Miracle-dz/UniFAR-FTUs huggingface dataset:
ARMAR-4: A 63 DOF torque controlled humanoid robot

We present the mechatronic design of the next generation of our humanoid robots, the humanoid robot ARMAR-4, a full body torque controlled humanoid robot with 63 active degrees of freedom, 63 actuators, 214 sensors, 76 microcontroller for low-level control, 3 PCs for perception, high-level control and balancing, a weight of 70 kg including batteries and total height of 170 cm. In designing the robot we follow an integrated approach towards the implementation of high performance humanoid robot systems, able to act and interact in the real world using only on-board sensors and computation power. Special attention was paid to the realization of advanced bimanual manipulation and locomotion capabilities. The paper presents the design concept of the robot and its mechatronic realization.
Dietary LA and sex effects on oxylipin profiles in rat kidney, liver, and serum differ from their effects on PUFAs[S]

A vast literature on fatty acids in mammals exists, but comparable compositional data on oxylipins is lacking. Weanling Sprague-Dawley rats were therefore provided control diets or diets with higher linoleic acid (LA) or with higher LA and α-linolenic acid (LA+ALA) for 6 weeks. Kidneys, livers, and serum were analyzed for oxylipins and fatty acids. The proportion of tissue oxylipins derived from LA was greater than the relative proportion of LA itself, whereas arachidonic acid (AA) oxylipins were overrepresented in serum. Higher dietary LA increased kidney LA and AA oxylipins, despite not altering LA or AA. In liver, both LA and AA and their oxylipins were higher, whereas in serum only LA oxylipins were higher with higher dietary LA. Higher LA resulted in a higher ratio of n-6/n-3 PUFA-derived oxylipins; adding ALA to the LA diet mitigated this and many, but not all, effects of the LA diet. Approximately 40% of oxylipins detected were influenced by sex and, unlike their PUFA precursors, most (>90%) of these were higher in males. These differences in dietary LA and sex on oxylipin and fatty acid profiles further our understanding of the effects of fatty acids and may have implications for dietary LA recommendations.
Pathogen‐Driven Outbreaks in Forest Defoliators Revisited: Building Models from Experimental Data

Models of outbreaks in forest‐defoliating insects are typically built from a priori considerations and tested only with long time series of abundances. We instead present a model built from experimental data on the gypsy moth and its nuclear polyhedrosis virus, which has been extensively tested with epidemic data. These data have identified key details of the gypsy moth–virus interaction that are missing from earlier models, including seasonality in host reproduction, delays between host infection and death, and heterogeneity among hosts in their susceptibility to the virus. Allowing for these details produces models in which annual epidemics are followed by bouts of reproduction among surviving hosts and leads to quite different conclusions than earlier models. First, these models suggest that pathogen‐driven outbreaks in forest defoliators occur partly because newly hatched insect larvae have higher average susceptibility than do older larvae. Second, the models show that a combination of seasonality and delays between infection and death can lead to unstable cycles in the absence of a stabilizing mechanism; these cycles, however, are stabilized by the levels of heterogeneity in susceptibility that we have observed in our experimental data. Moreover, our experimental estimates of virus transmission rates and levels of heterogeneity in susceptibility in gypsy moth populations give model dynamics that closely approximate the dynamics of real gypsy moth populations. Although we built our models from data for gypsy moth, our models are, nevertheless, quite general. Our conclusions are therefore likely to be true, not just for other defoliator‐pathogen interactions, but for many host‐pathogen interactions in which seasonality plays an important role. Our models thus give qualitative insight into the dynamics of host‐pathogen interactions, while providing a quantitative interpretation of our gypsy moth–virus data.
Estimation of Multivehicle Dynamics by Considering Contextual Information

