Miracle-dz/UniFAR-FTUs huggingface dataset:
Ridinilazole, a narrow spectrum antibiotic for treatment of Clostridioides difficile infection, enhances preservation of microbiota-dependent bile acids

Antibiotic treatment is a standard therapy for Clostridioides difficile infection, but dysbiosis of the gut microbiota due to antibiotic exposure is also a major risk factor for the disease. Following an initial episode of C. difficile infection, a relentless cycle of recurrence can occur, where persistent treatment-related dysbiosis predisposes the patient to subsequent relapse. This study uses a longitudinal study design to compare the effects of a narrow-spectrum (ridinilazole) or broad-spectrum antibiotic (vancomycin) on intestinal bile acid profiles and their associations with gut bacteria over the course of C. difficile infection treatment. At end-of-treatment (day 10), subjects receiving vancomycin showed a nearly 100-fold increase in the ratio of conjugated to secondary bile acids in their stool compared to baseline, whereas subjects receiving ridinilazole maintained this ratio near baseline levels. Correlation analysis detected significant positive associations between secondary bile acids and several Bacteroidales and Clostridiales families. These families were depleted in the vancomycin group but preserved at near baseline abundance in the ridinilazole group. Enterobacteriaceae, which expanded to a greater extent in the vancomycin group, correlated negatively and positively with secondary and conjugated primary bile acids, respectively. Bile acid ratios at end-of-treatment were significantly different between those who recurred and those who did not. These results indicate that a narrow-spectrum antibiotic maintains an intestinal bile acid profile associated with a lowered risk of recurrence.
Estimation of incubation period and serial interval of COVID-19: analysis of 178 cases and 131 transmission chains in Hubei province, China

Abstract A novel coronavirus disease, designated as COVID-19, has become a pandemic worldwide. This study aims to estimate the incubation period and serial interval of COVID-19. We collected contact tracing data in a municipality in Hubei province during a full outbreak period. The date of infection and infector–infectee pairs were inferred from the history of travel in Wuhan or exposed to confirmed cases. The incubation periods and serial intervals were estimated using parametric accelerated failure time models, accounting for interval censoring of the exposures. Our estimated median incubation period of COVID-19 is 5.4 days (bootstrapped 95% confidence interval (CI) 4.8–6.0), and the 2.5th and 97.5th percentiles are 1 and 15 days, respectively; while the estimated serial interval of COVID-19 falls within the range of −4 to 13 days with 95% confidence and has a median of 4.6 days (95% CI 3.7–5.5). Ninety-five per cent of symptomatic cases showed symptoms by 13.7 days (95% CI 12.5–14.9). The incubation periods and serial intervals were not significantly different between male and female, and among age groups. Our results suggest a considerable proportion of secondary transmission occurred prior to symptom onset. And the current practice of 14-day quarantine period in many regions is reasonable.
SstmpDB: a database of single-spanning transmembrane proteins

Membrane proteins represent ca. 20–30% of both eukaryotic and prokaryotic proteomes. They play crucial roles in cell survival and cell communication, as they function as transporters, receptors, anchors and enzymes. More than 30% of all prescribed drugs are targeting membrane proteins. Transmembrane proteins are either single-spanning membrane proteins or multi-spanning proteins. Single-spanning proteins can be classified into four types I, II, III and IV, depending on their topology and membrane targeting. They are very important functionally, involved in the presentation of antigens to the immune system, they are calcium-dependent cell adhesion proteins, they play a role in septum formation and they have many more specific, crucial roles. The purpose of this work was the construction of a database containing all single-spanning membrane proteins and their functional classification. This database is available at http://aias.biol.uoa.gr/sstmpdb
How do morphotypes and chemotypes relate to genotypes? The colonial ascidian Cystodytes (Polycitoridae)

