeast of Santa Cruz provinces). The analysis also reveals that dispersals were the predominant events, and they are related to Cenozoic dispersals to lower latitudes as global cooling advanced and new lands emerged.
Feasibility and outcomes of percutaneous radiofrequency ablation for intrahepatic recurrent hepatocellular carcinoma after liver transplantation: a single-center experience

Abstract Purpose To evaluate the feasibility, effectiveness, and treatment outcomes of percutaneous radiofrequency ablation (RFA) in the application of intrahepatic recurrent hepatocellular carcinoma (r-HCC) after liver transplantation (LT). Methods From April 2008 to December 2019, a total of 37 patients (34 male and 3 female, mean age: 48.7 ± 10.5 years) with 61 r-HCCs after LT treated by RFA as a first-line option were enrolled. The technical success, recurrence-free survival (RFS), overall survival (OS) and complications were evaluated. Results After the first session of RFA, three patients were detected with residual foci. All of them received additional session of RFA and two tumors were successfully ablated. Therefore, the technical success was 97.3% (36/37). During the follow-up period, a total of 7 tumors developed local tumor progression (LTP) after 2.2–10.8 months. The LTP rate was 11.7% for r-HCC in the transplanted liver. The median RFS was 4.8 months (95% confidence interval [CI]: 2.2–7.3 months). The 1-, 3-, and 5-year cumulative OS rates were 68.5%, 40.3%, and 40.3%, respectively. Multivariate analyses revealed that tumor size was the only independent predictor for RFS (hazard ratio [HR] = 2.557, 95% CI, 1.015–6.444; p = .046) and limited extrahepatic metastasis was the only independent prognostic factors of OS after RFA for post-LT r-HCC (HR = 4.031, 95%CI, 1.218–13.339; p = .022). Major complications after RFA occurred in two patients (2/37, 5.4%). Conclusion Percutaneous RFA is safe and effective for intrahepatic r-HCC after LT, especially for those without limited extrahepatic metastasis.
Large Subchorionic Cyst Located at Umbilical Cord Insertion with Vascular Displacing and Intracystic Hemorrhage/Hematoma: A Case Report

Abstract Background: Large subchorionic cysts usually arise close to the placental cord insertion site (PCIS) inducing traction on the umbilical cord, impairing blood flow and favoring fetal growth restriction (FGR). Intracystic hemorrhage/hematoma is likely due to the prothrombotic properties of X cells secretion (extravillous trophoblast), which line the cyst wall. Case report: We describe a large subchorionic cyst located exactly at the PCIS, displacing the umbilical cord vessel branches running along the cyst surface. The fetus presented with FGR. At 36 weeks of gestational age, the cyst measured 7.7 cm in maximum dimension showing a partially organized hemorrhage and a peripheral laminated thrombohematoma. The patient underwent elective cesarean section as the cyst and its vessels were at high risk of rupture during labor. Conclusion: Recognition of large subchorionic cysts close to or at the PCIS in a growth restricted fetus with subsequent expedited delivery may avoid a fatal event.
LIRO: Tightly Coupled Lidar-Inertia-Ranging Odometry

In recent years, thanks to the continuously reduced cost and weight of 3D lidar, the applications of this type of sensor in the community have become increasingly popular. Despite many progresses, estimation drift and tracking loss are still prevalent concerns associated with these systems. However, in theory these issues can be resolved with the use of some observations to fixed landmarks in the operation environments. This motivates us to investigate a sensor fusion scheme of lidar and inertia measurements with Ultra-Wideband (UWB) range measurements to such landmarks, which can be easily deployed in the environments with minimal cost and time. Hence, data from IMU, lidar and UWB are tightly-coupled with the robot's states on a sliding window based on their timestamps. Then, we construct a cost function comprising of factors from UWB, lidar and IMU preintegration measurements. Finally an optimization process is carried out to estimate the robot's position and orientation. It is demonstrated through some real world experiments that the method can effectively resolve the drift issue, while only requiring two or three anchors deployed in the environment.
Surgical Re-intervention Rates After Invasive Treatment for Lower Urinary Tract Symptoms due to Benign Prostatic Syndrome: A Comparative Study of More than 43,000 Patients with Long-Term Follow-Up.

