Miracle-dz/UniFAR-FTUs huggingface dataset:
A Compression Algorithm for DNA Sequences Using Approximate Matching for Better Compression Ratio to Reveal the True Characteristics of DNA

to be counted on. This requires a better model for computing the DNA content such that better data compression results can be achieved. In fact, it is our purpose to r eveal s uch s ubtleties, s uch a s crossover and mutation, in DNA sequences by using a more appropriate compression algorithm. In this article, we will present a DNA compression algorithm, GenCompress, based on approximate matching that gives the best compression results on standard benchmark DNA sequences. We will present t he d esign r ationale o f GenCompress based on approximate matching, discuss details of the algorithm, provide experimental results, and compare the results with the two most effective compression algorithms for DNA sequences (Biocompress-2 and Cfact).
An anti-amyloid therapy works for Alzheimer’s disease: why has it taken so long and what is next?

Hardy and Mummery discuss the recent positive findings in the clinical trial of lecanemab in early Alzheimer’s disease, and the implications for the amyloid hypothesis. They argue that the results mark a turning point for the Alzheimer’s field, but that taking anti-amyloid therapies into clinical practice will be challenging.
Proton auroral intensification induced by interplanetary shock on 7 November 2004

We report a shock-induced auroral intensification event observed by the IMAGE spacecraft on 7 November 2004. The comparison of simultaneous auroral snapshots, obtained from FUV-SI12 and FUV-SI13 cameras onboard IMAGE spacecraft, indicates the dominance of proton precipitation (rather than electron precipitation) throughout the auroral oval region. The proton aurora in the postnoon sector showed the most significant intensification, with luminosity increasing by 5 times or more. We describe the main characteristics of interplanetary parameters observed by the ACE and Geotail satellites and plasma parameters within the mapped precipitation region detected by the Los Alamos National Laboratory 1990-1995 satellite. The generation mechanism of postnoon proton auroral intensification is further investigated on the basis of these observations. The estimated increase of loss cone size was not enough to produce the required proton auroral precipitation enhancement. The expected oxygen band electromagnetic ion cyclotron waves (no available observation), in the highly fluctuating density region during the shock period, might contribute to the enhanced precipitation of auroral protons. Our new finding is that the shock-driven buildup of 1-10 keV proton fluxes could account for the observed proton auroral intensification.
The association between adverse events of COVID-19 vaccination and anxiety and willingness to receive a booster dose

ABSTRACT Many countries have initiated a booster dose for COVID-19 vaccination. However, little is known about the association between adverse events to vaccination and individual psychological status and willingness to receive the booster dose. From December 1, 2021 to February 1, 2022, 474 participants answered a questionnaire in a university town in China, and information about previous adverse events, anxiety status, and vaccination intention were collected. Chi-square test and logistic regression models were used to analyze the factors associated with willingness to receive booster dose of vaccine. Previous adverse events, such as pain at the injection site, fatigue, muscle pain and headache were associated with anxiety of the participants. About 76.2% of the participants were willing to receive booster dose of vaccine. However, adverse event was not associated with their willingness to receive the booster dose. Participants with age ≤25 were less willing to receive the booster dose, although the association was not statistically significant in the multivariable model. In conclusion, the adverse events of COVID-19 vaccination were associated with psychology status of the vaccinated people. It is still necessary to strengthen the public education on COVID-19 vaccination to improve the vaccination willingness of people, especially among the young people.
Phylogenetic patterns in regional flea assemblages from 6 biogeographic realms: strong links between flea and host phylogenetic turnovers and weak effects of phylogenetic originality on host specificity