Intraspecies variability is widespread in marine invertebrates. Size, colour, texture, general shape and secondary chemistry can differ quite drastically from one individual to another. Cystodytes dellechiajei (Polycitoridae) is a cosmopolitan colonial ascidian with several morphotypes, most of which differ in colour and spicular composition. New molecular tools enable us to assess the taxonomic status of these morphotypes. To determine whether variation observed in Mediterranean Cystodytes has a genetic basis, we sequenced 45 specimens from eight locations of the western Mediterranean and one from Mayotte (Indian Ocean), and obtained a 617 bp fragment of the mitochondrial gene COI. Fifteen different colour morphs were recorded and four kinds of spicules were found: disk‐shaped, sphere‐shaped, star‐shaped and discoidal, thick spicules with a toothed margin. Zooid morphology was remarkably uniform in the whole sample set. Different tree construction methods (distance‐based, parsimony‐based, and maximum‐likelihood‐based) yielded consistent results, and recognized six major clades, which had no correspondence with spicule shape and were only partially consistent with colour morphs. Results are discussed in the light of previous knowledge of the chemistry of blue, green, brown and purple colour morphs. In spite of the different colour patterns and spicular variability we concluded, on the basis of chemical and genetic data, that the morphological traits analysed were not consistent enough to be used to differentiate between Cystodytes species. We point out the importance of genetics and chemistry in assessing the taxonomic status of species with variable morphology.
A functional-structural model of upland rice root systems reveals the importance of laterals and growing root tips for phosphate uptake from wet and dry soils.

BACKGROUND AND AIMS Upland rice is often grown where water and phosphorus (P) are limited. To better understand the interaction between water and P availability, functional-structural models that mechanistically represent small-scale nutrient gradients and water dynamics in the rhizosphere are needed. METHODS Rice was grown in large columns using a P-deficient soil at three P supplies in the topsoil (deficient, suboptimal, non-limiting) in combination with two water regimes (field capacity versus drying periods). Root system characteristics, such as nodal root number, lateral types, interbranch distance, root diameters, and the distribution of biomass with depth, as well as water and P uptake were measured. Based on the observed root data 3D root systems were reconstructed by calibrating the structural architecure model CRootBox for each scenario. Water flow and P transport in the soil to each of the individual root segments of the generated 3D root architectures were simulated using a multiscale flow an transport model. Total water and P uptake were then computed by adding up the uptake by all the root segments. KEY RESULTS Measurements showed that root architecture was significantly affected by the treatments. The moist, high P scenario had 2.8 times the root mass, double the numer of nodal roots, and more S-type laterals than the dry, low P scenario. Likewise, measured plant P uptake increased over threefold by increasing P and water supply. However, drying periods reduced P uptake at high but not at low P supply. Simulation results adequately predicted P uptake in all scenarios when the Michaelis Menten constant (Km) was corrected for diffusion limitation. They showed that the key drivers for P uptake are the different types of laterals (i.e. S- and L-type) and growing root tips . The L-type laterals become more important for overall water and P uptake than the S-type laterals in the dry scenarios. This is true across all the P treatments, but the effect is more pronounced as the P availability decreases. CONCLUSIONS This functional-structural model can predict the function of specific rice roots in terms of P and water uptake under different P and water supplies, when the structure of the root system is known. A future challenge is to predict how root systems' structure responds to nutrient and water availability.
Thresholds

We examine the experience of Thresholds, a virtual reality (VR) recreation of the world's first photographic exhibition, which has toured to multiple museums. Following the method of performance-led research in the wild, we provide an account of the artist's design rationale and the experiences of visitors as the work toured. We reveal how the overlaying and juxtaposing of virtual and physical spaces established a VR architecture that underpinned the extended user experience. Overlaying was used to layer a virtual model onto a corresponding physical set to deliver physical sensations of touch and movement alongside visual and audio stimuli. Juxtaposition was used to embed the VR installation within the surrounding gallery space at each host museum, dealing with the challenges of entering, exiting, spectating, and invigilating the experience. We propose that museum designers can use these techniques to deliver VR installations that are compelling but also scalable and tourable.
Mobilization of pdif modules in Acinetobacter: A novel mechanism for antibiotic resistance gene shuffling?

