Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigating students’ difficulties with differential equations in physics

There are numerous cases in physics where the value of a quantity and changes in that quantity are related. For example, the speed of an object depends on its acceleration; the radioactivity of a sample depends on the amount of the sample present. Except in highly idealized settings, the analysis of these cases requires students to recognize, set up, and solve an ordinary differential equation (ODE). In many universities, including DCU, ODEs are studied in mathematics before they are applied in physics. However, the aims of mathematicians and physicists can be very different. Mathematics modules tend to emphasize the classification of ODEs and their theoretical aspects (questions of existence and uniqueness of solutions). Techniques for solving ODEs are also studied extensively, and typically students acquired a good instrumental understanding [1] of solving ODEs. However, in physics modules, modelling is often emphasized: students must apply mathematical knowledge to interpret a setting, recognize the need for and set up an ODE, solve it, and interpret the solution. Other potential reasons why ODEs present a problem for physics students include gaps in students’ mathematical knowledge, and conceptual issues with ODEs.
Immobilization of protease extracted from Bacillus sp. P45 on different supports

Immobilization is a direct tool which not only improves the activity and stability of enzymes, but also enables their reuse. Therefore, selecting methods and supports to obtain biocatalysts with high selectivity and thermal stability is an important step. This study aimed at evaluating the immobilization of partially purified protease from Bacillus sp. P45, by different methods with the use of the following carriers: Amberlite IR® 120, montmorillonite clay, chitosan, glutaraldehyde-activated chitosan, Eupergit® C, DEAE-Cellulose® and QAE-Sephadex®. It also aimed at determining the operational stability of the derivative. The best results were obtained with the use of glutaraldehyde-activated chitosan, Amberlite IR® 120 and montmorillonite clay, with loading capacities of 25.4, 6.2 and 2.3 U/g support, respectively. Regarding the operational stability of the derivative glutaraldehyde-activated chitosan, the enzyme was found to keep 53.5% of its residual activity after being reused four times.
Methods for powering bioelectronic microdevices

Bioelectronic microdevices are an emerging class of biomedical devices miniaturized at the scale of a millimeter or less, which promise new capabilities for monitoring and treating human disease. Although rapid progress has been made in the sensing and actuation capabilities of microdevices, a major technological challenge remains in the way that these devices are powered within the body. In this review, we revisit the power requirements of microdevices, describe current methods for storing, transferring or harvesting energy in microdevices, provide an overview of emerging powering approaches and discuss the promise of microdevices in biomedicine.
Features of acid–base balance of bone marrow

Context: Bone marrow (BM) pH has rarely been measured, and the long BM has barely been studied at all because intravital obtaining of the long BM is impossible due to the extreme strength of the long bone tissue. Aims: The study aimed to investigate the acid–base balance of the BM and to compare the acid–base properties of long BM and flat BM. Subjects and Methods: Forty flat BM samples were extracted by sternal puncture. Forty long BM samples were extracted from the femora in patients who had to have a limb amputated. A blood gas and acid–base status analyzer were used to determine pH. Results: Flat BM pH is similar to blood p; the long BM pH is acidic and ranges from 6.7 to 6.9. Hematopoietic stem cells occur in both acidic and slightly alkaline environments. The blood gas and acid–base status analyzer used in this study are suitable for determining the acid–base properties of BM. Conclusions: The acid–base status appears to be an important factor of stem cell differentiation. This paper can be of interest to biotechnologists and researchers who investigate possibilities to influence the differentiation and properties of the stem cells.
Neural Circuit Mechanism of Decision Uncertainty and Change-of-Mind

Decision-making is often accompanied by a degree of confidence on whether a choice is correct. Decision uncertainty, or lack in confidence, may lead to change-of-mind. Studies have identified the behavioural characteristics associated with decision confidence or change-of-mind, and their neural correlates. Although several theoretical accounts have been proposed, there is no neural model that can compute decision uncertainty and explain its effects on change-of-mind. We propose a neuronal circuit model that computes decision uncertainty while accounting for a variety of behavioural and neural data of decision confidence and change-of-mind, including testable model predictions. Our theoretical analysis suggests that change-of-mind occurs due to the presence of a transient uncertainty-induced choice-neutral stable steady state and noisy fluctuation within the neuronal network. Our distributed network model indicates that the neural basis of change-of-mind is more distinctively identified in motor-based neurons. Overall, our model provides a framework that unifies decision confidence and change-of-mind.
The effects of used motor oil on Myzus persicae and Arabidopsis thaliana

