Miracle-dz/UniFAR-FTUs huggingface dataset:
Paeonol protects against acute pancreatitis by Nrf2 and NF-κB pathways in mice.

OBJECTIVES Paeonol (PAE) is an active ingredient with anti-inflammatory and antioxidant properties. This study was designed to investigate the effect of PAE on acute pancreatitis (AP). METHODS AP was induced by the intraperitoneal injection of 20% l-arginine (4 g/kg) for 6 h. Mice were pretreated with PAE (25, 50 or 100 mg/kg) intragastrically for 5 days. The histological damage and alterations of biochemical indicators, inflammatory cytokines and oxidative stress factors in AP mice were detected. The Nrf2 and NF-κB pathways were examined to illustrate the potential mechanism. KEY FINDINGS In AP model, we found that PAE attenuated histological injury of pancreatic tissues, reduced the serum levels of α-amylase and increased Ca2+ contents in a dose-dependent manner. The white blood cell content, and IL-1β, IL-6 and TNF-α levels in the serum of AP mice were reduced by PAE. Furthermore, PAE caused a reduction of MPO and MDA levels, accompanied by an increase in SOD activity in the pancreas of AP mice. We also demonstrated that the alterations of Nrf2 and NF-κB pathways in AP mice were reversed by PAE. CONCLUSIONS PAE attenuates inflammation and oxidative stress in the development of AP by the regulation of Nrf2 and NF-κB pathways.
Does sternal body shape reflect family relationships? A study on a genealogically documented Central European osteological sample (19th–20th centuries)

In forensic contexts, sternal anatomical varieties represent useful tools for the identification of an individual, either by comparison of ante‐mortem and post‐mortem data, or by potential comparison of data from biologically related individuals. Sternal body variation is also used to detect the biological affinity of individuals in bioarchaeology. However, no study has been made available to date on the degree to which the overall shape of the sternal body reflects the degree of biological relatedness. We, therefore, analyzed the sternal body shape of 10 individuals with known genealogical data, members of one family over three generations including inbred individuals (19th–20th centuries, Bohemia, Czech Republic), and a control sample of 12 biologically unrelated individuals. First, closely biologically related individuals were compared with unrelated individuals based on 10 variables expressing the morphological characteristics of the sternum, and then all individuals were compared based on Fourier analysis depending on their degree of relationship. The results showed that there is a greater degree of shape similarity in biologically related individuals than in unrelated individuals, and variability decreases with an increasing degree of relatedness. Inbred individuals showed the lowest sternum‐shape distances and degree of variability, while unrelated individuals, showed the highest distances and variability. Moreover, in some cases, the documented relationships were also supported by a similar morphology of the ossified and fused xiphoid process. Thus, sternal shape analysis expands the possibilities for individual identification and the detection of the biological affinity of individuals for both the forensic sciences and bioarchaeology.
Streptococcus pyogenes can support or inhibit growth of Haemophilus influenzae by supplying or restricting extracellular NAD+

Nicotinamide adenine dinucleotide (NAD+) is an essential co-factor for cellular metabolism and serves as a substrate in enzymatic processes. NAD+ is produced by de novo synthesis or salvage pathways in nearly all bacterial species. Haemophilus influenzae lacks the capacity for de novo synthesis, so it is dependent on import of NAD+ from the external environment or salvage biosynthetic pathways for recycling of NAD+ precursors and breakdown products. However, the actual sources of NAD+ utilized by H. influenzae in the respiratory tract are not well defined. In this study, we found that a variety of bacteria, including species found in the upper airway of humans, released NAD+ that was readily detectable in extracellular culture fluid, and which supported growth of H. influenzae in vitro. By contrast, certain strains of Streptococcus pyogenes (group A streptococcus or GAS) inhibited growth of H. influenzae in vitro by secreting NAD+-glycohydrolase (NADase), which degraded extracellular NAD+. Conversely, GAS strains that lacked enzymatically active NADase released extracellular NAD+, which could support H. influenzae growth. Our results suggest that many bacterial species, including normal flora of the upper airway, release NAD+ into the environment. GAS is distinctive in its ability to both release and degrade NAD+. Thus, colonization of the airway with H. influenzae may be promoted or restricted by co-colonization with GAS in a strain-specific manner that depends, respectively, on release of NAD+ or secretion of active NADase. We suggest that, in addition to its role as a cytotoxin for host cells, NADase may serve a separate function by restricting growth of H. influenzae in the human respiratory tract.
Effects of psychosis-associated genetic markers on brain volumetry: a systematic review of replicated findings and an independent validation