PURPOSE No large-scale comparison of the four most established surgical approaches for LUTS due to benign prostate obstruction in terms of long-term efficacy is available. We compared photoselective vaporisation, laser enucleation and open simple prostatectomy to transurethral resection with regard to 5-year surgical re-intervention rates. MATERIALS AND METHODS 43.041 male patients with LUTS who underwent transurethral resection (n=34,526), photoselective vaporisation (n=3,050), laser enucleation (n=1,814) or open simple prostatectomy (n=3,651) between 2011 and 2013 were identified in pseudonymised claims and core data of the German local health care funds (AOK) and followed for 5 years. Surgical re-interventions for LUTS, urethral stricture or bladder neck contracture were evaluated. Surgical approach was related to re-intervention risk using the Kaplan-Meier method and Cox proportional-hazards models. RESULTS ,050 first re-interventions occurred within 5 years of primary surgery (Kaplan-Meier survival without re-intervention: 87.5%, 95%-CI: 87.2%-87.8%). Photoselective vaporisation carried an increased hazard of re-intervention (HR 1.31, 95%-CI: 1.17-1.46, p <0.001) relative to transurethral resection, open simple prostatectomy carried a lower hazard (HR 0.43, 95%-CI: 0.37-0.50, p <0.001) and LEP did not differ significantly (HR 0.84, 95%-CI: 0.66-1.08, p=0.2). This pattern was more pronounced regarding re-intervention for LUTS recurrence (photoselective vaporisation: HR 1.52, 95%-CI: 1.35-1.72, p <0.001; LEP: HR 0.84, 95%-CI: 0.63-1.14, p=0.3; open simply prostatectomy: HR 0.38, 95%-CI: 0.31-0.46, p <0.001; relative to transurethral resection). CONCLUSIONS 5-year re-intervention rates of transurethral resection and laser enucleation did not differ significantly, while photoselective vaporisation had a substantially higher rate. Open simple prostatectomy remains superior to transurethral resection with respect to long-term efficacy.
Extension of CNN-LSTM based reduced order surrogate for minimal turbulent channel flow

We investigate the applicability of machine learning based reduced order model (ML-ROM) to three-dimensional complex flows. As an example, we consider a turbulent channel flow at the friction Reynolds number of $Re_\tau = 110$ in a minimum domain which can maintain coherent structures of turbulence. Training data set are prepared by direct numerical simulation (DNS). The present ML-ROM is constructed by combining a three-dimensional convolutional neural network autoencoder (CNN-AE) and a long short-term memory (LSTM). The CNN-AE works to map high-dimensional flow fields into a low-dimensional latent space. The LSTM is then utilized to predict a temporal evolution of the latent vectors obtained by the CNN-AE. The combination of CNN-AE and LSTM can represent the spatio-temporal high-dimensional dynamics of flow fields by only integrating the temporal evolution of the low-dimensional latent dynamics. The reproduced turbulent flow fields by the present ML-ROM show statistical agreement with the reference DNS data in time-ensemble sense, which can also be found through an orbit-based analysis. The influences on vortical structures over the domain and a time interval for temporal prediction for the ML-ROM performance are also investigated. The potential and limitation of the present ML-ROM for turbulence analysis are discussed at the end of our presentation.
POMDP Manipulation Planning under Object Composition Uncertainty

Manipulating unknown objects in a cluttered environment is difficult because segmentation of the scene into objects, that is, object composition is uncertain. Due to this uncertainty, earlier work has concentrated on either identifying the "best" object composition and deciding on manipulation actions accordingly, or, tried to greedily gather information about the "best" object composition. Contrary to earlier work, we 1) utilize different possible object compositions in planning, 2) take advantage of object composition information provided by robot actions, 3) take into account the effect of different competing object hypotheses on the actual task to be performed. We cast the manipulation planning problem as a partially observable Markov decision process (POMDP) which plans over possible hypotheses of object compositions. The POMDP model chooses the action that maximizes the long-term expected task specific utility, and while doing so, considers the value of informative actions and the effect of different object hypotheses on the completion of the task. In simulations and in experiments with an RGB-D sensor, a Kinova Jaco and a Franka Emika Panda robot arm, a probabilistic approach outperforms an approach that only considers the most likely object composition and long term planning outperforms greedy decision making.
Ultrastructure of eggshell and embryological development of Salvator merianae (Squamata: Teiidae)

The objective of this study was to characterize the external morphology of Salvator meriane embryos in different stages of embryonic development and establish a relationship with the ultrastructure of the shell from oviductal transit to hatching. A total of 120 embryos were analyzed to describe their external morphology, and 78 eggs were used for the analysis of the shell. For embryonic development, the series was established according to the total length of the body. We established 40 embryonic stages from the primitive streak. In the early stages, the external morphological features are the C‐shaped body, the maxillary, and mandibular fusion processes with the frontal process and the fusion of the forelimb with the digital plate. In the middle stages, the eyelid appears, and there are claws on the toes, cornification of fingers, and the onset of pigmentation. The last stage of embryonic development is characterized by the beginning of the formation of the scales, appear the toenails, and finalize the entire pigmentation. Regarding the relationship that exists with the ultrastructure of the egg during development, it was possible to observe a marked change in the composition of the shell and well‐marked compaction during embryonic development, which may be related to the transport of calcium during embryonic ossification. Our results allowed us to show the complete sequence of embryonic development, determining the laying stage for this species. It was possible to establish a relationship with the ultrastructure of the eggshell from the oviductal transit to the moment of hatching.
Differential role of nicotinamide adenine dinucleotide deficiency in acute and chronic kidney disease.