Human drivers are endowed with an inborn ability to put themselves in the position of other drivers and reason about their behavior and intended actions. State-of-the-art driving-assistance systems, on the other hand, are generally limited to physical models and ad hoc safety rules. In order to drive safely amongst humans, autonomous vehicles need to develop an understanding of the situation in the form of a high-level description of the state of traffic participants. This paper presents a probabilistic model to estimate the state of vehicles by considering interactions between drivers immersed in traffic. The model is defined within a probabilistic filtering framework; estimation and prediction are carried out with statistical inference techniques. Memory requirements increase linearly with the number of vehicles, and thus, it is possible to scale the model to complex scenarios involving many participants. The approach is validated using real-world data collected by a group of interacting ground vehicles.
Genetic Fate Mapping Defines the Vascular Potential of Endocardial Cells in the Adult Heart

Rationale: Endocardium is the major source of coronary endothelial cells (ECs) in the fetal and neonatal hearts. It remains unclear whether endocardium in the adult stage is also the main origin of neovascularization after cardiac injury. Objective: To define the vascular potential of adult endocardium in homeostasis and after cardiac injuries by fate-mapping studies. Methods and Results: We generate an inducible adult endocardial Cre line (Npr3 [natriuretic peptide receptor C]-CreER) and show that Npr3-CreER efficiently and specifically labels endocardial cells but not coronary blood vessels in the adult heart. The adult endocardial cells do not contribute to any vascular ECs during cardiac homeostasis. To examine the formation of blood vessels from endocardium after injury, we generate 4 cardiac injury models with Npr3-CreER mice: myocardial infarction, myocardial ischemia–reperfusion, cryoinjury, and transverse aortic constriction. Lineage tracing experiments show that adult endocardium minimally contributes to coronary ECs after myocardial infarction. In the myocardial ischemia–reperfusion, cryoinjury, or transverse aortic constriction models, adult endocardial cells do not give rise to any vascular ECs, and they remain on the inner surface of myocardium that connects with lumen circulation. In the myocardial infarction model, very few endocardial cells are trapped in the infarct zone of myocardium shortly after ligation of coronary artery, indicating the involvement of endocardial entrapment during blood vessels formation. When these adult endocardial cells are relocated and trapped in the infarcted myocardium by transplantation or myocardial constriction model, very few endocardial cells survive and gain vascular EC properties, and their contribution to neovascularization in the injured myocardium remains minimal. Conclusions: Unlike its fetal or neonatal counterpart, adult endocardium naturally generates minimal, if any, coronary arteries or vascular ECs during cardiac homeostasis or after injuries.
The effectiveness of extracorporeal shockwave therapy in common lower limb conditions: a systematic review including quantification of patient-rated pain reduction

Objective To evaluate extracorporeal shockwave therapy (ESWT) in treating Achilles tendinopathy (AT), greater trochanteric pain syndrome (GTPS), medial tibial stress syndrome (MTSS), patellar tendinopathy (PT) and proximal hamstring tendinopathy (PHT). Design Systematic review. Eligibility criteria Randomised and non-randomised studies assessing ESWT in patients with AT, GTPS, MTSS, PT and PHT were included. Risk of bias and quality of studies were evaluated. Results Moderate-level evidence suggests (1) no difference between focused ESWT and placebo ESWT at short and mid-term in PT and (2) radial ESWT is superior to conservative treatment at short, mid and long term in PHT. Low-level evidence suggests that ESWT (1) is comparable to eccentric training, but superior to wait-and-see policy at 4 months in mid-portion AT; (2) is superior to eccentric training at 4 months in insertional AT; (3) less effective than corticosteroid injection at short term, but ESWT produced superior results at mid and long term in GTPS; (4) produced comparable results to control treatment at long term in GTPS; and (5) is superior to control conservative treatment at long term in PT. Regarding the rest of the results, there was only very low or no level of evidence. 13 studies showed high risk of bias largely due to methodology, blinding and reporting. Conclusion Low level of evidence suggests that ESWT may be effective for some lower limb conditions in all phases of the rehabilitation.
Waist circumference is associated with pulmonary function in normal-weight, overweight, and obese subjects.

