Miracle-dz/UniFAR-FTUs huggingface dataset:
Shape-Controlled Syntheses of Magnetite Microparticles and Their Magnetorheology

Magnetic microspheres in a concentrated suspension can be self-assembled to form chain structures under a magnetic field, resulting in an enhanced viscosity and elasticity of the suspension (i.e., the magnetorheological (MR) effect). Recently, interest has been raised about the relationship between nonspherical particles, such as octahedral particles and the MR effect. However, experimental studies have not made much progress toward clarifying this issue due to the difficulty associated with synthesizing microparticles with well-defined shapes and sizes. Here, we presented a method for the shape-controlled synthesis of magnetite (Fe3O4) microparticles and investigated the MR effects of two suspensions prepared from the two shape-controlled samples of Fe3O4 microparticles. Our method, which was based on the polyol method, enabled the preparation of spherical and octahedral Fe3O4 microparticles with similar sizes and magnetic properties, through a reduction of α-FeOOH in a mixed solvent of ethylene glycol (a polyol) and water. The water played an important role in both the phase transition (α-FeOOH to Fe3O4) and the shape control. No substantial difference in the MR effect was observed between an octahedral-particle-based suspension and a spherical-particle-based one. Therefore, in this study, the shape of the microparticles did not strongly influence the MR effect, i.e., the properties of the chain structures.
Untangling the Hypogeococcus pungens species complex (Hemiptera: Pseudococcidae) for Argentina, Australia, and Puerto Rico based on host plant associations and genetic evidence

Hypogeococcus pungens, a mealybug native of southern South America, is devastating native cacti in Puerto Rico and threatening cactus diversity in the Caribbean, and potentially in Central and North America. The taxonomic status of H. pungens is controversial since it has been reported feeding not only on Cactaceae but also on other plant families throughout its distribution range. However, in Australia, where the species had been exported from Argentina to control weedy American cacti, it was never found on host plants other than Cactaceae. These conflicting pieces of evidence not only cast doubt on the species identity that invaded Puerto Rico, but also have a negative impact on the search for natural enemies to be used in biological control programs against this pest. Here we present reproductive incompatibility and phylogenetic evidences that give support to the hypothesis that H. pungens is a species complex in which divergence appears to be driven by the host plants. The nuclear EF1α and 18S and the mitochondrial COI genes were used as markers to evaluate the phylogenetic relationships among H. pungens populations collected in Argentina, Australia and Puerto Rico feeding on Cactaceae and/or Amaranthaceae. Additionally, we conducted reciprocal crosses between mealybugs from both hosts. Species delimitation analysis revealed two well-supported putative species within H. pungens, one including mealybugs feeding on Amaranthaceae (H. pungens sensu stricto), and a new undescribed species using Cactaceae as hosts. Additionally, we found asymmetric reproductive incompatibility between these putative species suggesting recent reproductive isolation. The Bayesian species delimitation also suggested that the Australian mealybug population may derive from another undescribed species. Overall, the patterns of genetic differentiation may be interpreted as the result of recent speciation events prompted by host plant shifts. Finally, the finding of a single haplotype in the Puerto Rico population suggests only one invasive event. We still need to identify the geographical origin of the pest in order to enable the use of biological control to reduce the threat to cacti diversity in the Caribbean.
Transcriptional response of Lactococcus lactis during bacterial emulsification

Microbial surface properties are important for interactions with the environment in which cells reside. Surface properties of lactic acid bacteria significantly vary and some strains can form strong emulsions when mixed with a hydrocarbon. Lactococcus lactis NCDO712 forms oil-in-water emulsions upon mixing of a cell suspension with petroleum. In the emulsion the bacteria locate at the oil-water interphase which is consistent with Pickering stabilization. Cells of strain NCDO712 mixed with sunflower seed oil did not stabilize the oil droplets. This study shows that the addition of either ethanol or ammonium sulfate led to cell aggregation, which subsequently allowed stabilizing oil-in-water emulsions. From this, we conclude that bacterial cell aggregation is important for emulsion droplet stabilization. To determine how bacterial emulsification influences the microbial transcriptome RNAseq analysis was performed on lactococci taken from the oil-water interphase. In comparison to cells in suspension 72 genes were significantly differentially expressed with a more than 4-fold difference. The majority of these genes encode proteins involved in transport processes and the metabolism of amino acids, carbohydrates and ions. Especially the proportion of genes belonging to the CodY regulon was high. Our results also point out that in a complex environment such as food fermentations a heterogeneous response of microbes might be caused by microbe-matrix interactions. In addition, microdroplet technologies are increasingly used in research. The understanding of interactions between bacterial cells and oil-water interphases is of importance for conducting and interpreting such experiments.
Evaluation of an intervention addressing a reablement programme for older, community-dwelling persons in Sweden (ASSIST 1.0): a protocol for a feasibility study

