Miracle-dz/UniFAR-FTUs huggingface dataset:
Examination of genetic and pharmacological tools to study the proteasomal deubiquitinating enzyme ubiquitin‐specific protease 14 in the nervous system

Strategies for enhancing protein degradation have been proposed for treating neurological diseases associated with a decline in proteasome activity. A proteasomal deubiquitinating enzyme that controls substrate entry into proteasomes, ubiquitin‐specific protease 14 (USP14), is an attractive candidate for therapies that modulate proteasome activity. This report tests the validity of genetic and pharmacological tools to study USP14’s role in regulating protein abundance. Although previous studies implicated USP14 in the degradation of microtubule associate protein tau, tar DNA binding protein, and prion protein, the levels of these proteins were similar in our neurons cultured from wild type and USP14‐deficient mice. Neither loss nor over‐expression of USP14 affected the levels of these proteins in mice, implying that modifying the amount of USP14 is not sufficient to alter their steady‐state levels. However, neuronal over‐expression of a catalytic mutant of USP14 showed that manipulating USP14’s ubiquitin‐hydrolase activity altered the levels of specific proteins in vivo. Although pharmacological inhibitors of USP14’s ubiquitin‐hydrolase activity reduced microtubule associate protein tau, tar DNA binding protein, and prion protein in culture, the effect was similar in wild type and USP14‐deficient neurons, thus impacting their use for specifically evaluating USP14 in a therapeutic manner. While examining how targeting USP14 may affect other proteins in vivo, this report showed that fatty acid synthase, v‐rel reticuloendotheliosis viral oncogene homolog, CTNNB1, and synaptosome associated protein 23 are reduced in USP14‐deficient mice; however, loss of USP14 differentially altered the levels of these proteins in the liver and brain. As such, it is critical to more thoroughly examine how inhibiting USP14 alters protein abundance to determine if targeting USP14 will be a beneficial strategy for treating neurodegenerative diseases.
Pilot Study of the Relationship between Deck Level and Journey Duration on Plasma Cortisol, Epinephrine and Norepinephrine Levels in Italian Heavy Pigs

Simple Summary Journey duration, position of the animal in the vehicle and time spent in the lairage facilities before slaughtering can negatively affect pig welfare. The effects of journey duration and deck level on hormonal parameters were examined in this pilot study during three commercial truckloads. Plasma cortisol, epinephrine and norepinephrine increased with longer transportation time. The levels of the tested hormones were higher in pigs transported for 11 h than for 6.5 h or only 3 h. The loading position (deck level) of the animals on the truck strongly affected only norepinephrine. While the effects of journey duration on plasma cortisol levels were expected and in line with the literature, our findings on plasma catecholamines are novel and may be useful to monitor transportation stress responses in pigs. These preliminary findings need to be confirmed by future studies. Abstract The aim of this pilot study was to evaluate the relationship between journey duration, deck level and activation patterns of the hypothalamic-pituitary-adrenocortical axis (HPA) and sympathetic adrenal medullary system (SAM) in pigs. A total of 90 pigs were examined. The animals came from three different Italian farms associated with the same slaughterhouse located in Bari (Apulia region-Italy). A group of thirty animals was transported from Pordenone (11 h journey); a second group was transported from Terni (6.5 h journey); a third group was transported from Benevento (3 h journey). The animals were transported in the same vehicle, which complied with the structural characteristics indicated in the Council Regulation (EC) No. 1/2005. The truck was composed of a lorry and a trailer, each one divided into three decks. Only the animals transported in the trailer were tested for the study. Before transportation, blood samples were collected on each farm, at 6:00 a.m., from 30 pigs randomly selected out of 135 pigs ready to be transported. Blood samples were also collected during slaughter to evaluate plasma cortisol, epinephrine and norepinephrine, around 6:00 a.m. A journey duration of 11 h was associated with significantly higher plasma concentrations of stress hormones compared with shorter journeys. This increase was proportional to the journey duration, with the pigs travelling for 6.5 h displaying intermediate concentrations between those noticed after 3 h and 11 h journeys. The interaction between deck and journey distance was not significant on epinephrine, norepinephrine or cortisol levels collected at arrival. There was a significant effect of deck level on norepinephrine levels (p < 0.0001), a tendency to influence epinephrine levels (p = 0.073) but no effect on cortisol levels (p = 0.945). Overall, we observed that an 11 h-long journey seemed to impact negatively on pigs’ HPA-SAM activity, likely requiring the animals to spend more time in the lairage facilities to recover.
Association of the Qualitative Clock Drawing Test with Progression to Dementia in Non-Demented Older Adults