BACKGROUND Obesity is becoming a serious public health issue and is related to lung dysfunction. Because both weight and height are indicators of body size, body mass index (BMI) may not be an ideal index of obesity in prediction of pulmonary dysfunction. OBJECTIVE The objective of the study was to determine the predictability of waist circumference (WC) and BMI for pulmonary function in adults with and without excess body weight. DESIGN A cross-sectional study of 1674 adults aged > or = 18 y was conducted in a rural community. Height, weight, WC, and pulmonary function were measured. Multivariate analysis was conducted. RESULTS WC was negatively associated with forced vital capacity and forced expiratory volume in 1 s, and the associations were consistent across sex, age, and BMI categories. On average, a 1-cm increase in WC was associated with a 13-mL reduction in forced vital capacity and an 11-mL reduction in forced expiratory volume in 1 s. The association between WC and pulmonary function was consistent in subjects with normal weight, overweight, and obesity. In subjects with normal weight, BMI was positively associated with forced vital capacity and forced expiratory volume in 1 s. CONCLUSION WC, but not BMI, is negatively and consistently associated with pulmonary function in normal-weight, overweight, and obese subjects.
Comparison of methods to assess change in children's body composition.

BACKGROUND Little is known about how simpler and more available methods to measure change in body fatness compare with criterion methods such as dual-energy X-ray absorptiometry (DXA) in children. OBJECTIVE Our objective was to determine the ability of air-displacement plethysmography (ADP) and formulas based on triceps skinfold thickness (TSF) and bioelectrical impedance analysis (BIA) to estimate changes in body fat over time in children. DESIGN Eighty-six nonoverweight and overweight boys (n = 34) and girls (n = 52) with an average age of 11.0 +/- 2.4 y underwent ADP, TSF measurement, BIA, and DXA to estimate body fatness at baseline and 1 +/- 0.3 y later. Recent equations were used to estimate percentage body fat by TSF measurement (Dezenberg equation) and by BIA (Suprasongsin and Lewy equations). Percentage body fat estimates by ADP, TSF measurement, and BIA were compared with those by DXA. RESULTS All methods were highly correlated with DXA (P < 0.001). No mean bias for estimates of percentage body fat change was found for ADP (Siri equation) compared with DXA for all subjects examined together, and agreement between body fat estimation by ADP and DXA did not vary with race or sex. Magnitude bias was present for ADP relative to DXA (P < 0.01). Estimates of change in percentage body fat were systematically overestimated by BIA equations (1.37 +/- 6.98%; P < 0.001). TSF accounted for only 13% of the variance in percentage body fat change. CONCLUSION Compared with DXA, there appears to be no noninvasive and simple method to measure changes in children's percentage body fat accurately and precisely, but ADP performed better than did TSF or BIA. ADP could prove useful for measuring changes in adiposity in children.
Analysis of Known Linear Distributed Average Consensus Algorithms on Cycles and Paths

In this paper, we compare six known linear distributed average consensus algorithms on a sensor network in terms of convergence time (and therefore, in terms of the number of transmissions required). The selected network topologies for the analysis (comparison) are the cycle and the path. Specifically, in the present paper, we compute closed-form expressions for the convergence time of four known deterministic algorithms and closed-form bounds for the convergence time of two known randomized algorithms on cycles and paths. Moreover, we also compute a closed-form expression for the convergence time of the fastest deterministic algorithm considered on grids.
Metakaolin as a model system for understanding geopolymers

