Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein changes as robust signatures of fish chronic stress: a proteomics approach in fish welfare research

Background: In order to have a greater understanding of fish welfare, sensitive technological tools, such as proteomics, may assist the aquaculture industry as it allows an unbiased approach for the discovery of potential biomarkers for stress monitoring. Stress is characterized by a cascade of physiological responses that end-up inducing further changes at the whole-animal level that might either increase fitness or impair welfare. Monitorization of this dynamic process, up till now relies on indicators that are only a snapshot of the stress level experienced. Within this scope, using G ilthead seabream ( Sparus aurata ) as model, three chronic stress conditions, namely overcrowding, handling and hypoxia, were employed to evaluate the potential of the fish protein-based adaptations as reliable signatures of chronic stress, in contrast with the commonly used hormonal and metabolic indicators. Results: A large spectrum of biological variation regarding cortisol and glucose levels was observed, which values rose higher in net handled fish. In this sense, a potential pattern of stressor-specificity was evidenced since the magnitude of response and tolerance varied markedly from a permanent (crowding) to a repetitive stressor (handling). Gel-based proteomics analysis of the plasma proteome also revealed that net handled fish had the highest number of differential proteins, compared to the other trials . M ass spectrometric analysis, followed by gene ontology enrichment and protein-protein interaction analyses, characterized those as humoral components of the innate immune system and key elements on the response to stimulus. Conclusions: Overall, this study represents the first screening of more reliable signatures of physiological adaptation to chronic stress in fish, allowing the future development of novel biomarker models to monitor fish welfare.
Developmental Expression of SULT1C4 Transcript Variants in Human Liver: Implications for Discordance Between SULT1C4 mRNA and Protein Levels.

The cytosolic sulfotransferases (SULTs) metabolize a variety of xenobiotic and endogenous substrates. Several SULTs are expressed in the fetus, implying that these enzymes have important functions during human development. We recently reported that while SULT1C4 mRNA is abundant in prenatal human liver specimens, SULT1C4 protein is barely detectable. Two coding transcript variants (TVs) of SULT1C4 are indexed in GenBank, TV1 (full-length) and TV2 (lacking exons 3 and 4). The purpose of this study was to evaluate expression of the individual TVs as a clue for understanding the discordance between mRNA and protein levels. RT-PCR was initially performed to identify TVs expressed in intestinal and hepatic cell lines. This analysis generated fragments corresponding to TV1, TV2, and a third variant that lacked exon 3 (E3DEL). Using RT-qPCR assays designed to quantify TV1, TV2, or E3DEL individually, all three TVs were more highly expressed in prenatal than postnatal specimens. TV2 levels were ~5-fold greater than TV1, while E3DEL levels were minimal. RNA-seq analysis of another set of liver specimens confirmed that TV1 and TV2 levels were highest in prenatal liver, with TV2 higher than TV1. RNA-seq also detected a non-coding RNA, which was also more abundant in prenatal liver. Transfection of HEK293T cells with plasmids expressing individual Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys (DDK)-tagged SULT1C4 isoforms demonstrated that TV1 produced much more protein than did TV2. These data suggest that the lack of correspondence between SULT1C4 mRNA and protein levels in human liver is likely attributable to the inability of the more abundant TV2 to produce stable protein. SIGNIFICANCE STATEMENT: Cytosolic sulfotransferases (SULTs) metabolize a variety of xenobiotic and endogenous substrates, and several SULTs are highly expressed in the fetus, implying that they have important functions during human development. SULT1C4 is highly expressed in prenatal liver at the mRNA level but not the protein level. This study provides an explanation for this discordance by demonstrating that the predominant SULT1C4 transcript is a variant that produces relatively little protein.
Transcriptome profiling and protease inhibition experiments identify proteases that activate H3N2 influenza A and influenza B viruses in murine airways