Published: 02/07/2018 Used motor oil (UMO) is a highly toxic substance that enters the environment as runoff from roadways and other urbanized impermeable surfaces. The effects of various runoff contaminants on the environment have been studied extensively, with research focusing on efficient and effective methods of clean-up. This study serves to examine the effects of varying volumes of UMO on plants and the subsequent impacts on herbi-vores. Arabidopsis thaliana was used as the model plant organism due to its rapid life cycle and Myzus persicae was used as the model herbivore organism due to its high proliferation rate. The results showed a statistically significant effect (Foil(3,64)=3.3853, P=0.023) of UMO treatment on plant performance. There was also a statistically sig-nificant effect (F21, 256=2.4661, P=0.00052) due to the interaction of oil and day on the herbivore of the plant. The results indicate that contaminants can affect multiple tro-phic levels, which should be considered when looking at possible issues regarding the contamination of natural environments.
Crystallography of systems with long periods: a neutron-scattering study of sodium dodecyl sulfate/water mesophases

Diagrammes de diffraction des mesophases ordonnees de ce systeme lyotrope. L'espace reciproque des 6 mesophases change de facon continue des phases les plus hydratees (cylindres) aux phases les moins hydratees (bicouches). Le comportement orientationnel des bicouches de ces mesophases orientees permet d'identifier les plans cristallographiques. Deduction (approximative) du groupe d'espace
Error Rate Optimization and improved WSN Lifetime

—Wireless Sensor Network design for various purposes like military operation, environment monitoring, fire monitoring etc. As sensor nodes are small in size and deployment of nodes are also easy and it is very useful in different operation so growth of sensor network is very rapid. As size of sensor network is large consumption of the energy is also increased compare to before and sensor nodes are powered by small battery, which is also not re-chargeable which lead to early death of sensor node. Lifetime of the network is decreased and it affects the overall system performance. For the improvement of the network lifetime in the wireless sensor network clustering is a technique which is used. A new multi-objective adaptive swarm optimization (MASO) method for clustering is proposed in this paper and maximum number of cluster will be calculated, which is best suited for the network. Cluster head and cluster member is given to each cluster and the local information extraction task is performed. Cluster head collect all the extracted information from the member node after then it will be sent to the base station, the global information extraction from all the cluster head nodes is performed by the base station and generate some useful result. Error probability is considered in transmission of data packets in one hop communication is considered by author. Obtained result is compared with “Energy Aware Swarm Optimization with Inter cluster Search for Wireless Sensor Network”
HLA alleles associated with risk of ankylosing spondylitis and rheumatoid arthritis influence the gut microbiome

Objectives HLA alleles affect susceptibility to more than 100 diseases, but the mechanisms to account for these genotype-disease associations are largely unknown. HLA-alleles strongly influence predisposition to ankylosing spondylitis (AS) and rheumatoid arthritis (RA). Both AS and RA patients have discrete intestinal and faecal microbiome signatures. Whether these changes are cause or consequence of the diseases themselves is unclear. To distinguish these possibilities, we examine the effect of HLA-B27 and HLA-DRB1 RA-risk alleles on the composition of the intestinal microbiome in healthy individuals. Methods 568 samples from 6 intestinal sites were collected from 107 otherwise healthy unrelated subjects and stool samples from 696 twin pairs from the TwinsUK cohort. Microbiome profiling was performed using sequencing of the 16S rRNA bacterial marker gene. All patients were genotyped using the Illumina CoreExome SNP microarray, and HLA genotypes were imputed from these data. Results Association was observed between HLA-B27 genotype, and RA-risk HLA-DRB1 alleles, and overall microbial composition (P=0.0002 and P=0.00001 respectively). These associations were replicated in the TwinsUK cohort stool samples (P=0.023 and P=0.033 respectively). Conclusions This study shows that the changes in intestinal microbiome composition seen in AS and RA are at least partially due to effects of HLA-B27 and –DRB1 on the gut microbiome. These findings support the hypothesis that HLA alleles operate to cause or increase the risk of these diseases through interaction with the intestinal microbiome, and suggest that therapies targeting the microbiome may be effective in their prevention and/or treatment.
A modified air-assisted silicone oil removal from the anterior chamber

Silicone oil (SO) is a commonly used tamponading agent in retinal detachment surgeries. Inadvertent anterior migration of SO and complete anterior chamber (AC) oil fill in an aphakic or pseudophakic eye is occasionally encountered. This can cause secondary glaucoma with very high intraocular pressure and pain. In this scenario, an urgent silicone oil removal (SOR) is warranted. Since SO is buoyant, in the supine position, it tends to rise anteriorly. Hence, removal of SO trapped in the AC will invariably lead to further migration of oil from the posterior segment into the AC to replace the volume removed. Simultaneous replacement of AC volume is necessary to prevent this. We describe a modified technique of partial SOR that employs air to prevent recurrent migration of SO into AC.
A retrospective evaluation of automated optimization of deep brain stimulation parameters