Geopolymers are a class of amorphous aluminosilicate materials that exhibit a range of properties depending on synthesis parameters. Determining the molecular interactions responsible for the different characteristics experimentally is hindered by the compositional variation of the source materials. Computational methods are thus used to provide atom level insights, with metakaolin used as a model system to represent the Al/Si geopolymer matrix. The formation of metakaolin through the thermal de-hydroxylation of kaolinite was simulated with molecular dynamics using an interatomic potential model identified through testing of several models from the literature. The simulated metakaolin exhibited a 1:1 Al/Si ordering with a loss in periodicity due to the migration of aluminium ions through the structure. The change in the aluminium coordination as a function of de-hydroxylation results in a final structure composed of primarily 4-fold Al with up to 20% of the Al in a 5-fold coordination. A complex cavity network was identified and characterised in metakaolin and provided sites for the inclusion of sodium, potassium and calcium interstitial defect ions. The results showed that whilst ionic size controlled the final locations of the defect ions, ionic charge influenced the degree of interaction with the surrounding oxygen atoms and resulted in greater variations in the final defect site characteristics. Introducing hydroxyl groups into the structure caused the interactions of the defects with the aluminium to increase compared to silicon, demonstrating that the degree of source material hydration is as important as the type of metal cations present in the geopolymerisation reaction. A procedure for the generation of stable, partially hydrated metakaolin surfaces was developed and the resulting surfaces had a high degree of roughness that increased in the presence of water. The Al-terminated surfaces in metakaolin demonstrated the greatest level of interaction with water compared to Si, causing a surface puckering effect that resulted in a widening of the surface layers. The results indicate that water plays an important role, as the presence of water in the reaction mixture combined with high levels of structural disorder in the source materials increase their susceptibility to the caustic attack involved in geopolymerisation.
TeachEnG: a Teaching Engine for Genomics

Motivation Bioinformatics is a rapidly growing field that has emerged from the synergy of computer science, statistics, and biology. Given the interdisciplinary nature of bioinformatics, many students from diverse fields struggle with grasping bioinformatic concepts only from classroom lectures. Interactive tools for helping students reinforce their learning would be thus desirable. Here, we present an interactive online educational tool called TeachEnG (acronym for Teaching Engine for Genomics) for reinforcing key concepts in sequence alignment and phylogenetic tree reconstruction. Our instructional games allow students to align sequences by hand, fill out the dynamic programming matrix in the Needleman-Wunsch global sequence alignment algorithm, and reconstruct phylogenetic trees via the maximum parsimony and Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithms. With an easily accessible interface and instant visual feedback, TeachEnG will help promote active learning in bioinformatics. Availability and Implementation: TeachEnG is freely available at http://song.igb. illinois.edu/TeachEnG/. It is written in JavaScript and compatible with Firefox, Safari, Chrome, and Microsoft Edge. Contact: songi@illinois.edu
Gata4 potentiates second heart field proliferation and Hedgehog signaling for cardiac septation

Significance Dominant GATA4 mutations cause congenital heart defects in humans, but the mechanistic basis whereby Gata4 haploinsufficiency causes disease is unknown. We demonstrate that Gata4 is required in a subset of cardiac progenitor cells called the “second heart field” for cardiac septation. Furthermore, we identified two distinct pathways downstream of Gata4, phosphatase and tensin homolog (Pten)-modulated cell-cycle transition and Hedgehog signaling, which appear to act independently. Restoration of either Pten-mediated cell-cycle transition or Hedgehog signaling restored cardiac septation in Gata4-mutant mice, suggesting that defects in both pathways are required for disease causation. This work generates a working model for understanding the molecular basis of human congenital heart disease caused by dominant transcription factor mutations. GATA4, an essential cardiogenic transcription factor, provides a model for dominant transcription factor mutations in human disease. Dominant GATA4 mutations cause congenital heart disease (CHD), specifically atrial and atrioventricular septal defects (ASDs and AVSDs). We found that second heart field (SHF)-specific Gata4 heterozygote embryos recapitulated the AVSDs observed in germline Gata4 heterozygote embryos. A proliferation defect of SHF atrial septum progenitors and hypoplasia of the dorsal mesenchymal protrusion, rather than anlage of the atrioventricular septum, were observed in this model. Knockdown of the cell-cycle repressor phosphatase and tensin homolog (Pten) restored cell-cycle progression and rescued the AVSDs. Gata4 mutants also demonstrated Hedgehog (Hh) signaling defects. Gata4 acts directly upstream of Hh components: Gata4 activated a cis-regulatory element at Gli1 in vitro and occupied the element in vivo. Remarkably, SHF-specific constitutive Hh signaling activation rescued AVSDs in Gata4 SHF-specific heterozygous knockout embryos. Pten expression was unchanged in Smoothened mutants, and Hh pathway genes were unchanged in Pten mutants, suggesting pathway independence. Thus, both the cell-cycle and Hh-signaling defects caused by dominant Gata4 mutations were required for CHD pathogenesis, suggesting a combinatorial model of disease causation by transcription factor haploinsufficiency.
Fermentation in human subjects of nonstarch polysaccharides in mixed diets, but not in a barley fiber concentrate, could be predicted by in vitro fermentation using human fecal inocula.