Abstract Abstract We investigated phylogenetic patterns in flea assemblages from 80 regions in 6 biogeographic realms and asked whether (a) flea phylogenetic turnover is driven by host phylogenetic turnover, environmental dissimilarity or geographic distance; (b) the relative importance of these drivers differs between realms; and (c) the environmental drivers of flea phylogenetic turnover are similar to those of host phylogenetic turnover. We also asked whether the phylogenetic originality of a flea species correlates with the degree of its host specificity and whether the phylogenetic originality of a host species correlates with the diversity of its flea assemblages. We found that host phylogenetic turnover was the best predictor of flea phylogenetic turnover in all realms, whereas the effect of the environment was weaker. Environmental predictors of flea phylogenetic turnover differed between realms. The importance of spatial distances as a predictor of the phylogenetic dissimilarity between regional assemblages varied between realms. The responses of host turnover differed from those of fleas. In 4 of the 6 realms, geographic distances were substantially better predictors of host phylogenetic turnover than environmental gradients. We also found no general relationship between flea phylogenetic originality and its host specificity in terms of either host species richness or host phylogenetic diversity. We conclude that flea phylogenetic turnover is determined mainly by the phylogenetic turnover of their hosts rather than by environmental gradients. Phylogenetic patterns in fleas are manifested at the level of regional assemblages rather than at the level of individual species.
Biochemical characteristics of Myceliophthora thermophila recombinant β-glucosidase (MtBgl3c) applicable in cellulose bioconversion

Abstract The GH3 β-glucosidase gene of Myceliophthora thermophila (MtBgl3c) has been cloned and heterologously expressed in E. coli for the first time. This study highlights the important characteristics of recombinant MtBgl3c (rMtBgl3c) which make it a promising candidate in industrial applications. Optimization of the production of rMtBgl3c led to 28,000 U L−1. On purification, it has a molecular mass of ∼100 kDa. It is a broad substrate specific thermostable enzyme that exhibits pH and temperature optima at 5.0 and 55 °C, respectively. The amino acid residues Asp287 and Glu514 act as nucleophile and catalytic acid/base, respectively in the enzyme catalysis. Its low Km value (1.28 mM) indicates a high substrate affinity as compared to those previously reported. The rMtBgl3c displays a synergistic action with the commercial enzyme cocktail in the saccharification of sugarcane bagasse suggesting its utility in the cellulose bioconversion. Tolerance to solvents, detergents as well as glucose make this enzyme applicable in wine, detergent, paper and textile industries too.
A COSMOS study of the structure and content of NGC 6822

A COSMOS survey of deep Schmidt plates in four colors is used to examine the distribution of stars and unresolved light in the local group dwarf irregular galaxy NGC 6822. Global color-magnitude diagrams and luminosity functions are derived from background-subtracted data. These show more clearly than previous studies the prominence of the main sequence and the comparatively small number of red giants. Maps of stars separated by magnitude and by color, as well as CMDs for various areas, show a wide range in recent histories of star formation over the image.
Chronic Pain and Health Related Quality of Life Assessment One Year After Total Knee Arthroplasty.

OBJECTIVE To assess chronic pain prevalence, health related quality of life (HRQOL), and factors associated with HRQOL in patients at least one year after total knee arthrosplasty (TKA). STUDY DESIGN Descriptive study. PLACE AND DURATION OF STUDY Sancaktepe Martyr Prof. Dr. Ilhan Varank Education and Training Hospital, between June 2019 and June 2021. METHODOLOGY Patients, who had undergone elective TKA operation for the first time were included in the study. The identified patients were contacted by phone and asked to complete questionnaires including short form 12 version 2 (SF-12 v2) for HRQOL, having components, physical (PCS) and mental health score (MCS). Demographic and perioperative data were collected by reviewing the patients' medical records retrospectively. RESULTS Of the 122 selected patients, 105 (86%) patients accepted to take survey via telephone. According to MCS scores, all patients showed good mental health. Patients were classified according to their PCS; into low HRQOL (Group L, n=42) and high HRQOL (Group H, n=63). Six percent of patients had chronic pain and 60% had high HRQOL after TKA. Age, body mass index (BMI), and chronic obstructive pulmonary disease (COPD) were significantly higher in Group L. Postoperative numerical rating scale (NRS, p=0.007) and dolour neuropathic pain score (DN4, p=0.002) were significantly different between both groups. CONCLUSION Older age, high BMI, COPD, postoperative chronic pain, and postoperative neuropathic pain were associated with HRQOL after TKA. KEY WORDS Arthroplasty, Replacement, Knee, Pain, postoperative, Chronic pain, Neuralgia, Quality of Life.
Prolonged administration of a secretin receptor antagonist inhibits biliary senescence and liver fibrosis in Mdr2−/− mice