To evaluate the predictability of progression of cognitive impairment to dementia using qualitative clock drawing test (CDT) scores, we administered both the CDT using Cahn et al.’s qualitative scoring system and the Mini-Mental State Examination (MMSE) to assess cognitive function in non-demented older individuals attending a memory clinic at a university hospital. Patients visiting the clinic for assessment of cognitive function between January 2015 and December 2019 were enrolled, and only those who were diagnosed as not having dementia at the time of initial assessment completed a follow-up assessment at 1 y (n = 163). To examine any association of qualitative CDT score with progression to dementia, multiple logistic regression analysis was conducted with the change in diagnosis from non-dementia to dementia at 1 y as the dependent variable. A total of 26 participants (16.0%) were diagnosed as having converted to dementia. Multiple logistic regression analysis revealed that both the qualitative CDT score using Cahn et al.’s scoring system and the existence of conceptual deficits were significantly associated with progression to dementia at 1 y after initial assessment of cognitive function, irrespective of the MMSE score, among non-demented older individuals. The CDT may be a useful predictor of progression to dementia in primary care settings.
Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE): Position paper on diagnosis, prognosis, and treatment by the MNGIE International Network

Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is a rare autosomal recessive disease caused by TYMP mutations and thymidine phosphorylase (TP) deficiency. Thymidine and deoxyuridine accumulate impairing the mitochondrial DNA maintenance and integrity. Clinically, patients show severe and progressive gastrointestinal and neurological manifestations. The onset typically occurs in the second decade of life and mean age at death is 37 years. Signs and symptoms of MNGIE are heterogeneous and confirmatory diagnostic tests are not routinely performed by most laboratories, accounting for common misdiagnosis. Factors predictive of progression and appropriate tests for monitoring are still undefined. Several treatment options showed promising results in restoring the biochemical imbalance of MNGIE. The lack of controlled studies with appropriate follow‐up accounts for the limited evidence informing diagnostic and therapeutic choices. The International Consensus Conference (ICC) on MNGIE, held in Bologna, Italy, on 30 March to 31 March 2019, aimed at an evidence‐based consensus on diagnosis, prognosis, and treatment of MNGIE among experts, patients, caregivers and other stakeholders involved in caring the condition. The conference was conducted according to the National Institute of Health Consensus Conference methodology. A consensus development panel formulated a set of statements and proposed a research agenda. Specifically, the ICC produced recommendations on: (a) diagnostic pathway; (b) prognosis and the main predictors of disease progression; (c) efficacy and safety of treatments; and (f) research priorities on diagnosis, prognosis, and treatment. The Bologna ICC on diagnosis, management and treatment of MNGIE provided evidence‐based guidance for clinicians incorporating patients' values and preferences.
Solving an MHC allele–specific bias in the reported immunopeptidome

Identification of MHC class I–bound peptides by immunopurification of MHC complexes and subsequent analysis by mass spectrometry is crucial for understanding T cell immunology and immunotherapy. Investigation of the steps for the MHC ligand isolation process revealed biases in widely used isolation techniques toward peptides of lower hydrophobicity. As MHC ligand hydrophobicity correlates positively with immunogenicity, identification of more hydrophobic MHC ligands could potentially lead to more effective isolation of immunogenic peptides as targets for immunotherapies. We solved this problem by use of higher concentrations of acetonitrile for the separation of MHC ligands and their respective complexes. This increased overall MHC ligand identifications by 2-fold, increased detection of cancer germline antigen–derived peptides by 50%, and resulted in profound variations in isolation efficacy between different MHC alleles correlating with the hydrophobicity of their anchor residues. Overall, these insights enabled a more complete view of the immunopeptidome and overcame a systematic underrepresentation of these critical MHC ligands of high hydrophobicity.
Calycosin induces apoptosis via p38-MAPK pathway-mediated activation of the mitochondrial apoptotic pathway in human osteosarcoma 143B cells

