Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic modeling of soft continuum manipulators using lie group variational integration

This paper presents the derivation and experimental validation of algorithms for modeling and estimation of soft continuum manipulators using Lie group variational integration. Existing approaches are generally limited to static and quasi-static analyses, and are not sufficiently validated for dynamic motion. However, in several applications, models need to consider the dynamical behavior of the continuum manipulators. The proposed modeling and estimation formulation is obtained from a discrete variational principle, and therefore grants outstanding conservation properties to the continuum mechanical model. The main contribution of this article is the experimental validation of the dynamic model of soft continuum manipulators, including external torques and forces (e.g., generated by magnetic fields, friction, and the gravity), by carrying out different experiments with metal rods and polymer-based soft rods. To consider dissipative forces in the validation process, distributed estimation filters are proposed. The experimental and numerical tests also illustrate the algorithm’s performance on a magnetically-actuated soft continuum manipulator. The model demonstrates good agreement with dynamic experiments in estimating the tip position of a Polydimethylsiloxane (PDMS) rod. The experimental results show an average absolute error and maximum error in tip position estimation of 0.13 mm and 0.58 mm, respectively, for a manipulator length of 60.55 mm.
Positive Selection and Gene Expression Analyses from Salivary Glands Reveal Discrete Adaptations within the Ecologically Diverse Bat Family Phyllostomidae

Abstract The leaf-nosed bats (Phyllostomidae) are outliers among chiropterans with respect to the unusually high diversity of dietary strategies within the family. Salivary glands, owing to their functions and high ultrastructural variability among lineages, are proposed to have played an important role during the phyllostomid radiation. To identify genes underlying salivary gland functional diversification, we sequenced submandibular gland transcriptomes from phyllostomid species representative of divergent dietary strategies. From the assembled transcriptomes, we performed an array of selection tests and gene expression analyses to identify signatures of adaptation. Overall, we identified an enrichment of immunity-related gene ontology terms among 53 genes evolving under positive selection. Lineage-specific selection tests revealed several endomembrane system genes under selection in the vampire bat. Many genes that respond to insulin were under selection and differentially expressed genes pointed to modifications of amino acid synthesis pathways in plant-visitors. Results indicate salivary glands have diversified in various ways across a functional diverse clade of mammals in response to niche specializations.
Physiological synchrony in EEG, electrodermal activity and heart rate reflects shared selective auditory attention

Objective. Concurrent changes in physiological signals across multiple listeners (physiological synchrony—PS), as caused by shared affective or cognitive processes, may be a suitable marker of selective attentional focus. We aimed to identify the selective attention of participants based on PS with individuals sharing attention with respect to different stimulus aspects. Approach. We determined PS in electroencephalography (EEG), electrodermal activity (EDA) and electrocardiographic inter-beat interval (IBI) of participants who all heard the exact same audio track, but were instructed to either attend to the audiobook or to interspersed auditory events such as affective sounds and beeps that attending participants needed to keep track of. Main results. PS in all three measures reflected the selective attentional focus of participants. In EEG and EDA, PS was higher for participants when linked to participants with the same attentional instructions than when linked to participants instructed to focus on different stimulus aspects, but in IBI this effect did not reach significance. Comparing PS between a participant and members from the same or the different attentional group allowed for the correct identification of the participant’s attentional instruction in 96%, 73% and 73% of the cases, for EEG, EDA and IBI, respectively, all well above chance level. PS with respect to the attentional groups also predicted performance on post-audio questions about the groups’ stimulus content. Significance. Our results show that selective attention of participants can be monitored using PS, not only in EEG, but also in EDA and IBI. These results are promising for real-world applications, where wearables measuring peripheral signals like EDA and IBI may be preferred over EEG sensors.
Narrow-band imaging versus Lugol chromoendoscopy for esophageal squamous cell cancer screening in normal endoscopic practice: randomized controlled trial

