Miracle-dz/UniFAR-FTUs huggingface dataset:
Study on the Application of a New Method for the Viral Detection of Caliciviruses in Foodstuffs

Noroviruses (NoVs), transmitted mainly through the fecal-oral route, are particularly infectious and only a few virions carried by contaminated water or food are sufficient to cause the disease. These viruses may cause outbreaks of large proportions that could be limited if there is a quickly detection of the source of infection and if would be prohibited or restricted to the sick people the contact with others. Foods normally involved in this disease are edible bivalve molluscs (mussels, oysters and clams) that are often eaten raw or under-cooked and frozen soft fruits imported from areas with low hygienic conditions. We developed a rapid, reliable and sensitive method for the viral detection in foodstuffs using proteinase K, a serine protease, often used in molecular biology to digest proteins and remove contamination from nucleic acids preparations. We applied this method to clams infected with Feline Calicivirus (FCV) strain F9 (used as substitute of NoV, which isn't able to replicate in vitro) and to soft fruits infected with a NoV solution. The protocol consists of three steps: first we homogenized the foodstuffs, then we put the samples in a tube together with proteinase K for an hour at 37°C and finally we centrifuged the sample at 4300 rpm for 5 min. We noticed a cytotoxic effect of proteinase K on cell cultures for tests with FCV and to avoid the problem we will add a phase of inactivation of the enzyme with a proper inhibitor. For tests with NoV we used for the detection the Real- time PCR that allowed also a quantification of the samples. Coupling our protocol with Real-time PCR makes detection quicker and it was possible to detect even low concentrations of viruses. Besides a step with RNAse A will be introduced together with proteinase K to avoid false positive with real-time PCR.
Stable Determination of a Rigid Scatterer in Elastodynamics

We deal with an inverse elastic scattering problem for the shape determination of a rigid scatterer in the time-harmonic regime. We prove a local stability estimate of log log type for the identification of a scatterer by a single far-field measurement. The needed a priori condition on the closeness of the scatterers is estimated by the universal constant appearing in the Friedrichs inequality.
Long-term changes in mollusc communities of the Ognon river (France) over a 30-year period

The mollusc fauna of the Ognon river, one of the main tributaries of the Saone, surveyed for the fi rst time in 1977, was re-sampled in 2007 to assess long-term changes. Overall, the total number of collected individu- als increased by 33.6 % (55.2 % for gastropods and 23.7 % for bivalves) but total species richness remained stable during the period (40 vs. 39 species) although there was considerable species turnover: 8 disappearances offset by 7 appearances including that of the invasive Corbicula fl uminea which accounted for 30.4 % of the total number of individuals in 2007. The use of trend test, similarity index and principal component analyses (PCA) revealed radical changes in mollusc communities between years particularly in the upstream-downstream gradients of species rich- ness, total number of molluscs, and gastropods, bivalves, pulmonates, sphaeriid and unionid mussel densities. The upstream colonisation of several species was observed in the upper part of the river but in the lower part divergences in terms of species richness, density and structure increased in a downstream direction. The chronology of the changes observed strongly suggest that competition for food following the proliferation of C. fl uminea and the 2003 heatwave may be, responsible for the dramatic decline of native bivalves (Unionidae and Sphaeriidae, respectively). Given the magnitude of these changes, a return to a state prior to the disturbance of the malacological structure is hardly conceivable. However, the evolution towards a new relatively stable state is an alternative hypothesis.
Circulating Neutrophils of Nonalcoholic Steatohepatitis Patients Show an Activated Phenotype and Suppress T Lymphocytes Activity

Neutrophils or PolyMorphonuclear Neutrophils (PMNs) are key effector cells of the innate immune system and thanks to their remarkable plasticity, establish a cross talk with T cells modulating their survival and effector functions. During Nonalcoholic Steatohepatitis (NASH), the advanced form of hepatic steatosis or NAFL, PMNs infiltrate liver tissue, becoming a histological feature of NASH. Our aim was to evaluate the frequency of PMNs in NAFL and NASH patients in order to understand how they modulate the activity of circulating CD4+ and CD8+ T cells. In our cohort of patients, NASH patients displayed a higher frequency of circulating PMNs that was strongly correlated to liver enzymes, grade of steatosis, inflammation and fibrosis, the hepatocellular ballooning, and NAFLD Activity Score (NAS). Furthermore, even if ex vivo, in both groups of patients, PMNs shared the same phenotype of resting cells, after 24 hours of coculture with autologous CD4+ and CD8+ T cells, PMNs of NASH patients acquired a more active phenotype, becoming able to strongly inhibit proliferation and activation of CD4+ and CD8+ T cells. The higher ability of PMNs of NASH patients in suppressing CD4+ and CD8+ T cells, over time, might contribute in reducing the immunological defense of liver tissue against damages thus taking part in the progression of the NAFL disease toward NASH.
In Silico Design of Inhibitors for -Secretase: Implications for Alzheimer's Disease