Abstract Background Given psychotic illnesses' high heritability and associations with brain structure, numerous neuroimaging-genetics findings have been reported in the last two decades. However, few findings have been replicated. In the present independent sample we aimed to replicate any psychosis-implicated SNPs (single nucleotide polymorphisms), which had previously shown at least two main effects on brain volume. Methods A systematic review for SNPs showing a replicated effect on brain volume yielded 25 studies implicating seven SNPs in five genes. Their effect was then tested in 113 subjects with either schizophrenia, bipolar disorder, ‘at risk mental state’ or healthy state, for whole-brain and region-of-interest (ROI) associations with grey and white matter volume changes, using voxel-based morphometry. Results We found FWER-corrected (Family-wise error rate) (i.e. statistically significant) associations of: (1) CACNA1C-rs769087-A with larger bilateral hippocampus and thalamus white matter, across the whole brain; and (2) CACNA1C-rs769087-A with larger superior frontal gyrus, as ROI. Higher replication concordance with existing literature was found, in decreasing order, for: (1) CACNA1C-rs769087-A, with larger dorsolateral-prefrontal/superior frontal gyrus and hippocampi (both with anatomical and directional concordance); (2) ZNF804A-rs11681373-A, with smaller angular gyrus grey matter and rectus gyri white matter (both with anatomical and directional concordance); and (3) BDNF-rs6265-T with superior frontal and middle cingulate gyri volume change (with anatomical and allelic concordance). Conclusions Most literature findings were not herein replicated. Nevertheless, high degree/likelihood of replication was found for two genome-wide association studies- and one candidate-implicated SNPs, supporting their involvement in psychosis and brain structure.
Institutional choice among medical applicants: a profile paper for The United Kingdom Medical Applicant Cohort Study (UKMACS) prospective longitudinal cohort study

Purpose To generate a large cohort of those in 2019 seriously considering applying to study Medicine, collecting data on a range of socioeconomic and other demographic factors that influence choice of medical schools and to link to other datasets to form a longitudinal study of progress through medical school and careers in medicine. Design Cross-sectional questionnaire studies, part of the longitudinal UK Medical Applicant Cohort Study (UKMACS). Setting UK medical school admissions in 2020. Participants UK residents aged 16+ and seriously considering applying to study Medicine. The cohort was primarily drawn from those registering in 2019 for the U(K)CAT (University Clinical Aptitude Test (formerly the UK Clinical Aptitude Test)) with additional potential applicants responding to an open call. Participants consented to their data being linked within the UK Medical Education Database. Findings to date UKMACS Wave 1 questionnaire respondents consisted of 6391 consenting respondents from across the UK. In 2019, 14 980 of the 17 470 UK-domiciled medicine applicants were first-time applicants. The questionnaires show that many of these applicants have a need for more help and guidance to make informed choices, with less advantaged groups reporting themselves as being at a disadvantage when applying due to limited understanding of information and limited access to guidance to enable informed and effective decision-making. Future plans To link the cohort with successive Universities and Colleges Admissions Service and other datasets to analyse outcomes of applications and establish national longitudinal evidence to understand how medical choices are made and how they impact on educational, career and workforce outcomes.
Complete Genome Sequence of an Uncultivated Freshwater Bacteroidota Lineage

We report here a complete metagenome-assembled genome belonging to the AKYH767 order within the Bacteroidota phylum. The recovered genome stems from a nonaxenic Amoebozoa culture from Lake Zürich and was assembled as a circular element at a length of 4.1 Mbp and a coverage of 115×. ABSTRACT We report here a complete metagenome-assembled genome belonging to the AKYH767 order within the Bacteroidota phylum. The recovered genome stems from a nonaxenic Amoebozoa culture from Lake Zürich and was assembled as a circular element at a length of 4.1 Mbp and a coverage of 115×.
An interrupted time-series analysis of the effects of withdrawal of financial incentives on diagnosis of atrial fibrillation as resolved. Does withdrawal of an incentive reverse its unintended effects?