Cleavage of influenza virus hemagglutinin (HA) by host proteases is essential for virus infectivity. HA of most influenza A and B (IAV/IBV) viruses is cleaved at a monobasic motif by trypsin-like proteases. Previous studies have reported that transmembrane serine protease 2 (TMPRSS2) is essential for activation of H7N9 and H1N1pdm IAV in mice but that H3N2 IAV and IBV activation is independent of TMPRSS2 and carried out by as-yet-undetermined protease(s). Here, to identify additional H3 IAV- and IBV-activating proteases, we used RNA-Seq to investigate the protease repertoire of murine lower airway tissues, primary type II alveolar epithelial cells (AECIIs), and the mouse lung cell line MLE-15. Among 13 candidates identified, TMPRSS4, TMPRSS13, hepsin, and prostasin activated H3 and IBV HA in vitro. IBV activation and replication was reduced in AECIIs from Tmprss2/Tmprss4-deficient mice compared with WT or Tmprss2-deficient mice, indicating that murine TMPRSS4 is involved in IBV activation. Multicycle replication of H3N2 IAV and IBV in AECIIs of Tmprss2/Tmprss4-deficient mice varied in sensitivity to protease inhibitors, indicating that different, but overlapping, sets of murine proteases facilitate H3 and IBV HA cleavages. Interestingly, human hepsin and prostasin orthologs did not activate H3, but they did activate IBV HA in vitro. Our results indicate that TMPRSS4 is an IBV-activating protease in murine AECIIs and suggest that TMPRSS13, hepsin, and prostasin cleave H3 and IBV HA in mice. They further show that hepsin and prostasin orthologs might contribute to the differences observed in TMPRSS2-independent activation of H3 in murine and human airways.
Miller Fisher syndrome and polyneuritis cranialis in COVID-19

Objective To report 2 patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) who presented acutely with Miller Fisher syndrome and polyneuritis cranialis, respectively. Methods Patient data were obtained from medical records from the University Hospital “Príncipe de Asturias,” Alcalá de Henares, and the University Hospital “12 de Octubre,” Madrid, Spain. Results A 50-year-old man presented with anosmia, ageusia, right internuclear ophthalmoparesis, right fascicular oculomotor palsy, ataxia, areflexia, albuminocytologic dissociation, and positive testing for anti-GD1b–immunoglobulin G antibody. Five days previously, he had developed a cough, malaise, headache, low back pain, and fever. A 39-year-old man presented with ageusia, bilateral abducens palsy, areflexia, and albuminocytologic dissociation. Three days previously, he had developed diarrhea, a low-grade fever, and poor general condition. Oropharyngeal swab test for SARS-CoV-2 by qualitative real-time reverse transcriptase PCR assay was positive in both patients and negative in the CSF. The first patient was treated with IV immunoglobulin and the second with acetaminophen. Two weeks later, both patients made a complete neurologic recovery, except for residual anosmia and ageusia in the first case. Conclusions Our 2 cases highlight the rare occurrence of Miller Fisher syndrome and polyneuritis cranialis during the coronavirus disease 2019 (COVID-19) pandemic. These neurologic manifestations may occur because of an aberrant immune response to COVID-19. The full clinical spectrum of neurologic symptoms in patients with COVID-19 remains to be characterized.
Developmental regulation of microtubule‐based trafficking and anchoring of axonal mitochondria in health and diseases

Mitochondria are cellular power plants that supply most of the ATP required in the brain to power neuronal growth, function, and regeneration. Given their extremely polarized structures and extended long axons, neurons face an exceptional challenge to maintain energy homeostasis in distal axons, synapses, and growth cones. Anchored mitochondria serve as local energy sources; therefore, the regulation of mitochondrial trafficking and anchoring ensures that these metabolically active areas are adequately supplied with ATP. Chronic mitochondrial dysfunction is a hallmark feature of major aging‐related neurodegenerative diseases, and thus, anchored mitochondria in aging neurons need to be removed when they become dysfunctional. Investigations into the regulation of microtubule (MT)‐based trafficking and anchoring of axonal mitochondria under physiological and pathological circumstances represent an important emerging area. In this short review article, we provide an updated overview of recent in vitro and in vivo studies showing (1) how mitochondria are transported and positioned in axons and synapses during neuronal developmental and maturation stages, and (2) how altered mitochondrial motility and axonal energy deficits in aging nervous systems link to neurodegeneration and regeneration in a disease or injury setting. We also highlight a major role of syntaphilin as a key MT‐based regulator of axonal mitochondrial trafficking and anchoring in mature neurons.
Phenotypic diversity assessment within a major ex situ collection of wild endemic coffees in Madagascar.