β-secretase is regarded as one of the best characterized targets for Alzheimer's disease therapy. β-secretase 1 protease plays an important role in cleaving amyloid precursor protein and further the formation of pathogenic β-amyloid plaques in the brain, thereby causing Alzheimer's disease. The present work reports the docking studies of a series of analogues based derivatives of phenyl-piperazine, cyclic urea, N-phenyl-1-arylamide and Nphenylbenzenesulfonamide. The structure of âsecretase 1 complexed with a ligand, 2-amino6-propylpyrimidin-4(3H)-one was retrieved from Protein Data Bank and used in the present study. All the derivatives and clinically used drugs for Alzheimer's disease, such as, tacrine, razadyne, exelon and aricept were energy minimized and docked with the receptor. The docked positions of all derivatives were compared with tacrine as the standard drug. Four of the derivatives showed better docking score and identical hydrogen bonds with that of tacrine.
Assessment of air quality using several bio monitors of selected sites of Durgapur, Burdwan district by air pollution tolerance index approach

Rapid industrialization leads a great role over pollution. Vegetation can absorb particulate and other gaseous pollutants into their system but they also have some limitation and tend to show symptoms of damages after prolonged exposure. Several parameters including ambient air quality monitoring as well as ascorbic acid, pH, total chlorophyll, relative water content of ten different crop species at four different sites were analyzed to evaluate the Air Pollution Tolerance Index of Durgapur, Burdwan District, West Bengal, India.From the detailed study it was found that the highest APTI valueshowed in Polyalthialongifolia (176.14) at Durgapur College Campus, Nacicasesum (158.68) at Durgapur Projects Limited, Polyalthialongifolia (133.26) at Amaravati and Moringaoleifera (129.32) at Mamrabazar. Therefore these tree species could act as the bioindicators for pollutants and could be utilized as tolerant species towards combating air pollution.
Which Balance Subcomponents Distinguish Between Fallers and Non-Fallers in People with COPD?

Rationale Chronic obstructive pulmonary disease (COPD) is an increasingly prevalent lung disease linked to dysfunctional balance and an increased risk of falls. The Balance Evaluation Systems Test (BESTest) evaluates the six underlying subcomponents of functional balance. The aim of this study was to determine the specific balance subcomponents and cut-off scores that discriminate between fallers and non-fallers with COPD to guide fall risk assessment and prevention. Methods A secondary analysis of cross-sectional data from two prior studies in COPD was performed. Independent samples t-tests were used to explore the differences in the BESTest sub-system scores between fallers and non-fallers. Receiver operating characteristic curves were used to determine the optimal subcomponent cut-off scores that identified fallers, and the area under the curve (AUC) was used to assess test accuracy. Results Data from 72 subjects with COPD (mean age, 70.3 ± 7.4y; mean forced expiratory volume in 1 second, 38.9 ± 15.8% predicted) were analyzed. Two BESTest subcomponents, stability limits/verticality (fallers: 75.4%, non-fallers: 83.8%; p=0.002) and postural responses (fallers: 67.5%, non-fallers: 79.7%; p=0.008) distinguished between fallers and non-fallers. Stability limits/verticality had an AUC of 0.70 and optimal cut-off score of 73.8% for identifying fallers; postural responses had an AUC of 0.67 and optimal cut-off score of 69.4%. Conclusion The stability limits/verticality and postural responses subcomponents of the BESTest distinguished between fallers and non-fallers with COPD. The stability limits/verticality subcomponent can also be used to identify whether an individual with COPD is at risk of falling using a cut-off score of 73.8%. These findings suggest that specific subcomponents of balance could be targeted to optimize fall risk assessment and prevention in COPD.
Improving Establishment of Seeded Buffalograss