The fermentation of nonstarch polysaccharides (NSP) contained in a low fiber diet, two high fiber diets high or low in protein, and a barley fiber concentrate was determined in balance experiments in six women and in an in vitro batch system using fecal inocula obtained from these same women. In vitro fermentations were performed with fiber residues prepared from duplicates of the fiber-containing foods consumed during the balance trials. Fermentation of total NSP in humans was 83.8 +/- 0.9% (low fiber diet), 61.8 +/- 3.6% (high fiber diet high in protein), 59.2 +/- 3. 9% (high fiber diet low in protein) and 31.2 +/- 7.4% (barley fiber concentrate). Fermentation in vitro differed from fermentation in humans by -4.0 +/- 1.6% (low fiber diet, P < 0.05,), 4.9 +/- 3.7% (high fiber diet high in protein), 8.8 +/- 3.0% (high fiber diet low in protein, P < 0.01) and 19.7 +/- 8.0% (barley fiber concentrate, P < 0.05). Differences between in vivo and in vitro fermentation were most pronounced for NSP-glucose, i.e., cellulose. Production of short-chain fatty acids in vitro corresponded to the fermentability of NSP. The yield of short-chain fatty acids per gram of fermented NSP was similar for the diets (8.8-9.4 mmol) but lower for the barley fiber concentrate (7.4 mmol, P < 0.05). Although differences between the fermentation measured in humans and in vitro were significant for two diets, the magnitude of the differences was such that fermentation of NSP in mixed diets could be predicted with sufficient accuracy in vitro, whereas agreement between the fermentation in vivo and in vitro of NSP in the barley fiber concentrate was not satisfactory.
Brain Vacuolation Resulting From Administration of the Type II Ampakine CX717 Is An Artifact Related to Molecular Structure and Chemical Reaction With Tissue Fixative Agents

Ampakines are small molecule positive allosteric modulators of the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA). One class II ("low impact") ampakine, CX717, has been implicated to have a neurotoxic effect based on findings in nonclinical, long-term toxicity studies. The neurotoxicity concerns, which halted the clinical development of the molecule, arose due to a finding of extensive white matter vacuolation in multiple brain regions of animals that were administered high doses of CX717 in several test species (unpublished data). This work characterized the features and a potential mechanism by which ampakines induce vacuoles in brain tissue. Brain sections from adult rats given CX717 (750 mg/kg BID by oral gavage) exhibited no vacuoles with acute or short-term dosing. However, after 14 or more days of treatment, vacuoles were prominent in cerebellum, globus pallidus, and hippocampus. Vacuole margins were lined by glial fibrillary acidic protein (GFAP), and by transmission electron microscopy were shown to be astrocyte processes. CX717-associated vacuoles occurred in formaldehyde-fixed specimens but not flash-frozen samples. Time-course experiments showed that brain tissue slices from CX717-treated animals exhibit no vacuoles until immersed in formaldehyde fixative, whereupon vacuoles form and expand in a time-dependent manner. Chemical interactions in test tube experiments have demonstrated that the combination of CX717 and formalin in an aqueous solution produces an exothermic reaction. Taken together, the data indicate that CX717 does not induce vacuoles in vivo, but rather is associated with astrocyte vacuolation post mortem, likely as the ampakine reacts with formalin to produce gas pockets in brain parenchyma.