Introduction Older persons with functional limitations often need assistance from home care staff to thrive and continue to live in their home environments. Reablement, a proactive, preventative approach administered by home care staff, stimulating active engagement of the older person, is often recommended. Even though reablement has a potential to become a new rehabilitation model and has been implemented in different countries in various degrees, there is a lack of knowledge regarding the process of establishing reablement, the theoretical underpinnings and the conditionality and outcomes in different contexts. This knowledge is needed before full-scale recommendations can be made for implementation in specific contexts. Aim This study protocol aims to present a feasibility study of the intervention, ASSIST 1.0, a theory-based reablement programme, which includes coaching of home care staff and digitally based smart products, in a Swedish context. Methods and analysis This feasibility study will evaluate the perceived value and acceptability of ASSIST 1.0 intervention programme regarding fidelity, reach and dose, and potential outcomes by using a pretest and post-test design involving an intervention group and a control group (n=30) of older persons living at home, needing home care services. Qualitative interviews with home care staff delivering ASSIST and the older adults receiving the intervention as well as their significant others will be conducted to explore aspects affecting the intervention. Ethics and dissemination This study has been approved by the regional ethics board. The results of the feasibility study will form the base for refinement of the ASSIST programme and for the subsequent planning of a full-scale randomised controlled trial investigating the effect of the programme on a larger scale. Dissemination will include peer-reviewed publications and presentations at national and international conferences as well as information to involved stakeholders. Trial registration number NCT03505619
A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments

We present our assessment of tertiary structure predictions for hard targets in Critical Assessment of Structure Prediction round 13 (CASP13). The analysis includes (a) assignment and discussion of best models through scores‐aided visual inspection of models for each evaluation unit (EU); (b) ranking of predictors resulting from this evaluation and from global scores; and (c) evaluation of progress, state of the art, and current limitations of protein structure prediction. We witness a sizable improvement in tertiary structure prediction building on the progress observed from CASP11 to CASP12, with (a) top models reaching backbone RMSD <3 å for several EUs of size <150 residues, contributed by many groups; (b) at least one model that roughly captures global topology for all EUs, probably unprecedented in this track of CASP; and (c) even quite good models for full, unsplit targets. Better structure predictions are brought about mainly by improved residue‐residue contact predictions, and since this CASP also by distance predictions, achieved through state‐of‐the‐art machine learning methods which also progressed to work with slightly shallower alignments compared to CASP12. As we reach a new realm of tertiary structure prediction quality, new directions are proposed and explored for future CASPs: (a) dropping splitting into EUs, (b) rethinking difficulty metrics probably in terms of contact and distance predictions, (c) assessing also side chains for models of high backbone accuracy, and (d) assessing residue‐wise and possibly residue‐residue quality estimates.
Addiction as Learned Behavior Patterns

Individuals with substance use disorders (SUDs) have to cope with drug-related cues and contexts which can affect instrumental drug seeking, as shown with Pavlovian-to-instrumental transfer (PIT) tasks among humans and animals. Our review addresses two potential mechanisms that may contribute to habitual or even compulsive drug seeking and taking. One mechanism is represented by Pavlovian and PIT effects on drug intake. The other is a shift from goal-directed to habitual drug intake, which can be accessed via model-based versus model-free decision-making in respective learning tasks. We discuss the impact of these learning mechanisms on drug consumption. First, we describe how Pavlovian and instrumental learning mechanisms interact in drug addiction. Secondly, we address the effects of acute and chronic stress exposure on behavioral and neural PIT effects in alcohol use disorder (AUD). Thirdly, we discuss how these learning mechanisms and their respective neurobiological correlates can contribute to losing versus regaining control over drug intake. Utilizing mobile technology (mobile applications on smartphones including games that measure learning mechanisms, activity bracelets), computational models, and real-world data may help to better identify patients with a high relapse risk and to offer targeted behavioral and pharmacotherapeutic interventions for vulnerable patients.
Integrating aeration and rotation processes to accelerate composting of agricultural residues