Little information exists on dormant seeding of buffalograss [Buchloe dactyloides (Nutt.) Engelm. ] in the Midwest and central Great Plains of the United States. The objectives of these two studies were to determine how seeding rate affects establishment of ‘Sundancer’ buffalograss when dormant seeded, and to evaluate if cultivar or seeding date affects establishment of ‘Cody’, ‘Bowie’ or ‘Sundancer’ buffalograss when seeded at various dates during the winter and spring. ‘Sundancer’ buffalograss was dormant seeded at 146, 244, or 293 kg ha in late November in 2012 and 2013 and spring-seeded in early May in 2013 and 2014. Dormant seeding of buffalograss resulted in >80% cover by the following August in all studies. Increasing seeding rate had no effect on establishment of ‘Sundancer’, regardless of seeding date. Furthermore, there was no difference in turf cover by August following seeding of ‘Sundancer’, ‘Bowie’ or ‘Cody’ at 146 kg ha in late Nov., Jan., Mar., or May regardless of seeding date. Our results suggest that ‘Sundancer’, ‘Bowie’ or ‘Cody’ can be successfully dormant seeded at 146 kg ha from late November though late March, which allows establishment before the
Stiffness-matched biomaterial implants for cell delivery: clinical, intraoperative ultrasound elastography provides a ‘target’ stiffness for hydrogel synthesis in spinal cord injury

Safe hydrogel delivery requires stiffness-matching with host tissues to avoid iatrogenic damage and reduce inflammatory reactions. Hydrogel-encapsulated cell delivery is a promising combinatorial approach to spinal cord injury therapy, but a lack of in vivo clinical spinal cord injury stiffness measurements is a barrier to their use in clinics. We demonstrate that ultrasound elastography – a non-invasive, clinically established tool – can be used to measure spinal cord stiffness intraoperatively in canines with spontaneous spinal cord injury. In line with recent experimental reports, our data show that injured spinal cord has lower stiffness than uninjured cord. We show that the stiffness of hydrogels encapsulating a clinically relevant transplant population (olfactory ensheathing cells) can also be measured by ultrasound elastography, enabling synthesis of hydrogels with comparable stiffness to canine spinal cord injury. We therefore demonstrate proof-of-principle of a novel approach to stiffness-matching hydrogel-olfactory ensheathing cell implants to ‘real-life’ spinal cord injury values; an approach applicable to multiple biomaterial implants for regenerative therapies.
Autophagy and Tumor Database: ATdb, a novel database connecting autophagy and tumor

Abstract Autophagy is an essential cellular process that is closely implicated in diverse pathophysiological processes and a variety of human diseases, especially tumors. Autophagy is regarded as not only an anti-cancer process in tumorigenesis but also a pro-tumor process in progression and metastasis according to current research. It means the role of autophagy in tumor is considered to be complex, controversial and context dependent. Hence, a comprehensive database is of great significance to obtain an in-depth understanding of such complex correlations between autophagy and tumor. To achieve this objective, here we developed the Autophagy and Tumor Database (named as ATdb, http://www.bigzju.com/ATdb/#/) to compile the published information concerning autophagy and tumor research. ATdb connected 25 types of tumors with 137 genes required for autophagy-related pathways, containing 219 population filters, 2650 hazard ratio trend plots, 658 interacting microRNAs, 266 interacting long non-coding RNAs, 155 post-translational modifications, 298 DNA methylation records, 331 animal models and 70 clinical trials. ATdb could enable users to search, browse, download and carry out efficient online analysis. For instance, users can make prediction of autophagy gene regulators in a context-dependent manner and in a precise subpopulation and tumor subtypes. Also, it is feasible in ATdb to cluster tumors into distinguished groups based on the gene-related long non-coding RNAs to gain novel insights into their potential functional implications. Thus, ATdb offers a powerful online database for the autophagy community to explore the complex world of autophagy and tumor. Database URL: http://www.bigzju. com/ATdb/#/
Austrodiplostomum ostrowskiae n. sp. (Digenea: Diplostomidae: Diplostominae) from the Double-crested Cormorant, Phalacrocorax auritus (Phalacrocoracidae) from the Galveston, Texas Area of the Gulf of Mexico, U.S.A.

Abstract Approximately 1,350 specimens of an undescribed species of Austrodiplostomum (Diplostomidae: Diplostominae) were collected from 10 double-crested cormorants, Phalacrocorax auritus (Phalacrocoracidae), from the Galveston, Texas, U.S.A. , area. Austrodiplostomum compactum is synonymized with Austrodiplostomum mordax, the type species in the genus, leaving A. mordax as the only species remaining. Austrodiplostomum ostrowskiae n. sp. can be distinguished from A. mordax by having a small but distinct hindbody, shorter ceca, a uterus and vitelline fields that extend into the tribocytic organ, smaller eggs, and an anterior testis that is about the same width as the posterior testis in A. ostrowskiae n. sp. Five specimens of the neotropical cormorant, Phalacrocorax brasilianus, were also examined from the Galveston, Texas, U.S.A. , area during the study, but this host species was not found to be infected with a species of Austrodiplostomum.
Neuromuscular disease modeling on a chip