Background and Aims: Secretin (SCT) and secretin receptor (SR, only expressed on cholangiocytes within the liver) play key roles in modulating liver phenotypes. Forkhead box A2 (FoxA2) is required for normal bile duct homeostasis by preventing the excess of cholangiocyte proliferation. Short-term administration of the SR antagonist (SCT 5–27) decreased ductular reaction and liver fibrosis in bile duct ligated and Mdr2−/− [primary sclerosing cholangitis (PSC), model] mice. We aimed to evaluate the effectiveness and risks of long-term SCT 5–27 treatment in Mdr2−/− mice. Approach and Results: In vivo studies were performed in male wild-type and Mdr2−/− mice treated with saline or SCT 5–27 for 3 months and human samples from late-stage PSC patients and healthy controls. Compared with controls, biliary SCT/SR expression and SCT serum levels increased in Mdr2−/− mice and late-stage PSC patients. There was a significant increase in ductular reaction, biliary senescence, liver inflammation, angiogenesis, fibrosis, biliary expression of TGF-β1/VEGF-A axis, and biliary phosphorylation of protein kinase A and ERK1/2 in Mdr2−/− mice. The biliary expression of miR-125b and FoxA2 decreased in Mdr2−/− compared with wild-type mice, which was reversed by long-term SCT 5–27 treatment. In vitro, SCT 5–27 treatment of a human biliary PSC cell line decreased proliferation and senescence and SR/TGF-β1/VEGF-A axis but increased the expression of miR-125b and FoxA2. Downregulation of FoxA2 prevented SCT 5–27–induced reduction in biliary damage, whereas overexpression of FoxA2 reduced proliferation and senescence in the human PSC cell line. Conclusions: Modulating the SCT/SR axis may be critical for managing PSC.
Age‐related changes to adipose tissue and peripheral neuropathy in genetically diverse HET3 mice differ by sex and are not mitigated by rapamycin longevity treatment

Neural communication between the brain and adipose tissues regulates energy expenditure and metabolism through modulation of adipose tissue functions. We have recently demonstrated that under pathophysiological conditions (obesity, diabetes, and aging), total subcutaneous white adipose tissue (scWAT) innervation is decreased (‘adipose neuropathy’). With advanced age in the C57BL/6J mouse, small fiber peripheral nerve endings in adipose tissue die back, resulting in reduced contact with adipose‐resident blood vessels and other cells. This vascular neuropathy and parenchymal neuropathy together likely pose a physiological challenge for tissue function. In the current work, we used the genetically diverse HET3 mouse model to investigate the incidence of peripheral neuropathy and adipose tissue dysregulation across several ages in both male and female mice. We also investigated the anti‐aging treatment rapamycin, an mTOR inhibitor, as a means to prevent or reduce adipose neuropathy. We found that HET3 mice displayed a reduced neuropathy phenotype compared to inbred C56BL/6 J mice, indicating genetic contributions to this aging phenotype. Compared to female HET3 mice, male HET3 mice had worse neuropathic phenotypes by 62 weeks of age. Female HET3 mice appeared to have increased protection from neuropathy until advanced age (126 weeks), after reproductive senescence. We found that rapamycin overall had little impact on neuropathy measures, and actually worsened adipose tissue inflammation and fibrosis. Despite its success as a longevity treatment in mice, higher doses and longer delivery paradigms for rapamycin may lead to a disconnect between life span and beneficial health outcomes.
Sex and Season Affect Cortical Volumes in Free-Living Western Fence Lizards, Sceloporus occidentalis