XerCD‐dif site‐specific recombination is a well characterized system, found in most bacteria and archaea. Its role is resolution of chromosomal dimers that arise from homologous recombination. Xer‐mediated recombination is also used by several plasmids for multimer resolution to enhance stability and by some phage for integration into the chromosome. In the past decade, it has been hypothesized that an alternate and novel function exists for this system in the dissemination of genetic elements, notably antibiotic resistance genes, in Acinetobacter species. Currently the mechanism underlying this apparent genetic mobility is unknown. Multidrug resistant Acinetobacter baumannii is an increasingly problematic pathogen that can cause recurring infections. Sequencing of numerous plasmids from clinical isolates of A. baumannii revealed the presence of possible mobile modules: genes were found flanked by pairs of Xer recombination sites, called plasmid‐dif (pdif) sites. These modules have been identified in multiple otherwise unrelated plasmids and in different genetic contexts suggesting they are mobile elements. In most cases, the pairs of sites flanking a gene (or genes) are in inverted repeat, but there can be multiple modules per plasmid providing pairs of recombination sites that can be used for inversion or fusion/deletion reactions; as many as 16 pdif sites have been seen in a single plasmid. Similar modules including genes for surviving environmental toxins have also been found in strains of Acinetobacter Iwoffi isolated from permafrost cores; this suggests that these mobile modules are an ancient adaptation and not a novel response to antibiotic pressure. These modules bear all the hallmarks of mobile genetic elements, yet, their movement has never been directly observed to date. This review gives an overview of the current state of this novel research field.
The Closest of Human between Three Hominidae Based on 16S rRNA Sequence Homology

Recently some evolution scientists claim that modern human have a common ancestor with African apes and other hominidae. In order to dentify the relation between the human and African apes in molecular view here we present a comparison between the human 16s rRNA sequence and three other hominidae (chimpanzee, gorilla, and orangutan). In this study we compared the sequences of the 16s rRNA and the intraspecies sequences were compared for each hominidae and the phylogenic trees were constructed for all the species. CLUSTALW program was used for sequence alignment and phylogenic tree creation. Phylogenic trees were designed by the neighbor-joining method. Our findings confirmed a common ancestor for human and three hominidae (chimpanzee, gorilla, bonobo). Moreover, we found higher nucleotide diversity between the hominidae than the human. We could hypothesize that the hominidae derivative from a common ancestor in a prior time in comparison with human. Our phylogenic findings may indicate that gibbon and orangutan was the first twin that separated from the great ape ancestor. Therefore, this could indicate that gibbon and orangutan may not be considered as humans closest, but the chimpanzee and bonobo might be considered as human closet.
Outdoor air pollutants exposure associated with pulmonary function and EBC pH value in atopic asthmatic and non-asthmatic children

Abstract Objective Air pollution is associated with the prevalence of respiratory diseases. This study aimed to evaluate the impacts of outdoor air pollutants and indoor Dermatophagoides pteronyssinus 1 (Der p 1) exposure on levels of fractional exhaled nitric oxide (FeNO), exhaled breath condensate (EBC) pH, and pulmonary function in atopic children. Methods This study recruited 59 atopic mild-to-moderate asthmatic children and 23 atopic non-asthmatic children. Data on personal characteristics, FeNO, EBC pH, and pulmonary function were collected. Group 1 allergens of Der p 1 were measured on the tops of mattresses and on bedroom floors in the children’s homes, and outdoor air pollutant concentrations were estimated from air quality monitoring stations, using the ordinary kriging method. Results Exposure levels of outdoor air pollutants, except for particulate matter (PM)2.5, for the recruited children met outdoor air quality standards set by the Taiwan Environmental Protection Agency. The lag effect of outdoor PM10 exposure was negatively associated with the forced expiratory volume in one second (FEV1) [(Lag 1: β=–0.771, p = 0.028), and O3 (Lag 1–7: β=–2.02, p = 0.04, Lag 1–28: β=–3.213, p = 0.029)]. Median pulmonary function parameters differed significantly in forced vital capacity (FVC) (p = 0.004) and FEV1 (p = 0.024) values between atopic asthmatic and non-asthmatic children. No association was found between the FeNO/EBC pH level and exposure to Der p 1 allergen and air pollutants in the recruited children. Conclusions Outdoor PM10 and O3 exposure was associated with reduction in FEV1 in atopic asthmatic and non-asthmatic children.
Brucella melitensis, a latent “travel bacterium,” continual spread and expansion from Northern to Southern China and its relationship to worldwide lineages

