Miracle-dz/UniFAR-FTUs huggingface dataset:
Shared and specific biological signalling pathways for diabetic retinopathy, peripheral neuropathy and nephropathy by high-throughput sequencing analysis

Objectives We aimed to explore the shared and specific signalling pathways involved in diabetic retinopathy (DR), diabetic peripheral neuropathy (DPN) and diabetic nephropathy (DN). Methods Differentially expressed mRNAs and lncRNAs were identified by high-throughput sequencing. Subsequently, functional enrichment analysis, protein-protein interaction (PPI) analysis and lncRNAs-mRNAs networks were conducted to determine the pathogenic mechanisms underlying DR, DPN and DN. Results Twenty-six biological pathways were shared among DR, DPN and DN groups compared to the type 2 diabetes mellitus (T2DM) group without complications, and most of the shared pathways and core proteins were involved in immune and inflammatory responses of microvascular damage. Cytokine‒cytokine receptor interactions and chemokine signalling pathway were the most significant and specific pathways for DR, and the lncRNA‒mRNA regulatory networks affected DR by targeting these pathways. Sphingolipid metabolism and neuroactive ligand-receptor pathways were found to be specific for the pathogenesis of DPN. Moreover, multiple amino acid metabolic pathways were involved in the occurrence and progression of DN. Conclusions Diabetic retinopathy, DPN and DN exhibited commonality and heterogeneity simultaneously. The shared pathologic mechanisms underlying these diabetic complications are involved in diabetic microvascular damage via immune and inflammatory pathways. Our findings predict several biomarkers and therapeutic targets for these diabetic complications.
Image-Based Sexual Abuse as a Means of Coercive Control: Victim-Survivor Experiences

Scholars and practitioners increasingly acknowledge the ways that abusive partners create, distribute, or threaten to distribute intimate images without consent, yet little empirical research has comprehensively explored image-based sexual abuse within intimate partner contexts. This article responds to this gap and reports on the findings of a study involving interviews with 29 women and one gender-diverse person who experienced image-based sexual abuse as part of a pattern of “coercive control. ” The authors argue that abusive partners use intimate imagery as a means of exerting power and control, and as a tactic of intimidation, entrapment, and degradation. They note that law, policy, and practice responses should recognize the gendered nature of image-based sexual abuse and its growing use as a means of coercive control.
Effects of hydrogen peroxide and calcium hypochlorite on chemical oxygen demand solubilization and disintegration of waste activated sludge by electro-chemical pretreatment

ABSTRACT The combination of electrochemical (EC) pretreatment with hydrogen peroxide (HP) and calcium hypochlorite (CHC) was investigated in this study for their effect on soluble chemical oxygen demand (CODs) and disintegration degree (DD) of waste activated sludge (WAS). For this aim, response surface methodology (RSM) and Box–Behnken design (BBD) were applied the determination of the optimum operational conditions. Operational conditions were varied between 0.2 and 2.0 mmol/g SS for HP and CHC dosages, 1–5 A for the applied current, 2–10 for the initial pH, and 15–45 min for the treatment time. Obtained results for each treatment were accurate and significant with correlation coefficients (R2) of 0.8639% and 0.9189% for EC combined with HP pretreatment and EC combined with CHC pretreatment, respectively. According to the obtained results, CODs increased in comparison to the raw sludge (168 mg/L) noting that CODs for EC – CHC (1155 ± 21 mg/L) was higher than EC – HP (811.5 ± 15 mg/L) at optimized conditions (for EC-HP pretreatment: HP dosage: 0.34 mmol/g TSS, Applied current:5 A, Initial pH:10, Time: 45 min, For EC-CHC pretreatment: CHC dosage: 0.23 mmol/g TSS, Applied current:4.83 A, Initial pH:10, Time: 40 min). Besides, the DD in terms of COD, total nitrogen (TN) and total organic carbon (TOC) (DDCOD, DDTN and DDTOC) registered increased values after the application of the EC treatment with both oxidants. The highest DDCOD, DDTN and DDTOC values were obtained with EC-CHC pretreatment for 11.34%, 20.34% and 9.18% respectively compared to EC-HP pretreatment (DDCOD: 7.37%, DDTN: 15.18% and DDTOC: 6.94%). GRAPHICAL ABSTRACT
Lint‐O cooperates with L(3)mbt in target gene suppression to maintain homeostasis in fly ovary and brain