BACKGROUND Nicotinamide adenine dinucleotide (NAD+) is a ubiquitous coenzyme involved in electron transport and a co-substrate for sirtuin function. NAD+ deficiency has been demonstrated in the context of acute kidney injury (AKI). METHODS We studied the expression of key NAD+ biosynthesis enzymes in kidney biopsies from human allograft patients and patients with chronic kidney disease (CKD) at different stages. We used ischaemia-reperfusion injury (IRI) and cisplatin injection to model AKI, urinary tract obstruction [unilateral ureteral obstruction (UUO)] and tubulointerstitial fibrosis induced by proteinuria to investigate CKD in mice. We assessed the effect of nicotinamide riboside (NR) supplementation on AKI and CKD in animal models. RESULTS RNA sequencing analysis of human kidney allograft biopsies during the reperfusion phase showed that the NAD+ de novo synthesis is impaired in the immediate post-transplantation period, whereas the salvage pathway is stimulated. This decrease in de novo NAD+ synthesis was confirmed in two mouse models of IRI where NR supplementation prevented plasma urea and creatinine elevation and tubular injury. In human biopsies from CKD patients, the NAD+ de novo synthesis pathway was impaired according to CKD stage, with better preservation of the salvage pathway. Similar alterations in gene expression were observed in mice with UUO or chronic proteinuric glomerular disease. NR supplementation did not prevent CKD progression, in contrast to its efficacy in AKI. CONCLUSION Impairment of NAD+ synthesis is a hallmark of AKI and CKD. NR supplementation is beneficial in ischaemic AKI but not in CKD models.
Introducing differential RNA-seq mapping to track the early infection phase for Pseudomonas phage ɸKZ

ABSTRACT As part of the ongoing renaissance of phage biology, more phage genomes are becoming available through DNA sequencing. However, our understanding of the transcriptome architecture that allows these genomes to be expressed during host infection is generally poor. Transcription start sites (TSSs) and operons have been mapped for very few phages, and an annotated global RNA map of a phage – alone or together with its infected host – is not available at all. Here, we applied differential RNA-seq (dRNA-seq) to study the early, host takeover phase of infection by assessing the transcriptome structure of Pseudomonas aeruginosa jumbo phage ɸKZ, a model phage for viral genetics and structural research. This map substantially expands the number of early expressed viral genes, defining TSSs that are active ten minutes after ɸKZ infection. Simultaneously, we record gene expression changes in the host transcriptome during this critical metabolism conversion. In addition to previously reported upregulation of genes associated with amino acid metabolism, we observe strong activation of genes with functions in biofilm formation (cdrAB) and iron storage (bfrB), as well as an activation of the antitoxin ParD. Conversely, ɸKZ infection rapidly down-regulates complexes IV and V of oxidative phosphorylation (atpCDGHF and cyoABCDE). Taken together, our data provide new insights into the transcriptional organization and infection process of the giant bacteriophage ɸKZ and adds a framework for the genome-wide transcriptomic analysis of phage–host interactions.
Short Communication: Augmentation of cardioprotective effect of captopril by Costus speciosus against isoproterenol induced myocardial toxicity in rats

Al-Yahya AAI, Asad M, Sadaby A, Ibrahim KE. 2017. Short Communication: Augmentation of cardioprotective effect of captopril by Costus speciosus against isoproterenol induced myocardial toxicity in rats. Nusantara Bioscience 9: 295-299. This study determined the pharmacodynamic interaction of captopril, a known cardioprotective effect with methanolic extract of Costus speciosus rhizomes (Costaceae) that is known for its powerful antioxidant action during isoproterenol induced cardiac toxicity in rats. A methanolic extract of the rhizomes was prepared by maceration. Rats were administered the methanolic extract at two different doses of 200 mg/k or 400 mg/kg orally and captopril was administered orally at a dose of 30 mg/kg. All the drugs alone or in combination were once daily for two weeks. At the end of treatment period, two doses of isoproterenol (150 mg/kg, s.c) were administered to rats at 24 hr interval. Blood was withdrawn to estimate creatinine kinase-MB (CK-MB) activities. The heart tissue was subjected to histological examinations to determine the extent of damage. Isoproterenol induced severe damage to the myocardium that was indicated through an elevation in serum CK-MB activity and the same was confirmed by histological examinations. Costus speciosus at both the tested doses attenuated the damage produced by isoproterenol. Both the doses caused a decrease in the biomarker activity as well as reduced the myocardial damage as observed in histological examination. A similar effect was observed with captopril. The co-administration of captopril with either dose of Costus speciosus demonstrated excellent cardioprotection suggesting that combination of this herb with captopril augments its cardioprotective action. It was concluded that Costus speciosus shows dose-dependent cardioprotection and augments the cardioprotective effect of captopril during isoproterenol induced cardiotoxicity in rats.
Childhood adherence to a potentially healthy and sustainable Nordic diet and later overweight: The Norwegian Mother, Father and Child Cohort Study (MoBa)