Background The UK introduced financial incentives for management of atrial fibrillation (AF) in 2006, after which there was an increase in the proportion of patients with AF diagnosed as resolved. Removal of incentives in Scotland provides a natural experiment to investigate the effects of withdrawal of an incentive on diagnosis of resolved AF. Aim To investigate the effects of introduction and withdrawal of financial incentives on the diagnosis of resolved AF. Design & setting Cohort study in a large database of UK primary care records, before and after introduction of incentives in April 2006 in Scotland, England, and Northern Ireland, and their withdrawal in April 2016 in Scotland. Method Interrupted time-series analysis of monthly rates of resolved AF from January 2000–September 2019. Results A total of 251 526 adult patients with AF were included, of whom 14 674 were diagnosed as resolved AF. In April 2006 there were similar shift-changes in rates of resolved AF per 1000 in England 1.55 (95% confidence interval [CI] = 1.11 to 2.00) and Northern Ireland 1.54 (95% CI = 0.91 to 2.18), and a smaller increase in Scotland 0.79 (95% CI = 0.04 to 1.53). There were modest downward post-introduction trends in all countries. After Scotland’s withdrawal of the incentive in April 2016 there was a small, statistically non-significant, downward shift in rate of resolved AF per 1000 (0.39 [95% CI = -3.21 to 2.42]) and no change in post-removal trend. Conclusion Introduction of a financial incentive coincided with an increase in resolved AF but no evidence was found that its withdrawal led to a reduction.
Genome Characterization of Gordonia Phage Amore2

Novel Gordonia phage Amore2 was isolated from Pittsburgh, Pennsylvania and infects Gordonia terrae 3612. Amore2 was placed into Actinobacteria cluster CS1. Its genome is 73,842 bp with 105 predicted open reading frames and 56.6% GC content. The closest similarity of Amore2 is Gordonia phage Austin, with a 98% nucleotide identity. ABSTRACT Novel Gordonia phage Amore2 was isolated from Pittsburgh, Pennsylvania and infects Gordonia terrae 3612. Amore2 was placed into Actinobacteria cluster CS1. Its genome is 73,842 bp with 105 predicted open reading frames and 56.6% GC content. The closest similarity of Amore2 is Gordonia phage Austin, with a 98% nucleotide identity.
Effect of thermal and ultrasonic pretreatment on lactic acid fermentation of food waste

Food waste (FW) generation has become one of the largest environmental concerns for human society. Thanks to its chemical features and its high biodegradability, FW can be used as starting platform to produce biocommodities. Lactic acid (LA) is one of those chemicals that is gaining the attention of industry and research for its important role in polylactic acids production. To exploit better the organic content of FW, several FW pretreatments have been proposed in the literature, though none of them were aimed at influencing LA fermentation. Thermal and ultrasonic pretreatment effects on solubilization rates and LA production yields have been investigated in this batch study. The highest solubilization rate was achieved with 30 minutes ultrasonic pretreated FW resulting in a 15% increment in soluble COD (sCOD). The highest LA yield was obtained after 90-minute thermal pretreatment at 80 and 100°C at a yield of 0.49 g LA•g COD−1. This study shows that ultrasonic pretreatment generally performed better than thermal pretreatment when considering the increase in sCOD but caused a reduction in LA concentrations and yields after fermentation with high production of ethanol. The opposite trend was recorded in the thermal pretreated incubations, in which LA was present for 50% of the sCOD with higher LA concentrations of 2.90 g COD•L−1.
Glitch recoveries in radio-pulsars and magnetars