Loss‐of‐function mutations in Drosophila lethal(3)malignant brain tumor [l(3)mbt] cause ectopic expression of germline genes and brain tumors. Loss of L(3)mbt function in ovarian somatic cells (OSCs) aberrantly activates germ‐specific piRNA amplification and leads to infertility. However, the underlying mechanism remains unclear. Here, ChIP‐seq for L(3)mbt in cultured OSCs and RNA‐seq before and after L(3)mbt depletion shows that L(3)mbt genomic binding is not necessarily linked to gene regulation and that L(3)mbt controls piRNA pathway genes in multiple ways. Lack of known L(3)mbt co‐repressors, such as Lint‐1, has little effect on the levels of piRNA amplifiers. Identification of L(3)mbt interactors in OSCs and subsequent analysis reveals CG2662 as a novel co‐regulator of L(3)mbt, termed “L(3)mbt interactor in OSCs” (Lint‐O). Most of the L(3)mbt‐bound piRNA amplifier genes are also bound by Lint‐O in a similar fashion. Loss of Lint‐O impacts the levels of piRNA amplifiers, similar to the lack of L(3)mbt. The lint‐O‐deficient flies exhibit female sterility and tumorous brains. Thus, L(3)mbt and its novel co‐suppressor Lint‐O cooperate in suppressing target genes to maintain homeostasis in the ovary and brain.
Tau target identification reveals NSF‐dependent effects on AMPA receptor trafficking and memory formation

Microtubule‐associated protein tau is a central factor in Alzheimer's disease and other tauopathies. However, the physiological functions of tau are unclear. Here, we used proximity‐labelling proteomics to chart tau interactomes in primary neurons and mouse brains in vivo. Tau interactors map onto pathways of cytoskeletal, synaptic vesicle and postsynaptic receptor regulation and show significant enrichment for Parkinson's, Alzheimer's and prion disease. We find that tau interacts with and dose‐dependently reduces the activity of N‐ethylmaleimide sensitive fusion protein (NSF), a vesicular ATPase essential for AMPA‐type glutamate receptor (AMPAR) trafficking. Tau‐deficient (tau−/−) neurons showed mislocalised expression of NSF and enhanced synaptic AMPAR surface levels, reversible through the expression of human tau or inhibition of NSF. Consequently, enhanced AMPAR‐mediated associative and object recognition memory in tau−/− mice is suppressed by both hippocampal tau and infusion with an NSF‐inhibiting peptide. Pathologic mutant tau from mouse models or Alzheimer's disease significantly enhances NSF inhibition. Our results map neuronal tau interactomes and delineate a functional link of tau with NSF in plasticity‐associated AMPAR‐trafficking and memory.
A BAYESIAN VIEW ON FARADAY ROTATION MAPS-SEEING THE MAGNETIC POWER SPECTRUM IN CLUSTERS OF GALAXIES

Magnetic fields are an important ingredient of galaxy clusters and are indirectly observed on cluster scales as radio haloes and radio relics. One promising method to shed light on the properties of cluster wide magnetic fields is the analysis of Faraday rotation maps of extended extragalactic radio sources. We developed a Fourier analysis for such Faraday rotation maps in order to determine the magnetic power spectra of cluster fields. In an advanced step, here we apply a Bayesian maximum likelihood method to the RM map of the north lobe of Hydra A on the basis of our Fourier analysis and derive the power spectrum of the cluster magnetic field. For Hydra A, we measure a spectral index of -5/3 over at least one order of magnitude implying Kolmogorov type turbulence. We find a dominant scale of about 3 kpc on which the magnetic power is concentrated, since the magnetic autocorrelation length is ${\lambda}_B
RRAP: RPKM Recruitment Analysis Pipeline