Abstract Background Narrow-band imaging (NBI) is as sensitive as Lugol chromoendoscopy to detect esophageal squamous cell carcinoma (SCC) but its specificity, which appears higher than that of Lugol chromoendoscopy in expert centers, remains to be established in general practice. This study aimed to prove the superiority of NBI specificity over Lugol chromoendoscopy in the detection of esophageal SCC and high grade dysplasia (HGD) in current general practice (including tertiary care centers, local hospitals, and private clinics). Methods This prospective randomized multicenter trial included consecutive patients with previous or current SCC of the upper aerodigestive tract who were scheduled for gastroscopy. Patients were randomly allocated to either the Lugol or NBI group. In the Lugol group, examination with white light and Lugol chromoendoscopy were successively performed. In the NBI group, NBI examination was performed after white-light endoscopy. We compared the diagnostic characteristics of NBI and Lugol chromoendoscopy in a per-patient analysis. Results 334 patients with history of SCC were included and analyzed (intention-to-treat) from 15 French institutions between March 2011 and December 2015. In per-patient analysis, sensitivity, specificity, positive and negative likelihood values were 100 %, 66.0 %, 21.2 %, and 100 %, respectively, for Lugol chromoendoscopy vs. 100 %, 79.9 %, 37.5 %, and 100 %, respectively, for NBI. Specificity was greater with NBI than with Lugol (P = 0.002). Conclusions As previously demonstrated in expert centers, NBI was more specific than Lugol in current gastroenterology practice for the detection of early SCC, but combined approaches with both NBI and Lugol could improve the detection of squamous neoplasia.
Dietary quality differs among cannabis use groups: data from the National Health and Nutrition Examination Survey 2005–16

Abstract Objective: To describe diet quality (Healthy Eating Index 2010 (HEI-2010) and Healthy Eating Index 2015 (HEI-2015)) according to self-reported cannabis use among the National Health and Nutrition Examination Survey (NHANES) adult participants. Design: Utilizing cross-sectional data, we assessed diet quality with up to two 24-h diet recalls from NHANES participants. Usual intakes were estimated via the multivariate Markov Chain–Monte Carlo method. Diet quality scores were compared among never users, previous users and current users of cannabis. Setting: NHANES surveys from 2005 to 2016. Participants: Adult NHANES participants (17 855) aged 20–59 years with valid data for dietary recalls and drug use questionnaires. Results: Current adult cannabis users (ages 20–59 years) had significantly lower total diet quality (HEI-2010) scores (51·8 ± 0·7) compared with previous (56·2 ± 0·4) and never users (57·7 ± 0·4). Similar differences in total and individual HEI-2015 scores were observed. For the HEI-2015 scores, cannabis users had a significantly higher (better) sodium scores (4·1 ± 0·2) compared with never users (3·3 ± 0·1) and previous users (3·2 ± 0·1). Cannabis users scored lower compared with never users on total vegetables (3·1 ± 0·1 v. 3·7 ± 0·0), total fruit (2·1 ± 0·1 v. 3·0 ± 0·1) and whole fruit (2·2 ± 0·1 v. 3·3 ± 0·1) for the HEI-2015 index. Conclusions: Current cannabis users’ usual intakes reflect lower diet quality compared with never or previous users, particularly lower subcomponent scores of total vegetables, greens and beans, total fruit and whole fruit. Cannabis users should increase their intake of fruit and vegetables to improve overall diet quality.
Spirochetes in Crystalline Styles of Marine Bivalves: Group-Specific PCR Detection and 16S rRNA Sequence Analysis

ABSTRACT Although spirochetes were first detected in crystalline styles of bivalves more than 100 years ago, little is known about the characteristics of these consortia (commensalism or parasitism). The presence of spirochetes in bivalves can so far not be generalized. The purpose of this study was the detection and phylogenetic identification of spirochetes associated with crystalline styles of different marine bivalve species collected in temperate regions and Antarctica. Polymerase chain reaction amplification of spirochete 16S ribosomal gene sequences was performed. 16S ribosomal gene clones were identified by phylogenetic analysis, and the variability within each bivalve species was determined. The spirochetes were mainly related to yet uncultured or potentially pathogenic spirochetes from the marine environment. All identified spirochete clones fell into 2 families: the Spirochaetaceae with 2 genera, Cristispira and Spirochaeta, and the Brachyspiraceae, with the genus Braehyspira. The diversity of spirochetes in the crystalline style of each bivalve species was low. All clone sequences from crystalline styles of the oyster Crassostrea gigas clustered into the group of Cristispira species. Interestingly, these Cristispira spirochetes were previously found in Crassostrea virginica, another oyster species. The spirochete clones of each bivalve species formed distinct clusters. We therefore assume that the investigated bivalve species harbor distinct populations of spirochetes. Although spirochetes were not found in all the investigated samples, the occurrence of spirochetes was not random and implies a closer association between the bivalve species and the specific spirochete cluster.
Evaluating the outcomes of genetic rescue attempts