BACKGROUND AND AIMS Like other clades, the Coffea genus is highly diversified on the island of Madagascar. The 66 endemic species have colonized various environments and consequently exhibit a wide diversity of morphological, functional, phenological features and reproductive strategies. The trends of interspecific trait variation, which stems from interactions between genetically defined species and their environment, still needed to be addressed for Malagasy coffee trees. METHODS Data acquisition was done in the most comprehensive ex situ collection of Madagascan wild Coffea. The structure of endemic wild coffees maintained in ex situ collection was explored in terms of morphological, phenological, and functional traits. The environmental (natural habitat) effect was assessed on traits in species from distinct natural habitats. Phylogenetic signal (Pagel's λ, Blomberg's K) was used to quantify trait proximities among species according to their phylogenetic relatedness. KEY RESULTS Despite the lack of environmental difference in the ex situ collection, widely diverging phenotypes were observed. Phylogenetic signal was found to vary greatly across and even within trait categories. The highest values were exhibited by the ratio of internode mass to leaf mass, the length of the maturation phase and the LDMC. By contrast, traits weakly linked to phylogeny were either constrained by original natural environment (leaf size) or under selective pressures (phenological traits). CONCLUSIONS This study gives insight into complex patterns of trait variability found in an ex situ collection, and underlines the opportunities offered by living ex situ collections for research characterizing phenotypic variation.
Toward precision prescribing for methadone: Determinants of methadone deposition

Background Despite the World Health Organization listing methadone as an essential medication, effective dose selection is challenging, especially in racial and ethnic minority populations. Subtherapeutic doses can result in withdrawal symptoms while supratherapeutic doses can result in overdose and death. Although CYP3A4 was conventionally considered the principal methadone metabolizing enzyme, more recent data have identified CYP2B6 as the principal enzyme. CYP2B6 has ethnically-associated polymorphisms that affect the metabolic rate. Our objective was to investigate the effects of genetic and nongenetic factors on methadone metabolism. Methods We measured trough plasma methadone levels in 100 participants with opioid use disorder. We assessed methadone metabolism by calculating the metabolite ratio (major metabolite: 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine [EDDP] divided by methadone concentration). We assessed hepatic fibrosis and steatosis by transient elastography and CYP2B6 alleles, principally responsible for methadone metabolism. Mixed effects models modeled the data in 97 participants. Results Participants were largely male (58%), minority (61% African American) and non-Hispanic (68%). Forty percent were HCV mono-infected, 40% were uninfected, and 20% were HCV/HIV co-infected. Female sex had significant effects on (R)- and (S)-methadone metabolism (p = 0.016 and p = 0.044, respectively). CYP2B6 loss of function (LOF) alleles significantly affected (S)-methadone metabolism (p = 0.012). Body mass index (BMI) significantly affected (R)-methadone metabolism (p = 0.034). Methadone metabolism appeared to be lower in males, in individuals with LOF alleles, and elevated BMI. Conclusions Genetic analysis, especially in minority populations, is essential to delivering individualized treatments. Although the principal methadone metabolizing enzyme remains controversial, our results suggest that sex, CYP2B6 genotype, and BMI should be incorporated into multivariate models to create methadone dosing algorithms. Methadone dosing algorithms should facilitate medication delivery, improve patient satisfaction, and diminish overdose potential.
Fungal Decay of Wood : Soft Rot-Brown Rot-White Rot