A common method for quantifying microbial abundances in situ is through metagenomic read recruitment to genomes and normalizing read counts as reads per kilobase (of genome) per million (bases of recruited sequences) (RPKM). We created RRAP (RPKM Recruitment Analysis Pipeline), a wrapper that automates this process using Bowtie2 and SAMtools. ABSTRACT A common method for quantifying microbial abundances in situ is through metagenomic read recruitment to genomes and normalizing read counts as reads per kilobase (of genome) per million (bases of recruited sequences) (RPKM). We created RRAP (RPKM Recruitment Analysis Pipeline), a wrapper that automates this process using Bowtie2 and SAMtools.
Biomechanical Comparison of Fiber Tape Device Versus Transarticular Screws for Ligamentous Lisfranc Injury in a Cadaveric Model

Background: The preferred method of fixation and surgical treatment for ligamentous Lisfranc injuries is controversial. Transarticular screws, bridge plating, fusion, and flexible fixation have been described, yet none have demonstrated superiority. Furthermore, screw fixation and plating often require secondary surgery to remove implants, leading surgeons to seek alternative fixation methods. Purpose: To compare transarticular screws and a fiber tape construct under a spectrum of biomechanical loads by evaluating the diastasis at 3 joints in the Lisfranc complex. Study Design: Controlled laboratory study. Methods: Eight matched pairs of fresh, previously frozen lower extremity cadaveric specimens were fixed with either 2 cannulated transarticular crossed screws or a fiber tape construct with a supplemental intercuneiform limb. The diastasis between bones was measured at 3 midfoot joints in the Lisfranc complex: the Lisfranc articulation, the second tarsometatarsal joint, and the intercuneiform joint. Measurements were obtained for the preinjured, injured, and fixation conditions under static loading at 50% donor body weight. Specimens then underwent cyclic loading performed at 1 Hz and 100 cycles, based on 100-N stepwise increases in ground-reaction force from 100 to 2000 N, to simulate postoperative loading from the partial weightbearing stage to high-energy activities. Failure of fixation was defined as diastasis ≥2 mm at the Lisfranc articulation (second metatarsal–medial cuneiform joint). Results: There were no significant differences in diastasis detected at the Lisfranc articulation or the intercuneiform joint throughout all loading cycles between groups. All specimens endured loading up to 50% body weight + 1400 N. Up to and including this stage, there were 2 failures in the cannulated transarticular crossed-screw group and none in the fiber tape group. Conclusion: The fiber tape construct with a supplemental intercuneiform limb, which does not require later removal, may provide comparable biomechanical stability to cannulated transarticular crossed screws, even at higher loads. Clinical Relevance: Ligamentous Lisfranc injuries are common among athletes. Therefore, biomechanical evaluations are necessary to determine stable constructs that can limit the time to return to play. This study compares the biomechanical stability of 2 methods of fixation for ligamentous injury through a wide spectrum of loading, including those experienced by athletes.
Total-body PET: a new paradigm for molecular imaging.

Total body (TB) PET instruments have dramatically changed the paradigm of PET clinical and research studies. We consider TB-PET instruments to be those with an axial field-of-view (AFOV) of at least 60 cm so that these instruments not only have very high sensitivity compared with instruments of standard AFOV (< 30 cm), but also have the capability to image dynamic radiopharmaceutical distributions in the major organs of the body simultaneously. TB-PET instruments have only been in use since 2018, and it is remarkable how much interest has been created in that short time in both clinical and research settings. In this manuscript, we review the design and performance of these systems, noting common features, as well as differences. We also discuss general challenges and trade-offs to maximize the performance gains of TB-PET systems. We consider these new instruments to be the first generation of a new category of PET design and discuss some areas where we expect improvements and refinements in the coming years. The manuscript then summarizes what has been learned from the initial sites with TB-PET and explores potential research and clinical applications of TB-PET.
White matter microstructure and longitudinal relaxation time anisotropy in human brain at 3 and 7 T