Pulsar glitches are sudden increases in the spin frequency of an otherwise steadily spinning down neutron star. These events are thought to represent a direct probe of the dynamics of the superfluid interior of the star. However glitches can differ significantly from one another, not only in size and frequency, but also in the post-glitch response of the star. Some appear as simple steps in frequency, while others also display an increase in spin-down rate after the glitch. Others still show several exponentially relaxing components in the post-glitch recovery. We show that if glitches are indeed due to large-scale unpinning of superfluid vortices, the different regions in which this occurs and respective time-scales on which they recouple can lead to the various observed signatures. Furthermore, we show that this framework naturally accounts for the peculiar relaxations of glitches in Anomalous X-ray Pulsars.
A dynamic and expandable digital 3D-atlas maker for monitoring the temporal changes in tissue growth during hindbrain morphogenesis

Reconstruction of prototypic three-dimensional (3D) atlases at the scale of whole tissues or organs requires specific methods to be developed. We have established a digital 3D-atlas maker (DAMAKER) and built a digital 3D-atlas to monitor the changes in the growth of the neuronal differentiation domain in the zebrafish hindbrain upon time. DAMAKER integrates spatial and temporal data of cell populations, neuronal differentiation and brain morphogenesis, through in vivo imaging techniques paired with image analyses and segmentation tools. First, we generated a 3D-reference from several imaged hindbrains and segmented them using a trainable tool; these were aligned using rigid registration, revealing distribution of neuronal differentiation growth patterns along the axes. Second, we quantified the dynamic growth of the neuronal differentiation domain by in vivo neuronal birthdating experiments. We generated digital neuronal birthdating 3D-maps and revealed that the temporal order of neuronal differentiation prefigured the spatial distribution of neurons in the tissue, with an inner-outer differentiation gradient. Last, we applied it to specific differentiated neuronal populations such as glutamatergic and GABAergic neurons, as proof-of-concept that the digital birthdating 3D-maps could be used as a proxy to infer neuronal birthdate. As this protocol uses open-access tools and algorithms, it can be shared for standardized, accessible, tissue-wide cell population atlas construction.
VORTEX FORMATION AND EVOLUTION IN PLANET HARBORING DISKS UNDER THERMAL RELAXATION

We study the evolution of planet-induced vortices in radially stratified disks, with initial conditions allowing for radial buoyancy. For this purpose we run global two-dimensional hydrodynamical simulations, using the PLUTO code. Planet-induced vortices are a product of the Rossby wave instability (RWI) triggered in the edges of a planetary gap. In this work we assess the influence of radial buoyancy for the development of the vortices. We found that radial buoyancy leads to smoother planetary gaps, which generates weaker vortices. This effect is less pronounced for locally isothermal and quasi-isothermal (very small cooling rate) disks. We observed the formation of two generations of vortices. The first generation of vortices is formed in the outer wall of the planetary gap. The merged primary vortex induces accretion, depleting the mass on its orbit. This process creates a surface density enhancement beyond the primary vortex position. The second generation of vortices arise in this surface density enhancement, indicating that the bump in this region is sufficient to trigger the RWI. The merged secondary vortex is a promising explanation for the location of the vortex in the Oph IRS 48 system. Finally, we observed a nonmonotonic behavior for the vortex lifetimes as a function of the thermal relaxation timescale, agreeing with previous studies. The birth times of the secondary vortices also display a nonmonotonic behavior, which is correlated with the growth time of the primary vortex and its induced accretion.
Implementation of Quantum Computing Techniques on NMR Systems

This document is submitted as a partial requirement for the course Quantum Information and Computing, BITS Pilani. The phenomenon of NMR can be used to generate spin states of nuclei and these can be used as qubits for computational purposes, the speciality being, an ensemble of molecules must be utilized. According to [15], it is both the best, and the worst technologies in quantum computing, reasons being the ease at which unitary quantum gates can be implemented and the difficulty in exact measurements without disturbing the ensemble respectively.
THE MAGNETIC FIELD OF L1544. I. NEAR-INFRARED POLARIMETRY AND THE NON-UNIFORM ENVELOPE