Objective. We performed a retrospective analysis of an optimization algorithm for the computation of patient-specific multipolar stimulation configurations employing multiple independent current/voltage sources. We evaluated whether the obtained stimulation configurations align with clinical data and whether the optimized stimulation configurations have the potential to lead to an equal or better stimulation of the target region as manual programming, while reducing the time required for programming sessions. Approach. For three patients (five electrodes) diagnosed with essential tremor, we derived optimized multipolar stimulation configurations using an approach that is suitable for the application in clinical practice. To evaluate the automatically derived stimulation settings, we compared them to the results of the monopolar review. Main results. We observe a good agreement between the findings of the monopolar review and the optimized stimulation configurations, with the algorithm assigning the maximal voltage in the optimized multipolar pattern to the contact that was found to lead to the best therapeutic effect in the clinical monopolar review in all cases. Additionally, our simulation results predict that the optimized stimulation settings lead to the activation of an equal or larger volume fraction of the target compared to the manually determined settings in all cases. Significance. Our results demonstrate the feasibility of an automatic determination of optimal DBS configurations and motivate a further evaluation of the applied optimization algorithm.
Role of Religion in Psychotic Illness in the Israeli Ultra-Orthodox Jewish Population

Abstract This study aims to describe the role that religion and belief may play in members of the Israeli ultra-Orthodox Jewish population hospitalized in the Mayanei Hayeshua Medical Center and diagnosed with a psychotic disorder. Religion was judged essential by the patients in the management of their illness. Forty percent of the patients perceive their illness as their destiny, 26.7% as an “affliction of love,” and 33.3% as resulting from their sins. Sixty percent of patients explained that faith is a source of hope in their life, with 76.7% indicating that collective religious practices help them face their illness. Ninety percent expressed no conflict between consulting a psychiatrist and their religious beliefs. Collective religious practices were correlated with higher treatment credibility. The use of religious coping methods was correlated with lower anxiety and tension among women. Higher conflict between religion and consulting a psychiatrist was correlated with lower treatment credibility among men.
Dissection of P2X4 and P2X7 Receptor Current Components in BV-2 Microglia

Microglia cells represent the immune system of the central nervous system. They become activated by ATP released from damaged and inflamed tissue via purinergic receptors. Ionotropic purinergic P2X4 and P2X7 receptors have been shown to be involved in neurological inflammation and pain sensation. Whether the two receptors assemble exclusively as homotrimers or also as heterotrimers is still a matter of debate. We investigated the expression of P2X receptors in BV-2 microglia cells applying the whole-cell voltage-clamp technique. We dissected P2X4 and P2X7 receptor-mediated current components by using specific P2X4 and P2X7 receptor blockers and by their characteristic current kinetics. We found that P2X4 and P2X7 receptors are activated independently from each other, indicating that P2X4/P2X7 heteromers are not of functional significance in these cells. The pro-inflammatory mediators lipopolysaccharide and interferon γ, if applied in combination, upregulated P2X4, but not P2X7 receptor-dependent current components also arguing against phenotypically relevant heteromerization of P2X4 and P2X7 receptor subunits.
Put Some Guts into It: Intestinal Organoid Models to Study Viral Infection

The knowledge about enteric viral infection has vastly increased over the last eight years due to the development of intestinal organoids and enteroids that suppose a step forward from conventional studies using cell lines. Intestinal organoids and enteroids are three-dimensional (3D) models that closely mimic intestinal cellular heterogeneity and organization. The barrier function within these models has been adapted to facilitate viral studies. In this review, several adaptations (such as organoid-derived two-dimensional (2D) monolayers) and original intestinal 3D models are discussed. The specific advantages and applications, as well as improvements of each model are analyzed and an insight into the possible path for the field is given.
Assessing the Ability of Developmentally Precocious Estrogen Signaling to Recapitulate Ovarian Transcriptomes and Follicle Dynamics in Alligators from a Contaminated Lake

Background: Concern has grown in recent decades over anthropogenic contaminants that interfere with the functioning of endocrine hormones. However, mechanisms connecting developmental processes to pathologies associated with endocrine-disrupting chemical (EDC) exposure are poorly understood in naturally exposed populations. Objectives: We sought to a) characterize divergence in ovarian transcriptomic and follicular profiles between alligators originating from a historically EDC-contaminated site, Lake Apopka, and a reference site; b) test the ability of developmentally precocious estrogen exposure to recapitulate site-associated patterns of divergence; and c) test whether treatment with exogenous follicle-stimulating hormone (FSH) is capable of rescuing phenotypes associated with contaminant exposure and/or embryonic estrogen treatment. Methods: Alligators eggs were collected from a contaminated site and a reference site, and a subset of eggs from the reference site were treated with estradiol (E2) during embryonic development prior to gonadal differentiation. After hatching, alligators were raised under controlled laboratory settings for 5 months. Juveniles from both sites were divided and treated with exogenous FSH. Histological analyses and RNA-sequencing were conducted to characterize divergence in ovarian follicle dynamics and transcriptomes between sites, between reference and E2-treated animals, and between FSH-treated and nontreated animals. Results: We observed broad site-of-origin divergence in ovarian transcriptomes and reductions in ovarian follicle density between juvenile alligators from Lake Apopka and the reference site. Treating embryos from the reference site with E2 overwhelmingly recapitulated transcriptional and histological alterations observed in Lake Apopka juveniles. Ovarian phenotypes observed in Lake Apopka alligators or resulting from estrogen treatment were only partially rescued by treatment with exogenous FSH. Discussion: Recapitulation of ovarian abnormalities by precocious E2 revealed a relatively simple mechanism underlying contaminant-induced pathologies in a historical example of environmental endocrine disruption. Findings reported here support a model where the developmental timing of estrogen signaling has the potential to permanently alter ovarian organization and function. https://doi.org/10.1289/EHP6627
Role of the H subunit C-terminal domain in the assembly of the vacuolar H+-ATPase