Augmenting gene flow is a powerful tool for the conservation of small, isolated populations. However, genetic rescue attempts have largely been limited to populations at the brink of extinction, in part due to concerns over negative outcomes (e.g., outbreeding depression). Increasing habitat fragmentation may necessitate more proactive genetic management. Broader application of augmented gene flow will, in turn, require rigorous evaluation to increase confidence and identify pitfalls in this approach. To date, there has been no assessment of best monitoring practices for genetic rescue attempts. We used genomically explicit, individual‐based simulations to examine the effectiveness of common approaches (i.e., tests for increases in fitness, migrant ancestry, heterozygosity, and abundance) for determining whether genetic rescue or outbreeding depression occurred. Statistical power to detect the effects of gene flow on fitness was high (≥0.8) when effect sizes were large, a finding consistent with those from previous studies on severely inbred populations. However, smaller effects of gene flow on fitness can appreciably affect persistence probability but current evaluation approaches fail to provide results from which reliable inferences can be drawn. The power of the metrics we examined to evaluate genetic rescue attempts depended on the time since gene flow and whether gene flow was beneficial or deleterious. Encouragingly, the use of multiple metrics provided nonredundant information and improved inference reliability, highlighting the importance of intensive monitoring efforts. Further development of best practices for evaluating genetic rescue attempts will be crucial for a responsible transition to increased use of translocations to decrease extinction risk.
Enhancement of Skin Wound Healing by rhEGF-Loaded Carboxymethyl Chitosan Nanoparticles

The self-assembly of hydrophobically modified polymers has become a research hotspot due to its wide application in the biomedical field. Recombinant human epidermal growth factors (rhEGFs) are molecules that are able to enhance wound healing; however, they have a short half-life and require sustained action to enhance their mitogenic effect on epithelial cells. Here, we proposed a new delivery system to avoid the inhibition of rhEGF by various enzymes, thus improving its bioavailability and sustained release. The amphiphilic polymer was composed of conjugated linoleic acid (CLA) and carboxymethyl chitosan (CMCS), which were further characterized by fourier transformed infrared spectroscopy (FTIR) and 1H nuclear magnetic resonance (1H NMR). Then, the self-assembly behavior of CLA–CMCS (CC) polymer in water was observed in which the particle size of CC decreased from 196 to 155 nm with the degree of CLA substitution increasing. The nanoparticles were loaded with rhEGF and the maximum rhEGF loading efficiency (LE) of CC3 nanoparticles was 82.43 ± 3.14%. Furthermore, CC nanoparticles (NPs) exhibited no cytotoxicity for L929 cells, and cell proliferation activity was well preserved after rhEGF loading to CC-NPs and was comparable to that of free rhEGF. Topically applied rhEGF:CC-NPs significantly accelerated the wound-closure rate in full thickness, which was most probably due to its sustained release and enhanced skin permeation. In conclusion, carboxymethyl chitosan-based nanoparticles were constructed and showed good cytocompatibility. Moreover, these findings also demonstrated the therapeutic potential of rhEGF:CC-NPs as a topical wound-healing drug carrier.
Larval Anisakis simplex (Rudolphi, 1809, det. Krabbe, 1878) and larval Hysterothylacium sp. (Nematoda: Ascaridoidea) in euphausiids (Crustacea: Malacostraca) in the North-East Atlantic and northern North Sea