Wood decay by fungi is typically classified into three types: soft rot, brown rot and white rot. Brown rot fungi are the most prevalent with regard to attack on coniferous, structural wood products in North America. The wood decayed by brown rot fungi is typically brown and crumbly and it is degraded via both non-enzymatic and enzymatic systems. A series of celluloytic enzymes are employed in the degradation process by brown rot fungi, but no lignin degrading enzymes are typically involved. White rot fungi are typically associated with hardwood decay and their wood decay patterns can take on different forms. White rotted wood normally has a bleached appearance and this may either occur uniformly, leaving the wood a spongy or stringy mass, or it may appear as a selective decay or a pocket rot. White rot fungi possess both cellulolytic and lignin degrading enzymes and these fungi therefore have the potential to degrade the entirety of the wood structure under the correct environmental conditions. Soft rot fungi typically attack higher moisture, and lower lignin content wood and can create unique cavities in the wood cell wall. Less is known about the soft rot degradative enzyme systems, but their degradative mechanisms are reviewed along with the degradative enzymatic and non-enzymatic systems known to exist in the brown rot and white rot fungi. As we learn more about the non-enzymatic systems involved in both brown and white rot degradative systems, it changes our perspective on the role of enzymes in the decay process. This in turn is affecting the way we think about controlling decay in wood preservation and wood protection schemes, as well as how we may apply fungal decay mechanisms in bioindustrial processes.
Reduced uptake of [11C]‐ABP688, a PET tracer for metabolic glutamate receptor 5 in hippocampus and amygdala in Alzheimer’s dementia

Metabotropic glutamate receptors play a critical role in the pathogenesis of Alzheimer's disease due to their involvement in processes of memory formation, neuroplasticity, and synaptotoxity. The objective of the current study was to study mGluR5 availability measured by [11C]‐ABP688 (ABP) in patients with clinically diagnosed Alzheimer's dementia (AD).
Isolation of infectious, non-fibrillar and oligomeric prions from a genetic prion disease

Gerstmann-Sträussler-Scheinker disease (GSS) is characterized by atypical N- and C-terminal cleaved protease-resistant PrPSc. Vanni et al. report that PrPSc oligomers purified from patients with GSS are authentic – but non-fibrillar – prions, thus uncovering the minimal prion protein domain able to encode infectious prions.
Successful treatment of ureteric calculi with constitutional homoeopathic medicine Lycopodium clavatum: A Case report

Introduction Formation of stone in the urinary tract, kidney, ureter and bladder is called as Urolithiasis. Formation of urinary stones is very common. About 5-15% population are affected with urinary stone, and, therefore, causes high morbidity in comparison to the above types of stone formation. Shock wave lithotripsy and ureteroscopy along with conservative treatments are the most common approaches for the treatment of calculi, although considered as expressive in one hand, and on the other hand, such interventions may lead to complications. Therefore, alternative medicines give a second thought for the treatment of urolithiasis because it avoids surgical interventions. Here we present a case study for the successful treatment of urolithiasis by a homoeopathic medicine Lycopodium clavatum in a 43 years old male. Case Profile A 43-year-old male patient with intense pain in the right loin for 5-6 days, increased frequency of urination, ineffectual urination, severe pain during urination, and finally with the pain score was 9, was considered for treatment in the present study. Based on his complete case history, Lycopodium clavatum at potencies of 0/1 to 0/6 was prescribed to him. Conclusion Correct homoeopathic organ specific or constitutional formulation(s) selected based on specific important symptoms can also be efficacious in diseases such as ureteric stone. Constitutional medicine Lycopodium clavatum is usually prescribed when the patient is with right side pain with ureteric stone and it is justified in the present case report. Randomized control trial is suggested to ascertain the results obtained in the present study i.e. successful treatment of urolithiasis with the constitutional homeopathic formulation Lycopodium clavatum.
Time-lapse imaging of HeLa spheroids in soft agar culture provides virtual inner proliferative activity

Cancer is a complex disease caused by multiple types of interactions. To simplify and normalize the assessment of drug effects, spheroid microenvironments have been utilized. Research models that involve agent measurement with the examination of clonogenic survival by monitoring culture process with image analysis have been developed for spheroid-based screening. Meanwhile, computer simulations using various models have enabled better predictions for phenomena in cancer. However, user-based parameters that are specific to a researcher’s own experimental conditions must be inputted. In order to bridge the gap between experimental and simulated conditions, we have developed an in silico analysis method with virtual three-dimensional embodiment computed using the researcher’s own samples. The present work focused on HeLa spheroid growth in soft agar culture, with spheroids being modeled in silico based on time-lapse images capturing spheroid growth. The spheroids in silico were optimized by adjusting the growth curves to those obtained from time-lapse images of spheroids and were then assigned virtual inner proliferative activity by using generations assigned to each cellular particle. The ratio and distribution of the virtual inner proliferative activities were confirmed to be similar to the proliferation zone ratio and histochemical profiles of HeLa spheroids, which were also consistent with those identified in an earlier study. We validated that time-lapse images of HeLa spheroids provided virtual inner proliferative activity for spheroids in vitro. The present work has achieved the first step toward an in silico analysis method using computational simulation based on a researcher’s own samples, helping to bridge the gap between experiment and simulation.
Striatal network modeling in Huntington’s Disease