The hippocampus plays an important role in spatial navigation and spatial learning across a variety of vertebrate species. Sex and seasonal differences in space use and behavior are known to affect hippocampal volume. Similarly, territoriality and differences in home range size are known to affect the volume of the reptile hippocampal homologues, the medial and dorsal cortices (MC, DC). However, studies have almost exclusively investigated males and little is known about sex or seasonal differences in MC and/or DC volumes in lizards. Here, we are the first to simultaneously examine sex and seasonal differences in MC and DC volumes in a wild lizard population. In Sceloporus occidentalis, males display territorial behaviors that are more pronounced during the breeding season. Given this sex difference in behavioral ecology, we expected males to have larger MC and/or DC volumes than females and for this difference to be most pronounced during the breeding season when territorial behavior is increased. Male and female S. occidentalis were captured from the wild during the breeding season and the post-breeding season and were sacrificed within 2 days of capture. Brains were collected and processed for histology. Cresyl-violet-stained sections were used to quantify brain region volumes. In these lizards, breeding females had larger DC volumes than breeding males and nonbreeding females. There was no sex or seasonal difference in MC volumes. Differences in spatial navigation in these lizards may involve aspects of spatial memory related to breeding other than territoriality that affect plasticity of the DC. This study highlights the importance of investigating sex differences and including females in studies of spatial ecology and neuroplasticity.
Broad protective vaccination against systemic Escherichia coli with autotransporter antigens

Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading cause of adult life-threatening sepsis and urinary tract infections (UTI). The emergence and spread of multidrug-resistant (MDR) ExPEC strains result in a considerable amount of treatment failure and hospitalization costs, and contribute to the spread of drug resistance amongst the human microbiome. Thus, an effective vaccine against ExPEC would reduce morbidity and mortality and possibly decrease carriage in healthy or diseased populations. A comparative genomic analysis demonstrated a gene encoding an invasin-like protein, termed sinH, annotated as an autotransporter protein, shows high prevalence in various invasive ExPEC phylogroups, especially those associated with systemic bacteremia and UTI. Here, we evaluated the protective efficacy and immunogenicity of a recombinant SinH-based vaccine consisting of either domain-3 or domains-1,2, and 3 of the putative extracellular region of surface-localized SinH. Immunization of a murine host with SinH-based antigens elicited significant protection against various strains of the pandemic ExPEC sequence type 131 (ST131) as well as multiple sequence types in two distinct models of infection (colonization and bacteremia). SinH immunization also provided significant protection against ExPEC colonization in the bladder in an acute UTI model. Immunized cohorts produced significantly higher levels of vaccine-specific serum IgG and urinary IgG and IgA, findings consistent with mucosal protection. Collectively, these results demonstrate that autotransporter antigens such as SinH may constitute promising ExPEC phylogroup-specific and sequence-type effective vaccine targets that reduce E. coli colonization and virulence.
A qualitative peptide biomarker approach to identify piscine gelatine in products to support food security

Abstract Due to allergy concerns, it is mandatory under EU law to declare in food products all ingredients derived from fish. Gelatine is prepared from the waste collagen of animal carcasses, including piscine, bovine and porcine materials, and is an ingredient in a wide range of foods. The Elliott Review into the integrity and assurance of food supply networks highlighted requirements for analytical surveillance methods to support due diligence, food safety and authenticity. We present the development of a method to extract gelatine from foods and determine the presence of piscine gelatine by liquid chromatography-tandem mass spectrometry using a suite of sixteen piscine marker peptides. The method has been successfully applied to gelatine granules, capsules and composite retail food products. While a study is required to determine parameters including the limit of detection of this method, the data indicate the method is reproducible between replicates of sub-samples and applies to a range of piscine gelatines collected over 16 years. Once validation studies are complete, there is potential for enforcement officers to apply the technology to verify the authenticity of fish products to support consumers in ensuring food safety and also food provenance relating to animal origin.
Preparing for Reality: A Randomized Trial on Immersive Virtual Reality for Bronchoscopy Training