A high degree of structural order by white matter (WM) fibre tracts creates a physicochemical environment where water relaxations are rendered anisotropic. Recently, angularly dependent longitudinal relaxation has been reported in human WM. We have characterised interrelationships between T1 relaxation and diffusion MRI microstructural indices at 3 and 7 T. Eleven volunteers consented to participate in the study. Multishell diffusion MR images were acquired with b‐values of 0/1500/3000 and 0/1000/2000 s/mm2 at 1.5 and 1.05 mm3 isotropic resolutions at 3 and 7 T, respectively. DTIFIT was used to compute DTI indices; the fibre‐to‐field angle (θFB) maps were obtained using the principal eigenvector images. The orientations and volume fractions of multiple fibre populations were estimated using BedpostX in FSL, and the orientation dispersion index (ODI) was estimated using the NODDI protocol. MP2RAGE was used to acquire images for T1 maps at 1.0 and 0.9 mm3 isotropic resolutions at 3 and 7 T, respectively. At 3 T, T1 as a function of θFB in WM with high fractional anisotropy and one‐fibre orientation volume fraction or low ODI shows a broad peak centred at 50o, but a flat baseline at 0o and 90o. The broad peak amounted up to 7% of the mean T1. At 7 T, the broad peak appeared at 40o and T1 in fibres running parallel to B0 was longer by up to 75 ms (8.3% of the mean T1) than in those perpendicular to the field. The peak at 40o was approximately 5% of mean T1 (i.e., proportionally smaller than that at 54o at 3 T). The data demonstrate T1 anisotropy in WM with high microstructural order at both fields. The angular patterns are indicative of the B0‐dependency of T1 anisotropy. Thus myelinated WM fibres influence T1 contrast both by acting as a T1 contrast agent and rendering T1 dependent on fibre orientation with B0.
Complete Genome Sequence of a Suckermouth Catfish Outbreak Isolate, Aeromonas hydrophila Strain LP0103

Aeromonas hydrophila is the most common opportunistic pathogen that plagues freshwater and euryhaline fishponds. Here, we present the complete genome sequence of A. hydrophila strain LP0103, which was isolated from a bacterial septicemia outbreak among suckermouth catfish (Pterygoplichthys pardalis) at Lotus Pond in Kaohsiung City, Taiwan. ABSTRACT Aeromonas hydrophila is the most common opportunistic pathogen that plagues freshwater and euryhaline fishponds. Here, we present the complete genome sequence of A. hydrophila strain LP0103, which was isolated from a bacterial septicemia outbreak among suckermouth catfish (Pterygoplichthys pardalis) at Lotus Pond in Kaohsiung City, Taiwan.
Gamma2, GammalA, and GammalM Antinuclear Factors in Human Sera *

The term "immunoglobulin" is used to refer to one or more of the three classes of serum protein, gammalA, gammaim, and gamma2, each of which is known to contain antibodies. The 7yAand y1Mimmunoglobulins have also been referred to as beta2A and beta2M, their electrophoretic mobilities being intermediate between the principal gamma and beta peaks in serum protein electrophoresis. ylA-globulin, like Y2-globulin, is approximately 7 S in its ultracentrifugal characteristics, but differs significantly from 'y2-globulin by other chemical and immunochemical criteria. ylM-globulin is a macro-gamma globulin that has an ultracentrifugation sedimentation coefficient of approximately 19 S. Determination of the immunochemical class of globulins responsible for the various autoreactivities found in various diseases may be important for our better understanding of the mechanisms of disease. The antinuclear factors (ANF), which are apparently autoantibodies to nuclear constituents, are found in the sera of patients with systemic lupus erythematosus (LE) and less frequently in other so-called connective tissue diseases, particularly rheumatoid arthritis (RA). Goodman, Fahey, and Malmgren (1) characterized ANF in two LE sera as globulins of both 7 S and 19 S type. Baum and Ziff (2) showed that ANF in LE sera were eluted from DEAE cellulose both
Animal welfare for wild herbivore management