Previous studies have demonstrated that calycosin is a natural phytoestrogen with a similar structure to estrogen, which can inhibit cell proliferation and induce apoptosis in a variety of tumors. Calycosin exerts potential pharmacological effects on osteosarcoma cells by inducing apoptosis. The aim of the present study was to elucidate the specific molecular mechanism of calycosin-induced apoptosis in osteosarcoma cells. Cell proliferation was determined by an MTT assay. Annexin V/PI and JC-1 staining were used to detect apoptosis and mitochondrial dysfunction, respectively, by flow cytometry. Western blot analysis was used to detect the expression of caspases or mitochondrial proteins. The results revealed that calycosin reduced the cell viability of human osteosarcoma 143B cells, induced apoptosis and increased the loss of mitochondrial membrane potential (MMP). In addition, calycosin increased the expression of the proapoptotic antiapoptotic proteins cleaved caspase-3, cleaved caspase-9, cleaved poly(ADP-ribose) polymerase and Bcl-2-associated X protein (Bax), and decreased the expression of the antiapoptotic proapoptotic protein B-cell lymphoma-2 (Bcl-2), thus altering the Bax/Bcl-2 ratio. In addition, the expression levels of cytochrome c were markedly decreased in the mitochondria and increased in the cytoplasm following calycosin treatment. Furthermore, calycosin treatment induced p38-mitogen-activated protein kinase (MAPK) phosphorylation, whereas the p38-MAPK inhibitor BIRB 796 markedly reversed cell viability, apoptosis and loss of MMP in 143B cells. These results suggested that calycosin inhibited osteosarcoma 143B cell growth via p38-MAPK regulation of mitochondrial-dependent intrinsic apoptotic pathways.
Loop-Mediated Isothermal Amplification (LAMP) Assay for Rapid and Accurate Confirmatory Diagnosis of HTLV-1/2 Infection

Laboratory diagnosis of human T-lymphotropic viruses (HTLV) 1 and 2 infection is performed by serological screening and further confirmation with serological or molecular assays. Thus, we developed a loop-mediated isothermal nucleic acid amplification (LAMP) assay for the detection of HTLV-1/2 in blood samples. The sensitivity and accuracy of HTLV-1/2 LAMP were defined with DNA samples from individuals infected with HTLV-1 (n = 125), HTLV-2 (n = 19), and coinfected with HIV (n = 82), and compared with real-time polymerase chain reaction (qPCR) and PCR-restriction fragment length polymorphism (RFLP). The overall accuracy of HTLV-1/2 LAMP (95% CI 74.8–85.5%) was slightly superior to qPCR (95% CI 69.5–81.1%) and similar to PCR-RFLP (95% CI 79.5–89.3%). The sensitivity of LAMP was greater for HTLV-1 (95% CI 83.2–93.4%) than for HTLV-2 (95% CI 43.2–70.8%). This was also observed in qPCR and PCR-RFLP, which was associated with the commonly lower HTLV-2 proviral load. All molecular assays tested showed better results with samples from HTLV-1/2 mono-infected individuals compared with HIV-coinfected patients, who present lower CD4 T-cell counts. In conclusion, HTLV-1/2 LAMP had similar to superior performance than PCR-based assays, and therefore may represent an attractive alternative for HTLV-1/2 diagnosis due to reduced working time and costs, and the simple infrastructure needed.
Dynamics of stress protein expression in leishmania-infected macrophages: evidence for selective induction and recognition of leishmania heat shock protein 60