The vacuolar H+-ATPase (V-ATPase) is regulated by reversible disassembly into autoinhibited V1-ATPase and Vo proton channel sectors, a process that is poorly understood on the molecular level. V-ATPase is a rotary motor and recent structural analysis revealed that disassembled V1 and Vo are in different rotary states, a mismatch that is likely responsible for the inability to reconstitute holo V-ATPase from its functional sectors in vitro. Here, using the model organism S. cerevisiae, we show that a key impediment for binding of autoinhibited V1 to Vo is the conformation of the inhibitory C-terminus of subunit H (HCT). Using biolayer interferometry and biochemical analysis, we show that selective disruption of HCT’s binding site on V1 allows in vitro assembly of a structurally and functionally coupled V-ATPase complex. The resultant mutant V-ATPase, however, does not disassemble as readily as the wild type enzyme, highlighting the importance of HCT’s conformation in the mechanism of reversible disassembly. These findings pave the way for identifying molecules that allow for therapeutic modulation of aberrant V-ATPase activity in the disease state.
Aromatic and Heteroaromatic Compounds

Part 1 Introduction: history of aromatic and heteroaromatic diazo compounds nomenclature general references. Part 2 Methods for the preparation of aromatic and heteroaromatic diazo compounds: diazotization of amines with alkali nitrite in dilute aqueous mineral acids diazotization in concentrated mineral acid isolation of diazonium salts diazotization of 2- and 4-aminophenols formation of diazonium salts under anhydrous conditions other reactions involving formation of aromatic diazonium ions. Part 3 Kinetics and mechanism of diazotization: historical development influence of acidity on the rate and mechanism of diazotization in aqueous sulfuric and perchloric acids nucleophilic catalysis of diazotization transformation of the N-Nitrosoamine intermediate into the diazonium ion. Part 4 The structure of diazonium compounds: introductory remarks structure of arenediazonium salts theoretical investigations. Part 5 Acid-base and isomerization reactions of diazo compounds in water: the aromatic diazonium ion as a dibasic acid the combined system of acid-base addition, (Z)/(E)- and prototropic isomerization reactions of arenediazonium ions kinetics and equilibria of arenediazonium ions in water. Part 6 Additions of other nucleophiles to arenediazonium ions: O-Coupling S-coupling N-coupling P-coupling C-coupling intramolecular coupling. Part 7 Structural and mechanistic aspects of additions of nucleophiles to diazonium ions: (Z)/(E)-isomerism investigations on reactivities by the interpretation of substituent effects - the Hammett and related equations the electronic influence of the diazonio group as a substituent influence of substituents on the addition of nucleophiles to arenediazonium ions. Part 8 Dediazoniation of arenediazonium ions: introduction to dediazoniation in general multiplicity of pathways and products the D[N] + A[N] mechanism of dediazoniation molecular orbital investigations on heterolytic dediazoniations and on aryl cations dediazoniations via aryne intermediates dediazoniation initiated by an electron transfer solvent effects in competitive homolytic and heterolytic dediazoniation dediazoniation in alkaline aqueous solutions dediazoniation in highly nucleophilic solvents and in the presence of good nucleophiles dediazoniation in alcohols. Part 9 Logic, psychology, and serendipity of scientific discoveries - an interlude. Part 10 Applications of heterolytic and homolytic dediazoniations in organic syntheses: hydro-de-diazoniation hydroxy- and mercapto-de-diazoniations and related reactions fluoro-de-diazoniation chloro-, bromo-, and cyano-de-diazoniations - the Sandmeyer reaction iodo-de-diazoniation and related reactions azido-de-diazoniation dediazoniation in the presence of carbonyl, sulfonyl, and related compounds replacement of the diazonio group by alkenes and alkynes - the Meerwein reaction arylation of aromatic compounds - the Gomberg-Bachmann and related reactions. (Part contents).