ABSTRACT Brucellosis caused by Brucella melitensis is considered to be one of the most important zoonotic diseases in China. In this study, Conventional bio-typing, MLVA (multiple locus variable-number tandem repeat analysis), and WGS (whole-genome sequencing)-SNP (single nucleotide polymorphism) were used to study the genetic similarity of B. melitensis in northern and southern China and analyze its relationship with worldwide lineages. Currently, the distribution of species/biovars of B. melitensis has obviously changed, and B. melitensis has become the dominant species in southern regions of China. Strains from the southern had a common geographic origin with strains from the northern. Many MLVA-16 events were shared in the genotypes of the southern and northern strains, suggest that genotypic movement occurred from north to south. Based on WGS-SNP analysis, strains from different provinces were closely related and may have descended from one common ancestor, suggests that the southern strains originated from northern China. These data indicate that B. melitensis is a latent “travel bacterium” that spread and expanded from North China to South China. Moreover, B. melitensis strains from China are also genetically related to strains from other Asian regions (Kazakhstan, Russia, Mongolia, and India). The movement of infected sheep and their products requires control.
Religious coping and psychosocial adjustment in patients with cystic fibrosis

The role of religious coping (RC) in psychosocial outcomes and health-related quality of life (HRQoL) in adults with cystic fibrosis has not been addressed. Multivariate regressions evaluated the effects of baseline RC on depressive and anxiety symptoms and HRQoL at 3-month follow-up in 123 adult cystic fibrosis patients. Higher positive RC attenuated the effects of perceived stress on greater depressive and anxiety symptoms. Negative RC predicted less vitality and social HRQoL, as well as more digestion symptoms. Positive RC may buffer the impact of stress on patients’ psychological distress, whereas negative RC may contribute to lower health-related quality of life.
Effect of sample preparation on in situ estimates of protein degradability for white clover herbages

The amount of crude protein in white clover solubilised during ingestion by cows was determined by collecting swallowed boluses in rumen fistulated cows. Six experiments were then conducted to determine the effects of sample preparation on in situ estimates of rumen degradability of crude protein in white clover (Trifolium repens L.) herbages. Different methods of preparation were compared with chopped fresh herbage, a recommended method when this type of feed is incubatedin situ. Samples of white clover were either: (i) chopped fresh to 10 mm lengths (FRS), (ii) frozen, freeze-dried and ground (FRZ/D), (iii) oven-dried at 45°C for 48 h and ground (OD45C), (iv) oven-dried at 60°C for 48 h and ground (OD60C), or (v) minced fresh in a food processor (MNC). The immediate solubilities of crude protein from MNC preparations most closely approximated measures of the proportion (0.28–0.37) of crude protein solubilised during ingestion by cows, while immediate solubilities of crude protein from FRS preparations were low (0.09–0.19). The effective rumen degradability of protein for FRS was lower (P<0.05) than for MNC, FRZ/D or the oven-dried preparations. The effects of the method of preparation of fresh clover on estimates of rumen degradable protein and undegraded dietary protein were compared assuming cows were producing <15 L milk/day. In the 2 experiments comparing FRS and MNC preparations, the average estimates of rumen degradable protein and undegraded dietary protein were 158 and 83 g/kg DM, respectively, for FRS, compared with 189 and 52 g/kg DM for MNC. Over the 4 experiments comparing fresh and dried preparations, estimates of rumen degradable protein and undegraded dietary protein for FRS were 140 and 101 g/kg DM, respectively, and differed from those for FRZ/D of 156 and 70 g/kg DM. The implications of such differences have been discussed in relation to use of the in situ technique. It was concluded that no method of sample preparation will be ideal and it is likely the preferred method of sample preparation for in situ studies will vary for fresh herbages compared with conserved forages and concentrates.
The effect of inclusion level and basal diet on the determination of the digestible and metabolisable energy content of soybean oil and its digestibility when fed to growing pigs