The magnetic field (B-field) of the starless dark cloud L1544 has been studied using near-infrared (NIR) background starlight polarimetry (BSP) and archival data in order to characterize the properties of the plane-of-sky B-field. NIR linear polarization measurements of over 1700 stars were obtained in the H band and 201 of these were also measured in the K band. The NIR BSP properties are correlated with reddening, as traced using the Rayleigh–Jeans color excess (H–M) method, and with thermal dust emission from the L1544 cloud and envelope seen in Herschel maps. The NIR polarization position angles change at the location of the cloud and exhibit their lowest dispersion there, offering strong evidence that NIR polarization traces the plane-of-sky B-field of L1544. In this paper, the uniformity of the plane-of-sky B-field in the envelope region of L1544 is quantitatively assessed. This allows evaluation of the approach of assuming uniform field geometry when measuring relative mass-to-flux ratios in the cloud envelope and core based on averaging of the radio Zeeman observations in the envelope, as done by Crutcher et al. In L1544, the NIR BSP shows the envelope B-field to be significantly non-uniform and likely not suitable for averaging Zeeman properties without treating intrinsic variations. Deeper analyses of the NIR BSP and related data sets, including estimates of the B-field strength and testing how it varies with position and gas density, are the subjects of later papers in this series.
A Scanner Deeply: Predicting Gaze Heatmaps on Visualizations Using Crowdsourced Eye Movement Data

Visual perception is a key component of data visualization. Much prior empirical work uses eye movement as a proxy to understand human visual perception. Diverse apparatus and techniques have been proposed to collect eye movements, but there is still no optimal approach. In this paper, we review 30 prior works for collecting eye movements based on three axes: (1) the tracker technology used to measure eye movements; (2) the image stimulus shown to participants; and (3) the collection methodology used to gather the data. Based on this taxonomy, we employ a webcam-based eyetracking approach using task-specific visualizations as the stimulus. The low technology requirement means that virtually anyone can participate, thus enabling us to collect data at large scale using crowdsourcing: approximately 12,000 samples in total. Choosing visualization images as stimulus means that the eye movements will be specific to perceptual tasks associated with visualization. We use these data to propose a Scanner Deeply, a virtual eyetracker model that, given an image of a visualization, generates a gaze heatmap for that image. We employ a computationally efficient, yet powerful convolutional neural network for our model. We compare the results of our work with results from the DVS model and a neural network trained on the Salicon dataset. The analysis of our gaze patterns enables us to understand how users grasp the structure of visualized data. We also make our stimulus dataset of visualization images available as part of this paper's contribution.
Effect of biological DMARDs and JAK inhibitors in pain of chronic inflammatory arthritis

ABSTRACT Introduction The advent of biological disease‐modifying anti‐rheumatic drugs (bDMARDs) and, more recently, of Janus kinase inhibitors (JAKi) has had a major impact on the long-term outcomes of chronic inflammatory arthritis (IA). However, the persistence of pain, even in patients with a complete pharmacological control of peripheral inflammation, represents an important clinical challenge in the treatment of IA. Areas covered In this review, we provide an overview of possible mechanisms underlying pain in IA and its assessment, as well as the effects of bDMARDs and JAKi on pain management. Expert opinion The overall data showed a good effect of bDMARDs and JAKi on pain, which is more pronounced for JAKi. However, it is challenging to distinguish the effect on the different types of pain (nociceptive, neuropathic, and nociplastic).
Interstellar Hydrides

Interstellar hydrides – that is, molecules containing a single heavy element atom with one or more hydrogen atoms – were among the first molecules detected outside the solar system. They lie at the root of interstellar chemistry, being among the first species to form in initially-atomic gas, along with molecular hydrogen and its associated ions. Because the chemical pathways leading to the formation of interstellar hydrides are relatively simple, the analysis of the observed abundances is relatively straightforward and provides key information about the environments where hydrides are found. Recent years have seen rapid progress in our understanding of interstellar hydrides, thanks largely to far-IR and submillimeter observations performed with the Herschel Space Observatory. In this review, we will discuss observations of interstellar hydrides, along with the advanced modeling approaches that have been used to interpret them, and the unique information that has thereby been obtained. 1 ar X iv :1 60 1. 02 98 5v 1 [ as tr oph . G A ] 1 2 Ja n 20 16