Background: Bronchoscopy is an essential procedure in the diagnosis and treatment of pulmonary diseases. However, the literature suggests that distractions affect the quality of bronchoscopy and affect inexperienced doctors more than experienced. Objectives: The objective of the study was as follows: does simulation-based bronchoscopy training with immersive virtual reality (iVR) improve the doctors’ ability to handle distractions and thereby increase the quality, measured in procedure time, structured progression score, diagnostic completeness (%), and hand motor movements of a diagnostic bronchoscopy in a simulated scenario. Exploratory outcomes were heart rate variability and a cognitive load questionnaire (Surg-TLX). Methods: Participants were randomized. The intervention group practiced in an iVR environment with a head-mounted display (HMD) while using the bronchoscopy simulator, while the control group trained without the HMD. Both groups were tested in the iVR environment using a scenario with distractions. Results: 34 participants completed the trial. The intervention group scored significantly higher in diagnostic completeness (100 i.q.r. 100–100 vs. 94 i.q.r. 89–100, p value = 0.03) and structured progress (16 i.q.r. 15–18 vs. 12 i.q.r. 11–15, p value 0.03) but not in procedure time (367 s standard deviation [SD] 149 vs. 445 s SD 219, p value = 0.06) or hand motor movements (−1.02 i.q.r. −1.03–[−1.02] versus −0.98 i.q.r. −1.02–[–0.98], p value = 0.27). The control group had a tendency toward a lower heart rate variability (5.76 i.q.r. 3.77–9.06 vs. 4.12 i.q.r. 2.68–6.27, p = 0.25). There was no significant difference in total Surg-TLX points between the two groups. Conclusion: iVR simulation training increases the quality of diagnostic bronchoscopy in a simulated scenario with distractions compared with conventional simulation-based training.
Ranolazine exerts atrial antiarrhythmic effects in a rat model of monocrotaline‐induced pulmonary hypertension

Atrial arrhythmias are a hallmark of heart diseases. The antiarrhythmic drug ranolazine with multichannel blocker properties is a promising agent to treat atrial arrhythmias. We therefore used the rat model of monocrotaline‐induced pulmonary‐hypertension to assess whether ranolazine can reduce the incidence of ex vivo atrial arrhythmias in isolated right atrium. Four‐week‐old Wistar rats were injected with 50 mg/kg of monocrotaline, and isolated right atrium function was studied 14 days later. The heart developed right atrium and right ventricular hypertrophy, and the ECG showed an increased P wave duration and QT interval, which are markers of the disease. Moreover, monocrotaline injection caused enhanced chronotropism and faster kinetics of contraction and relaxation in isolated right atrium. Additionally, in a concentration‐dependent manner, ranolazine showed chronotropic and ionotropic effects upon isolated right atrium, with higher potency in the control when compared with experimental model. Using a burst pacing protocol, the isolated right atrium from the monocrotaline‐treated animals was more susceptible to develop arrhythmias, and ranolazine was able to attenuate the phenotype. Thus, we concluded that the rat model of monocrotaline‐induced pulmonary‐hypertension develops right atrium remodelling, which increased the susceptibility to present ex vivo atrial arrhythmias, and the antiarrhythmic drug ranolazine ameliorated the phenotype.
Imaging through fog and rain

The main aerosol effect on imaging performance is brightness reduction through scattering losses. This is fairly well understood and modeled. However, one phenomenon that is almost always overlooked is the blurring of images that can result from forward-scattered radiation, i.e., the radiation reaching the image plane after being scattered by airborne particles. The paper describes a new and efficient method of calculation of the forward-scattering effect on the point spread and modulation transfer functions. Solutions are presented that show the dependence of the aerosol blurring effect on particle concentration, particle size, geometry, and size of object features. The paper also reports on a simple experiment for measuring the visible point spread function through fog and rain. In most cases, the measurements are in good agreement with the model predictions. As it turns out, our measurements performed at ranges of 500 and 900 m and optical depths of up to seven show significant aerosol blurring effects only for rain and for some advection fogs with a sufficient number of particles in the size range of about 100 μm.
Associations Between ADHD, Sleep Problems, and Mental Health Symptoms in Adolescents

Objective: This study examined associations between objective and subjective sleep parameters, and mental health symptoms (internalizing symptoms, externalizing symptoms, and irritability) and whether these relationships differed for adolescents with and without ADHD. Method: Participants were 373 adolescents aged 10 to 19 years (M = 13.21, SD = 2.37). Sleep was measured both via actigraphy and self- and parent-report scales. Mental health symptoms were measured via a range of validated measures. Results: Few relationships were detected when examining actigraphy variables. Subjective sleep parameters were associated with almost all mental health variables. Some relationships were moderated by ADHD status, generally consistent with stronger relationships between subjective sleep quality and mental health in the non-ADHD group. Conclusion: Sleep problems, particularly subjective difficulties, are associated with a range of mental health outcomes, regardless of the presence of ADHD. Sleep problems may be a beneficial intervention target for adolescents experiencing mental health issues.