Heat shock protein (HSP) expression was examined in murine bone marrow-derived macrophages infected with stationary phase promastigotes of Leishmania donovani. Immunoblotting with a rabbit polyclonal antiserum raised against HSP60 from Heliothis virescens (moth), revealed the de novo appearance of proteins with subunit sizes of M r 65,000 and 67,000 in leishmania infected macrophages. Expression of the novel M r 65,000 and 67,000 proteins in infected cells was coordinately regulated and at 24 hr of infection reached maximal levels of 52-100% increases above initial levels at 3 hr. Proteins with identical electrophoretic mobilities and which were similarly regulated in response to heat were also detected in leishmania promastigotes. The appearance of these proteins in macrophages was specific to leishmania infection in that neither protein was detected in non-infected cells either in the basal state or following several treatments including: (i) infection with Y. pseudotuberculosis, (ii) phagocytosis of S. aureus, (iii) NaAsC>2, or (iv) heat shock. A monoclonal antibody that recognizes both mammalian HSP70 and HSP70 from Plasmodia detected single isoforms of both leishmania and murine HSP70 in infected cells and neither protein changed quantitatively during infection. Levels of host heat shock proteins 60, 70 and 90 did not change in response to infection, however, marked induction of the mammalian stress protein heme oxygenase-1 was observed under these conditions. Further evidence for selective expression of the M r 65,000 and 67,000 heat-regulated leishmania proteins was provided by the finding that as their concentration was increasing, the abundance of the leishmania surface protease gp63 in infected cells was noted to decrease. The prominence of leishmania HSP60 within infected macrophages suggested the possibility that it might be a target of the host response. To facilitate further studies concerned with the role of this protein in the host response and in the pathogenesis of the leishmaniases, the HSP60 gene of Leishmania major was cloned, sequenced and expressed. A XEMBL-3 L. major genomic library was screened with a PCR-generated DNA probe derived from a highly conserved region of the leishmania HSP60 gene. A single clone that hybridized strongly was selected and characterized. Sequence analysis revealed the presence of an open reading frame
Alterations of Phospholipids Synthesis in Mitochondrial Membrane of the Liver Cells in the Dynamics of Chronic Emotional Painful Stress Development

At chronic emotional painful stress, regardless of the duration of stress, content of lysophosphatidylcholine, phosphatidic acid and phosphatidylserine increases in liver mitochondria. In this case, content of phosphatidylinositol, conversely, decreases slightly in early stress, and then depending on the duration of the stress, the reduction of the phospholipid increases.
Improvement of Deblocking Filter for AVS3

AVS3 is the third generation audio video coding standard (AVS). And the performance of AVS3 base profile is improved by 20% compared to the H.265. This paper proposes improvements to the deblocking scheme of AVS3, which has been adopted in the AVS3 baseline profile. The deblocking scheme in AVS2 has defects, including unreasonable filtering conditions and filtering coefficients. The deblocking filter in AVS3 also has the same drawback because it inherits the deblocking scheme from AVS2. These defects lead to unsatisfactory subjective quality of the AVS3 deblocking filter. Hence this paper improves the subjective quality of the AVS3 deblocking filter by reasonably modifying the filtering conditions and filter operation. In addition, to reduce the complexity of deblocking filter in AVS3, the proposed method simplifies the filtering operation of chroma deblocking. We implement the method on top of the AVS3 reference software (HPM-2.1), and the experimental result shows that subjective quality is significantly improved. The proposed method achieves 0.28% BD-rate reduction under Random Access (RA) configuration and 0.21% BD-rate reduction under ALL INTRA (AI) configuration.
Range-Doppler Reconstruction for Off-grid Target Using Frequency Agile Radar

Frequency agile radars (FARs) have outstanding performance in electronic counter-countermeasures. Many compressed sensing based algorithms have been developed for range-Doppler reconstruction in FAR. However, conventional compressed sensing paradigms suffer from the off-grid (OG) issue. To address this issue, we theoretical analyze the effect of off-grid problem and develop a novel algorithm called 2MOMP to estimate range and Doppler jointly. Several simulations validate the theoretical findings and demonstrate the effectiveness of mitigating OG effect.
Two-phase flows for sedimentation of suspensions

We present a two-phase flow model that arises from energetic-variational arguments and study its implication for the sedimentation of buoyant particles in a viscous fluid inside a HeleShaw cell and also compare corresponding simulation results to experiments. Based on a minimal dissipation argument, we provide a simplified 1D model applicable to sedimentation and study its properties and the numerical discretization. We also explore different aspects of its numerical discretization in 2D. The focus is on different possible stabilization techniques and their impact on the qualitative behavior of solutions. We use experimental data to verify some first qualitative model predictions and discuss these experiments for different stages of batch sedimentation.
The Influence of Certain Biological and Environmental Factors on Insecticide Tolerance of the Lygus Bug, Lygus hesperus