ABSTRACT Over 26000 specimens representing five euphausiid species collected, mostly in 1969, in the North-East Atlantic and northern North Sea were examined for parasites. Hysterothylacium sp. larvae were rare, occurring in only two euphausiid samples from inshore localities; the 9 larvae found (3.8 to 12.3 mm long) are described and illustrated. Infection with larval Anisakis simplex was virtually restricted to Thysanoessa spp. and appeared to be discontinuous. Infection was absent to the west of Scotland, and rare to the north of Scotland and at the Faroes. Larval A. simplex was not uncommon in offshore regions of the northern North Sea at depths between 100 and 200 m; the prevalence rate there for individual euphausiid species in individual samples was mostly 0 to 40% but an exceptionally high rate of 78.0% was recorded. Larvae in euphausiids do not become encapsulated but appear to remain active. Experimental observations on the sedimentation rate of A. simplex eggs and hatched larvae in sea water at 10°C are discussed in relation to embryonation and hatching at different temperatures, and depth of the sea. New host records are claimed for larval A. simplex in Nyctiplutnes couchii, and for larval Hysterothylacium sp. in Thysanoessa inermis. No individual euphausiid harboured more than one parasite, either larval nematode or ellobiopsid (see also SMITH, 1981). Morphological and morphometric observations on larval A. simplex from euphausiids are reported elsewhere (SMITH, 1983).
Molecular Evolution of Cadherin-Related Neuronal Receptor/Protocadherin α (CNR/Pcdhα) Gene Cluster in Mus musculus Subspecies

The mouse cadherin-related neuronal receptor/protocadherin (CNR/Pcdh) gene clusters are located on chromosome 18. We sequenced single-nucleotide polymorphisms (SNPs) of the CNR/Pcdh(alpha)-coding region among 12 wild-derived and four laboratory strains; these included the four major subspecies groups of Mus musculus: domesticus, musculus, castaneus, and bactrianus. We detected 883 coding SNPs (cSNPs) in the CNR/Pcdh(alpha) variable exons and three in the constant exons. Among all the cSNPs, 586 synonymous (silent) and 297 nonsynonymous (amino acid exchanged) substitutions were found; therefore, the K(a)/K(s) ratio (nonsynonymous substitutions per synonymous substitution) was 0.51. The synonymous cSNPs were relatively concentrated in the first and fifth extracellular cadherin domain-encoding regions (ECs) of CNR/Pcdh(alpha). These regions have high nucleotide homology among the CNR/Pcdh(alpha) paralogs, suggesting that gene conversion events in synonymous and homologous regions of the CNR/Pcdh(alpha) cluster are related to the generation of cSNPs. A phylogenetic analysis revealed gene conversion events in the EC1 and EC5 regions. Assuming that the common sequences between rat and mouse are ancestral, the GC content of the third codon position has increased in the EC1 and EC5 regions, although biased substitutions from GC to AT were detected in all the codon positions. In addition, nonsynonymous substitutions were extremely high (11 of 13, K(a)/K(s) ratio 5.5) in the laboratory mouse strains. The artificial environment of laboratory mice may allow positive selection for nonsynonymous amino acid variations in CNR/Pcdh(alpha) during inbreeding. In this study, we analyzed the direction of cSNP generation, and concluded that subspecies-specific nucleotide substitutions and region-restricted gene conversion events may have contributed to the generation of genetic variations in the CNR/Pcdh genes within and between species.
Subtypes of Alcohol Dependence and 36-Year Mortality.