Medium spiny neurons (MSNs) comprise over 90% of cells in the striatum. In vivo MSNs display coherent burst firing cell assembly activity patterns, even though isolated MSNs do not burst fire intrinsically. This activity is important for the learning and execution of action sequences and is characteristically dysregulated in Huntington’s Disease (HD). However, how dysregulation is caused by the various neural pathologies affecting MSNs in HD is unknown. Previous modeling work using simple cell models has shown that cell assembly activity patterns can emerge as a result of MSN inhibitory network interactions. Here, by directly estimating MSN network model parameters from single unit spiking data, we show that a network composed of much more physiologically detailed MSNs provides an excellent quantitative fit to wild type (WT) mouse spiking data, but only when network parameters are appropriate for the striatum. We find the WT MSN network is situated in a regime close to a transition from stable to strongly fluctuating network dynamics. This regime facilitates the generation of low-dimensional slowly varying coherent activity patterns and confers high sensitivity to variations in cortical driving. By re-estimating the model on HD spiking data we discover network parameter modifications are consistent across three very different types of HD mutant mouse models (YAC128, Q175, R6/2). In striking agreement with the known pathophysiology we find feedforward excitatory drive is reduced in HD compared to WT mice, while recurrent inhibition also shows phenotype dependency. We show that these modifications shift the HD MSN network to a sub-optimal regime where higher dimensional incoherent rapidly fluctuating activity predominates. Our results provide insight into a diverse range of experimental findings in HD, including cognitive and motor symptoms, and may suggest new avenues for treatment.
Replacement and desmoplastic histopathological growth patterns in cutaneous melanoma liver metastases: frequency, characteristics, and robust prognostic value

Among visceral metastatic sites, cutaneous melanoma (CM) metastasises initially to the liver in ~14–20% of cases. Liver metastases in CM patients are associated with both poor prognosis and poor response to immunotherapy. Histopathological growth patterns (HGPs) of liver metastases of the replacement and desmoplastic type, particularly from colorectal cancer and uveal melanoma (UM), may impart valuable biological and prognostic information. Here, we have studied HGP in 43 CM liver metastases resected from 42 CM patients along with other prognostic factors from three institutions. The HGPs (replacement, desmoplastic, pushing) were scored at the metastasis–liver interface with two algorithms: (1) 100% desmoplastic growth pattern (dHGP) and any (≥1%) replacement pattern (any‐rHGP) and (2) >50% dHGP, >50% rHGP or mixed (<50% dHGP and/or rHGP, pushing HGP). For 1 patient with 2 metastases, an average was taken to obtain 1 final HGP yielding 42 observations from 42 patients. 22 cases (52%) had 100% dHGP whereas 20 (48%) had any replacement. Cases with rHGP demonstrated vascular co‐option/angiotropism. With the development of liver metastasis, only rHGP (both algorithms), male gender and positive resection margins predicted diminished overall survival (p = 0.00099 and p = 0.0015; p = 0.034 and p = 0.024 respectively). On multivariate analysis, only HGP remained significant. 7 of 42 (17%) patients were alive with disease and 21 (50%) died with follow‐up after liver metastases ranging from 1.8 to 42.2 months (mean: 20.4 months, median: 19.0 months). 14 (33%) patients with previously‐treated metastatic disease had no evidence of disease at last follow up. In conclusion, we report for the first time replacement and desmoplastic HGPs in CM liver metastases and their prognostic value, as in UM and other solid cancers. Of particular importance, any rHGP significantly predicted diminished overall survival while 100% dHGP correlated with increased survival. These results contribute to a better understanding of the biology of CM liver metastases and potentially may be utilised in managing patients with these metastases.