The active phase of conventional static composting systems varies dramatically, ranging from several weeks to several months. Therefore, this study was to examine the effect of a combined continuous aeration-rotation process on shortening the active phase of composted material. A mixture of tomato plant residues with 20%-chicken manure (v/v) was composted in two identical pilot-scale bioreactors. One of them was static, and the other was continuously rotated at 3 rpm; each was supplied with continuous aeration. Compost temperatures (Tc) were measured throughout the composting process; the moisture content (MC) and carbon/nitrogen ratio (C/N) were measured at the beginning and end of the experiment. The quality and stage of compost were evaluated at the end of the experiment using Dewar, Solvita, and visual tests. Continuous aeration-rotation significantly reduced the active phase period to 4.5 days, increased the compost temperature (Tc) to 60°C after 3 days of operation, and remained at 50–65°C for approximately 3 consecutive days (thermophilic stage). In contrast, compost in the static bioreactor remained in the mesophilic stage (Tc < 45°C). During the composting process, the C/N ratio was reduced from 30/1 to 23/1 in the rotating bioreactor, while it remained at 30/1 in the static bioreactor, indicating that the nitrogen content was not a limiting factor affecting the composting process. The MC was within the optimum range for microorganisms (58–61%) for both bioreactors. After the active phase had ended in the rotating bioreactor, the compost was inactive and ready for further maturation, while compost from the static bioreactor was still immature and active. These results show that the proposed method can be done on a commercial scale to significantly reduce the composting period and to enhance the compost stability and productivity.
Flexible bodies-Restricted lives: A qualitative exploratory study of embodiment in living with joint hypermobility syndrome/Ehlers-Danlos syndrome, hypermobility type.

PURPOSE The aim of this study was to explore embodiment as a meaning-making experience in the daily life of Norwegian adults living with joint hypermobility syndrome/Ehlers-Danlos syndrome, hypermobility type (JHS/EDS-HT). The work of Drew Leder and his distinction between bodily dis- and dys-appearance contributes to the description and analysis of individuals' bodily experiences of living with this chronic illness. METHODS An explorative and qualitative design was applied to in-depth interviews with seven participants. The theoretical framework was phenomenological, and the method of analysis was thematic, involving descriptive and interpretative approaches. RESULTS Participants' bodily experiences were closely connected to a timeline viewing their illness in the past, the present and from future perspectives. The following central themes emerged from the data: (a) visible to invisible signs of a former body; (b) standing up and falling down of a present body; and (b) future thoughts of an inner and outer body. CONCLUSIONS The study found that living with JHS/EDS-HT revealed complex experiences of having flexible bodies and restricted lives. Our findings also showed a meaning-making process of embodied experiences that evolved over time, as well as a sliding transition from social to personal dys-appearance. In the course of time, a bodily disruptions in social interactions comes to the fore, with invisible symptoms such as pain and fatigue. Individual bodily suffering determines the existence of hope or hopelessness regarding recovery from this condition.
Structures of the Neisseria meningitides methionine‐binding protein MetQ in substrate‐free form and bound to l‐ and d‐methionine isomers

The bacterial periplasmic methionine‐binding protein MetQ is involved in the import of methionine by the cognate MetNI methionine ATP binding cassette (ABC) transporter. The MetNIQ system is one of the few members of the ABC importer family that has been structurally characterized in multiple conformational states. Critical missing elements in the structural analysis of MetNIQ are the structure of the substrate‐free form of MetQ, and detailing how MetQ binds multiple methionine derivatives, including both l‐ and d‐methionine isomers. In this study, we report the structures of the Neisseria meningitides MetQ in substrate‐free form and in complexes with l‐methionine and with d‐methionine, along with the associated binding constants determined by isothermal titration calorimetry. Structures of the substrate‐free (N238A) and substrate‐bound N. meningitides MetQ are related by a “Venus‐fly trap” hinge‐type movement of the two domains accompanying methionine binding and dissociation. l‐ and d‐methionine bind to the same site on MetQ, and this study emphasizes the important role of asparagine 238 in ligand binding and affinity. A thermodynamic analysis demonstrates that ligand‐free MetQ associates with the ATP‐bound form of MetNI ∼40 times more tightly than does liganded MetQ, consistent with the necessity of dissociating methionine from MetQ for transport to occur.
Effects of reducing growth rate via diet dilution on bone mineralization, performance and carcass yield of coccidia-infected broilers.

Coccidiosis and rapid growth rate (GR) compromise bone mineralization in modern broilers. We tested the hypothesis that reducing GR via diet dilution during peak bone development will improve bone mineralization in both infected and uninfected broilers. A total of 384 male Ross 308 chicks were allocated to a basal grower diet (3,107 kcal/kg ME and 19.4% CP) diluted with 0, 5, 10, or 15% lignocellulose (n = 12 pens/treatment, 8 birds/pen) at day 10 of age. Prior to this, birds in each group received half the intended diet-dilution levels (day 8 to 10 of age) and a common starter diet (day 1 to 7 of age). At day 13 of age (day 0 post-infection, pi), birds were orally inoculated with either 7,000 sporulated Eimeria maxima oocysts (I) or water (C), forming a 4 diet-dilution level × 2 infection status factorial experiment. Performance was measured over 12 days pi and scaled to BW at infection (day 0 pi) to account for a priori BW differences. At day 12 pi (day 25 of age), 1 bird/pen (a total of 6 birds/treatment) was sampled to assess tibia and femur mineralization relative to BW, and carcass yield. There was no interaction (P > 0.05) between infection status and diet-dilution level on ADFI/BW measured over day 1 to 12 pi, or on any bone variable. ADG/BW pi decreased (P < 0.01) with diet dilution amongst C birds, but was statistically similar (P > 0.05) amongst I birds. I compared to C birds had reduced breast meat (P < 0.05) and eviscerated carcass yield (P < 0.01), femur (P < 0.05) and tibia (P < 0.01) breaking strength (BS), and femur ash weight (AW) (P < 0.05). Diet dilution did not affect carcass yield, but improved femur BS (P < 0.001), and tended to improve (P < 0.1) femur and tibia AW. Overall, diet dilution significantly affected femur, more than tibia, variables: relative BS, robusticity index, and ash percentage. Reducing GR affected broiler long bone mineralization to a similar degree in the presence or absence of coccidiosis.
A comparison of stereotactic and tomosynthesis‐guided localisation of impalpable breast lesions