BACKGROUND Chronic, heavy alcohol use is associated with multiple health problems, including premature death. Further, the clinical presentation of alcohol dependence may differentially affect and predict the long-term health consequences of affected individuals. Subtypes of alcohol dependence based upon treatment intake information can help identify homogenous groups of patients for treatment purposes, but have not been used to predict long-term outcomes. The current study examined mortality in a 36-year posttreatment interval among 4 subtypes of alcohol-dependent patients based upon their initial intake data. METHODS Extensive baseline data were collected from n = 316 male and female patients receiving inpatient treatment for alcohol dependence between 1980 and 1982. Four alcohol dependent subtypes (Del Boca & Hesselbrock, Alcohol Health Res World, 20:56, 1996) derived from the baseline data were used to examine the 1-year posttreatment drinking status and the risk of death 36 years postdischarge. Public records were used to determine patient deaths in the 36 years since discharge. RESULTS At the 36-year follow-up interval since discharge, 68.4% of the sample had died. The 4 subtypes were found to be associated with different rates of resumption of regular drinking in the first year posttreatment and a differential risk of mortality. An increased risk for returning to regular drinking (once a week or more) and early death were associated with subtypes defined, in part, by conduct problems and externalizing disorders. Regardless of subtype membership, women had the highest risk of death following treatment. CONCLUSIONS This study demonstrates the clinical usefulness of subtypes of alcohol dependence for examining different alcohol use outcomes, including predicting mortality. The increased risks for returning to regular drinking once a week or more and early death posttreatment among subtypes associated with conduct problems and externalizing disorders suggest the need for continued monitoring and possible additional intervention postdischarge.
Fine lexical tuning in infant directed speech to typically developing children

Abstract Do parents fine-tune the MLU of utterances with a particular word as the word is on the verge of appearing in the child's production? We analyzed a corpus of spontaneous interactions of 30 dyads. The children were in the initial stages of their lexical development, and the parents’ utterances containing the words the children eventually acquired were selected. The main finding is that the MLU of the parental utterances containing the target words gradually decreased up to the point of the children's first production of those words. This suggests that parents fine-tune their utterances to support the children's linguistic development.
Effects of Two Invasive Weeds on Arthropod Community Structure on the Central Plateau of New Zealand

Heather (Calluna vulgaris) and broom (Cytisus scoparius), originally from Europe, are the main invasive plants on New Zealand’s North Island Central Plateau, where they threaten native flora and fauna. Given the strong link between arthropod communities and plants, we explored the impact of these invasive weeds on the diversity and composition of associated arthropod assemblages in this area. The arthropods in heather-invaded areas, broom-invaded areas, and areas dominated by the native species mānuka (Leptospermum scoparium) and Dracohyllum (Dracophyllum subulatum) were collected and identified to order. During summer and autumn, arthropods were collected using beating trays, flight intercept traps and pitfall traps. Diversity indices (Richness, Shannon’s index and Simpson’s index) were calculated at the order level, and permutational multivariate analysis (PERMANOVA) was used to explore differences in order-level community composition. Our results show a significant variation in community composition for all trapping methods in both seasons, whereas invasive plants did not profoundly impact arthropod order richness. The presence of broom increased arthropod abundance, while heather was linked to a reduction. Under all possible plant pairings between heather, broom, mānuka, and Dracophylum, the impact of neighbouring plant identity on arthropod community composition was further explored for the samples collected using beating trays. The results suggest that during plant invasion, arthropod communities are affected by neighbouring plant identity and that impacts vary between arthropod sampling methods and seasons.
An improving DNA isolation method for identification of anaerobic bacteria in human colostrum and faeces samples

The efficiency, with which the lysis of 20 anaerobic bacterial samples [8 different bacterial species isolated from 4 colostrum and 4 infants (which are fed only by breast milk and from 3 to 30-day-old) faeces] were lysed, was tested using a reference or an improving method that involves higher levels of lysozyme (Sigma-Aldrich) and proteinase K solution (Sigma-Aldrich). Eight species were lysed with the efficiency of > 87% by the reference methods. Also, the lytic efficiency for Bifidobacterium bifidum BB-12 was > 90%. Accordingly, since the DNA samples isolated by the improved methods can reflect nearly the true genomic information in the microbial flora, the improved methods should be appropriate for genomic analyses, that is, not only for bacteria in the human intestine, but also for bacteria in other human samples, such as colostrum. The study reports that the extraction method used to produce DNA of suitable quantity and quality for subsequent PCR is based on detection applications. The procedures are reliable and reproducible, in typically planning a success rate of over 90%. In summary, it develops a fast and reliable genomic DNA extraction protocol for anaerobic bacteria. Key words: Lactobacilli, DNA isolation