This thesis describes an approach for scientific assessment of animal welfare relevant to the management of wild herbivores. The research identifies animal welfare risks and uses quantified animal-based measures to examine welfare outcomes. The requirement for evidence-based approaches is emphasised, particularly through transparent, independent assessments. The thesis is presented as a series of case studies assessing a variety of management techniques (lethal and non-lethal) applied to wild Australian herbivores. Case study species include European rabbits, feral horses, free-ranging cattle, and eastern grey kangaroos. Management techniques examined include ground-based and helicopter-based shooting, chemical immobilisation and fertility control. Quantifying the duration of stress experienced by animals and the frequency of adverse animal welfare events for several management techniques permitted robust welfare assessment and comparison. Analysis of large datasets of animal-based measures allowed identification of explanatory variables (e.g. the skill of shooters) that may influence welfare outcomes. Limitations were identified for approaches currently used to assess welfare impacts, particularly for wildlife fertility control. An improved welfare assessment framework was developed that emphasised consideration of positive welfare states and the importance of natural behaviour. Animal welfare regulation was examined, and limitations were identified for a popular approach in wildlife management, use of procedural documents. Two key recommendations are made for future studies in this field. Firstly, animal welfare assessment should be evidence-based and outcomes should be quantified using animalbased measures, rather than the eminence-based subjectivity inherent in deeming practices to be either humane or inhumane. Secondly, the duration of stress and frequency of adverse welfare events offer a robust template for quantifying welfare outcomes. This approach does not attempt to quantify intensity of stress (which is not easily measured) but is practical for field studies and could be used to compare techniques, to designate desirable welfare standards, and to facilitate incremental improvements.
Validation of the RunScribe inertial measurement unit for walking gait measurement

Introduction The use of portable gait measurement systems in research is appealing to collect real-world data at low-cost, low participant burden, and without requirement for dedicated lab space. Most commercially available inertial measurement units (IMU’s) designed for running only capture temporospatial data, the ability to capture biomechanics data such as shock and motion metrics with the RunScribe IMU makes it the closest to a lab alternative. The RunScribe system has been validated in running, however, is yet to be validated for walking. Method Qualisys motion capture, AMTI force plates, and Delsys Trigno accelerometers were used as gold standard lab measures for comparison against the RunScribe IMU. Twenty participants completed 10 footsteps per foot (20 total) measured by both systems simultaneously. Variables for validation included: Vertical Ground reaction force (GRF), instantaneous GRF rate, pronation excursion, pronation velocity, total shock, impact force, braking force. Interclass correlation (ICC) was used to determine agreement between the measurement systems, mean differences were used to evaluate group level accuracy. Results ICC results showed moderate agreement between measurement systems when both limbs were averaged. The greatest agreement was seen for GRF rate, pronation excursion, and pronation velocity (ICC = 0.627, 0.616, 0.539), low agreement was seen for GRF, total shock, impact shock, braking shock (ICC = 0.269, 0.351, 0.244, 0.180). However mean differences show the greatest level of accuracy for GRF, GRF rate, and impact shock. Discussion Results show mixed agreement between the RunScribe and gold standard lab measures, and varied agreement across left and right limbs. Kinematic variables showed the greatest agreement, however GRF had the lowest relative mean difference for group results. The results show acceptable levels of agreement for most variables, however further work must be done to assess the repeatability and sensitivity of the RunScribe to be applied within areas such as footwear testing and gait retraining protocols.
Maternal dietary folate intake with folic acid supplements and wheeze and eczema in children aged 2 years in the Japan Environment and Children’s Study

Maternal intake of folic acid supplements is reportedly associated with the risk of early-onset allergies in offspring. However, only a few studies have considered the intake of both folic acid supplements and dietary folate. Here, the relationship between maternal intake of folic acid supplements and allergic symptoms such as wheeze and eczema in offspring was analyzed while considering dietary folate intake. We examined 84,361 mothers and 85,114 children in the Japan Environment and Children’s Study. The participants were divided into three groups depending on maternal folic acid supplementation (“no use,” “occasional use,” and “daily use”). Each group was then subdivided into three groups based on total folic acid and dietary folate intake. Outcomes were determined considering the wheeze and eczema status of each child at the age of 2 years. The status was based on the International Study of Asthma and Allergies in Childhood. It was found that 22.1% of the mothers took folic acid supplements daily. In contrast, 56.3% of the mothers did not take these supplements. Maternal intake of folic acid supplements was not associated with wheeze and eczema in the offspring. In contrast, only dietary folate intake was positively associated with wheeze at the age of 2 (adjusted odds ratio, 1.103; 95% confidence interval, 1.003–1.212). However, there is no scientific evidence of a biological mechanism that clarifies this result. Potential confounders such as other nutrition, outdoor/indoor air pollution, and genetic factors may have affected the results. Therefore, further studies on the association between maternal intake of folic acid and allergic symptoms at the age of 3 or above are needed to confirm the results of this study. Trial registration UMIN Clinical Trials Registry (number: UMIN000030786)