This experiment was conducted to determine the effect of inclusion level and type of basal diet on the digestible (DE) and metabolisable (ME) energy content of soybean oil and its digestibility when fed to growing pigs. Thirty-six barrows (Duroc × Landrace × Yorkshire weighing 34.2 ± 3.8 kg) were randomly allotted to a 2 × 3 factorial arrangement involving two basal diets and three levels of soybean oil (0%, 5% and 10%). One basal diet was based on corn and soybean meal. The other basal diet was based on corn starch and casein. The barrows were housed in individual metabolism crates to facilitate separate collection of faeces and urine, and were fed the assigned test diets at 4% of initial bodyweight per day. A 5-day total collection of faeces and urine followed a 7-day diet-adaptation period. The DE and ME contents of soybean oil were significantly affected by the dietary inclusion level (P < 0.05), but not by the type of basal diet. The DE contents of soybean oil at the 5% and 10% inclusion level were 34.99 and 37.63 MJ/kg, respectively, for the corn–soybean meal basal diet and 33.72 and 35.21 MJ/kg, respectively, for the corn starch–casein basal diet. The respective corresponding values for ME were 33.91, 37.07, 33.06 and 34.83 MJ/kg. The DE values calculated from regression equation were 38.05 and 37.85 MJ/kg, respectively, for corn–soybean meal and corn starch–casein basal diet. The DE value calculated from regression equation was greater than the values determined from the difference method for corn starch–casein basal diet. The value of endogenous loss for acid-hydrolysed ether extract was greater (P < 0.05) for corn–soybean meal basal diet than for corn starch–casein (13.06 g/kg of dry matter intake for corn–soybean meal basal diet and 1.37 g/kg of dry matter intake for corn starch–casein basal diet, respectively). The values of the true total tract digestibility and apparent total tract digestibility of soybean oil determined from the corn–soybean meal basal diet were not different from those determined from the corn starch–casein basal diet (true total tract digestibility: 97.1% and 95.4%; apparent total tract digestibility: 95.8% and 95.3%, respectively). In conclusion, the DE and ME values of soybean oil are affected by its inclusion level but not by basal diet. The type of basal diet did not affect the digestibility of soybean oil, but affected the endogenous loss of acid-hydrolysed ether extract for soybean oil.
Fuel to the fire: The escalating interplay of attachment and maltreatment in the transgenerational transmission of psychopathology in families living in refugee camps

Abstract Maltreatment by parents can be conceptualized as pathogenic escalations of a disturbed parent–child relationship that have devastating consequences for children's development and mental health. Although parental psychopathology has been shown to be a risk factor both for maltreatment and insecure attachment representations, these factors` joint contribution to child psychopathology has not been investigated. In a sample of Burundian refugee families living in refugee camps in Western Tanzania, the associations between attachment representations, maltreatment, and psychopathology were examined by conducting structured interviews with 226 children aged 7 to 15 and both their parents. Structural equation modeling revealed that children's insecure attachment representations and maltreatment by mothers fully mediated the relation between maternal and child psychopathology [model fit: comparative fit index (CFI) = 0.96; root mean square error of approximation (RMSEA) = 0.05]. A direct association between paternal and child psychopathology was observed (model fit: CFI = 0.96; RMSEA = 0.05). The findings suggest a vicious cycle, wherein an insecure attachment to a mother suffering from psychopathology may be linked to children's risk to be maltreated, which may reinforce insecure representations and perpetuate the pathogenic relational experience. Interventions targeting the attachment relationship and parental mental health may prevent negative child outcomes.