Impalpable breast cancers require precise pre‐operative lesion localisation to minimise re‐excision rates. Conventional techniques include hookwire insertion using stereotactic guidance. Newer techniques include the use of tomosynthesis guidance and the use of iodine‐125 seeds. This study compares the accuracy of lesion localisation with hookwire or seed insertion using prone stereotactic or upright tomosynthesis guidance.
Prevalence and determinants of initiation of breastfeeding within one hour of birth: An analysis of the Bangladesh Demographic and Health Survey, 2014

Background Breastfeeding within one hour of birth is a critical component of newborn care and is estimated to avert 22% of neonatal mortality globally. Understanding the determinants of early initiation of breastfeeding (EIBF) is essential for designing targeted and effective breastfeeding promotion programmes. The aim of this study was to determine the prevalence and determinants of early initiation of breastfeeding among Bangladeshi women. Methods This paper analyses the data from the Bangladesh Demographic and Health Survey, 2014. Analysis was based on responses of women who had at least one live birth in the two years preceding the survey (n = 3,162) collected using a structured questionnaire. The primary outcome was breastfeeding initiation within one hour of birth ascertained by women’s self-report. Explanatory variables included woman’s age, education, religion, household wealth, place of residence and place of delivery, birth order, child’s size, antenatal care (ANC), postnatal care (PNC) and skin-to-skin contact. Associations between variables were assessed by simple and multivariable logistic regressions. Results Of the 3,162 recently delivered mothers, 51% initiated breastfeeding within one hour of delivery. Prevalence of EIBF varied significantly between different types of mode of delivery, among different geographical regions and among women who had PNC with their newborn. Women who had caesarean section (C-section) were less likely to initiate breastfeeding early after birth than women who had normal vaginal delivery (NVD) (AOR: 0.32, 95% CI 0.23 0.43; p value < 0.001). Women who had received PNC with their newborns within one hour of delivery were more likely to breastfeed their babies within one hour of birth compared to those who did not (AOR: 1.61, 95% CI 1.26 2.07; p value < 0.001). Mother’s age, education, religion, household wealth index, place of residence and place of delivery, birth order, number of antenatal visits, child’s size and skin-to-skin contact were not significantly associated with EIBF. Conclusions Findings from this study suggest that investing more effort in ensuring immediate PNC of mother-newborn pair can increase EIBF. Solutions should be explored to increase EIBF among mothers who undergo C-section as C-section is rising rapidly in Bangladesh. Further research is needed to explore the regional differences in the country, including specific cultural practices that influence EIBF.
Heart failure prevalence in the general population: SOBOTA‐HF study rationale and design

Epidemiological heart failure (HF) data in the era of natriuretic peptides and echocardiography are scarce. The primary aim of this study is to evaluate the HF prevalence in the general population. We will also investigate natriuretic peptide cut‐off for diagnosis of HF. Finally, we will be able to identify left ventricular function phenotypes and study relations between cardiac function, clinical presentation, and health‐related quality of life.
Method for coregistration of optical measurements of breast tissue with histopathology: the importance of accounting for tissue deformations

Abstract. For the validation of optical diagnostic technologies, experimental results need to be benchmarked against the gold standard. Currently, the gold standard for tissue characterization is assessment of hematoxylin and eosin (H&E)-stained sections by a pathologist. When processing tissue into H&E sections, the shape of the tissue deforms with respect to the initial shape when it was optically measured. We demonstrate the importance of accounting for these tissue deformations when correlating optical measurement with routinely acquired histopathology. We propose a method to register the tissue in the H&E sections to the optical measurements, which corrects for these tissue deformations. We compare the registered H&E sections to H&E sections that were registered with an algorithm that does not account for tissue deformations by evaluating both the shape and the composition of the tissue and using microcomputer tomography data as an independent measure. The proposed method, which did account for tissue deformations, was more accurate than the method that did not account for tissue deformations. These results emphasize the need for a registration method that accounts for tissue deformations, such as the method presented in this study, which can aid in validating optical techniques for clinical use.