Many factors appear to influence DDT tolerance of the lygus bug, Lygus hesperus Knight. Lygus bugs collected from alfalfa seed fields during the period of bloom and seed set are more tolerant of DDT than those collected from alfalfa hay fields. Lygus bugs reared in the laboratory on green string beans are more tolerant of DDT than those from either alfalfa hay or seed fields Adult females are more tolerant than males. Tolerance to DDT increases progressively with each nymphal instar from third instar to adult. DDT is shown to have a negative temperature coefficient of action, while toxaphene has a positive temperature coefficient of action. Increase in DDT tolerance closely parallel increases in total body lipids. Differences in tolerances of two sexes could not be explained on the basis of differences in total body lipids. Analyses of body lipids of L. hesperus have shown that at least 7 fatty acids are present. They are myristic, palmitic, palmitoleic, stearic, oleic, linoleic, and linolenic. No significant qualitative or quantitative differences in fat composition of the two sexes were apparent. Slight difference in amounts of the fatty acids were found in insects taken from different hosts at various times of the year, but it is believed that these differences would not account for the observed differences in susceptibility to DDT.
Genetic diversity and population structure of cotton (Gossypium spp.) of the New World assessed by SSR markers

A global analysis of cotton (Gossypium spp.) genetic diversity is the first step to understanding its geographical distribution, dissemination, genetic relatedness, and population structure. To assess the genetic diversity and population structure in Gossypium species, 111 cotton accessions representing five allotetraploids (AD1–AD5 genomes), 23 Asiatic diploids of the Old World (A1 and A2 genomes), and 82 diploids of the New World subgenus Houzingenia (D1–D11 genomes) species were assessed using simple sequence repeats (SSR) markers with wide genome coverage. The mean genetic distance (GD) between the two most important New World tetraploid cottons (Upland (Gossypium hirsutum L.) and Pima (Gossypium barbadense L.)) was 0.39. Among the three shrub type sections (Houzingenia, Integrifolia, and Caducibracteolata) and three arborescent sections (Erioxylum, Selera, and Austroamericana), the GD ranged between 0.19 and 0.41. Phylogenetic analyses clustered all species into distinct phylogenetic groups, which we.
Bioreduction and Mechanistic Aspects Involved in the Synthesis of Silver Nanoparticles Using Holarrhena antidysenterica

An important aspect of nanobiotechnology concerns the development of biologically inspired experimental protocols. In this paper, we report biosynthesis and mechanistic aspects involved in the fabrication of silver nanoparticles (AgNPs) using leaf extract of Holarrhena antidysenterica. The plant H. antidysenterica is popularly known as kutja. It is majorly used for the treatment of diarrhoea and dysentery. In the study leaf extract of H. antidysenterica is used for the synthesis of AgNPs. Transmission Electron Microscopy (TEM) and Elemental Spectroscopy Imaging (ESI) were performed to ascertain the formation of AgNPs. The TEM study indicated AgNPs with spherical and quasispherical morphology with size range of 2 nm to 70 nm. Possible mechanism for the synthesis of AgNPs from above plant has also been proposed. The reduction of silver ions appeared to be due to the redox activities of ascorbic/dehydroascorbic acid and terpenoids while, proteins were identified as the capping agent for AgNPs. In the present study, we report fast, eco-friendly and one-step extracellular synthesis of AgNPs.
Pectinoidea (Mollusca: Bivalvia: Pectinidae: Propeamussiidae) from Hansa Bay, Papua new Guinae

Abstract Thirty five species of Pectinoidea (33 Pectinidae, 2 Propeamussiidae) are described from Hansa Bay, Papua New Guinea. Serratovola pallula n. sp. is here introduced as new to science. Lectotypes are designated of Pecten cloacatus Reeve, 1853 and Pecten tricarinatus Anton, 1838, and type localities are designated for Pecten vexillum Reeve, 1853, Pecten spectabilis Reeve, 1853, and Ostrea squamosa Gmelin, 1791.