Abstract The New Nordic Diet (NND) is a potentially healthy and sustainable dietary pattern represented by locally available and traditionally consumed foods in the Northern countries. The diet has been commonly examined in adult populations, but less is known regarding its potential associations with overweight/obesity in children. We have previously developed child diet scores measuring compliance to the NND at child age 6 and 18 months and 3 and 7 years. In this study, we aimed to describe child and maternal characteristics and assess potential associations between the age‐specific diet scores and child overweight at 8 years. This study is based on the Norwegian Mother, Father and Child Cohort Study (MoBa), including 14,989 mother–child pairs and uses data from the Medical Birth Registry of Norway (MBRN). The scores measured NND compliance as a total score and categorized into low, medium and high NND compliance at each age point. Using logistic regression models, we investigated the association between each age‐specific score and the odds of overweight at 8 years. In crude analyses, adherence to the NND at 6 months was inversely associated with odds of overweight at 8 years in the continuous score (odds ratio = 0.95, 95% CI [0.91, 0.98]) and when comparing high versus low NND adherence (odds ratio = 0.81, 95% CI [0.70, 0.94]). The association was almost entirely attenuated in the adjusted models. In conclusion, child NND adherence up to 7 years of age was not associated with odds of overweight at 8 years in adjusted analyses.
Multiple imputation methods for handling missing values in longitudinal studies with sampling weights: Comparison of methods implemented in Stata

Many analyses of longitudinal cohorts require incorporating sampling weights to account for unequal sampling probabilities of participants, as well as the use of multiple imputation (MI) for dealing with missing data. However, there is no guidance on how MI and sampling weights should be implemented together. We simulated a target population based on the Australian Bureau of Statistics Estimated Resident Population and drew 1000 random samples dependent on three design variables to mimic the Longitudinal Study of Australian Children. The target analysis was the weighted prevalence of overweight/obesity over childhood. We evaluated the performance of several MI approaches available in Stata, based on multivariate normal imputation (MVNI), fully conditional specification (FCS) and twofold FCS: a weighted imputation model, imputing missing data separately for each quintile sampling weight grouping, including the design stratum indicator in the imputation model, and using sampling weights as a covariate in the imputation model. Approaches based on available cases and inverse probability weighting (IPW), with time‐varying weights, were also compared. We observed severe issues of convergence with FCS and twofold FCS. All MVNI‐based approaches performed similarly, producing minimal bias and nominal coverage, except for when imputation was conducted separately for each quintile sampling weight group. IPW performed equally as well as MVNI‐based approaches in terms of bias, however, was less precise. In similar longitudinal studies, we recommend using MVNI with the design stratum as a covariate in the imputation model. If this is unknown, including the sampling weight as a covariate is an appropriate alternative.
Gut dysbiosis induced by cardiac pressure overload enhances adverse cardiac remodeling in a T cell-dependent manner

ABSTRACT Despite the existing association of gut dysbiosis and T cell inflammation in heart failure (HF), whether and how gut microbes contribute to T cell immune responses, cardiac fibrosis and dysfunction in HF remains largely unexplored. Our objective was to investigate whether gut dysbiosis is induced by cardiac pressure overload, and its effect in T cell activation, adverse cardiac remodeling, and cardiac dysfunction. We used 16S rRNA sequencing of fecal samples and discovered that cardiac pressure overload-induced by transverse aortic constriction (TAC) results in gut dysbiosis, characterized by a reduction of tryptophan and short-chain fatty acids producing bacteria in WT mice, but not in T cell-deficient mice (Tcra−/- ) mice. These changes did not result in T cell activation in the gut or gut barrier disruption. Strikingly, microbiota depletion in WT mice resulted in decreased heart T cell infiltration, decreased cardiac fibrosis, and protection from systolic dysfunction in response to TAC. Spontaneous reconstitution of the microbiota partially reversed these effects. We observed decreased cardiac expression of the Aryl hydrocarbon receptor (AhR) and enzymes associated with tryptophan metabolism in WT mice, but not in Tcra−/- mice, or in mice depleted of the microbiota. These findings demonstrate that cardiac pressure overload induced gut dysbiosis and T cell immune responses contribute to adverse cardiac remodeling, and identify the potential contribution of tryptophan metabolites and the AhR to protection from adverse cardiac remodeling and systolic dysfunction in HF. Graphical abstract