ABSTRACT Organs-on-chips are broadly defined as microfabricated surfaces or devices designed to engineer cells into microscale tissues with native-like features and then extract physiologically relevant readouts at scale. Because they are generally compatible with patient-derived cells, these technologies can address many of the human relevance limitations of animal models. As a result, organs-on-chips have emerged as a promising new paradigm for patient-specific disease modeling and drug development. Because neuromuscular diseases span a broad range of rare conditions with diverse etiology and complex pathophysiology, they have been especially challenging to model in animals and thus are well suited for organ-on-chip approaches. In this Review, we first briefly summarize the challenges in neuromuscular disease modeling with animal models. Next, we describe a variety of existing organ-on-chip approaches for neuromuscular tissues, including a survey of cell sources for both muscle and nerve, and two- and three-dimensional neuromuscular tissue-engineering techniques. Although researchers have made tremendous advances in modeling neuromuscular diseases on a chip, the remaining challenges in cell sourcing, cell maturity, tissue assembly and readout capabilities limit their integration into the drug development pipeline today. However, as the field advances, models of healthy and diseased neuromuscular tissues on a chip, coupled with animal models, have vast potential as complementary tools for modeling multiple aspects of neuromuscular diseases and identifying new therapeutic strategies. Summary: Modeling neuromuscular diseases is challenging due to their complex etiology and pathophysiology. Here, we review the cell sources and tissue-engineering procedures that are being integrated as emerging neuromuscular disease models.
Hardfats as crystallization modifiers of cocoa butter

Hardfats, or fully hydrogenated oils, consist of materials with homogeneous composition, composed of high melting point triacylglycerol. Hardfats are regarded as relatively new materials, and remain unexplored in lipid technology, notwithstanding being low-cost industrial products. They can behave as modulators of the crystallization process, acting as preferential nuclei for ordering the crystal lattice and inducing specific polymorphic habits, with great potential for use in crystallization processes. This work evaluated the influence of the addition of different hardfats on the crystallization patterns of cocoa butter (CB). Fully hydrogenated oils with significantly different chemical composition, obtained from palm kernel oil (FHPKO), palm oil (FHPO), cottonseed oil (FHCO), soybean oil (FHSO), and crambe oil (FHCrO), were considered. Blends of CB/hardfats, at concentrations of 1%, 3%, and 5% (by weight) were produced and the crystallization isotherms, thermal behavior, and polymorphism determined. Hardfats FHPO, FHCO, FHSO, and FHCrO proved to be effective additives to modulate the crystallization characteristics of CB, in respect to crystallization kinetics and thermal behavior. Only the hardfat from crambe oil, FHCrO, presented stabilizing effect on the polymorphism of CB, delaying the transition V VI. Practical applications: The use of hardfats as crystallization additives in products containing CB, for technological adjustment of CB formulations in order to harmonize events like solidification kinetics, thermal behavior, and polymorphism. Hardfats may act as potential modulators of CB crystallization, with the purpose to obtain higher quality products at significantly reduced cost in industrial processing.
Foot stiffening during the push-off phase of human walking is linked to active muscle contraction, and not the windlass mechanism

The rigidity of the human foot is often described as a feature of our evolution for upright walking and is bolstered by a thick plantar aponeurosis that connects the heel to the toes. Previous descriptions of human foot function consider stretch of the plantar aponeurosis via toe extension (windlass mechanism) to stiffen the foot as it is levered against the ground for push-off during walking. In this study, we applied controlled loading to human feet in vivo, and studied foot function during the push-off phase of walking, with the aim of carefully testing how the foot is tensioned during contact with the ground. Both experimental paradigms revealed that plantar aponeurosis strain via the ‘windlass mechanism' could not explain the tensioning and stiffening of the foot that is observed with increased foot-ground contact forces and push-off effort. Instead, electromyographic recordings suggested that active contractions of ankle plantar flexors provide the source of tension in the plantar aponeurosis. Furthermore, plantar intrinsic foot muscles were also contributing to the developed tension along the plantar aspect of the foot. We conclude that active muscular contraction, not the passive windlass mechanism, is the foot's primary source of rigidity for push-off against the ground during bipedal walking.
Unraveling an emerging disease associated with disturbed aquatic environments: The case of Buruli ulcer

Buruli ulcer (Mycobacterium ulcerans infection) is an emerging disease of developing tropical and subtropical countries. This environmental mycobacterium causes severe morbidity in communities associated with rivers and standing water bodies (particularly those created as a result of human environmental disturbance such as deforestation and agriculture) and subsequent water quality changes. Neither the reservoir nor the mode of transmission is known, but data from laboratory studies suggest that biting aquatic insects may be involved. M ulcerans has been shown to colonize and grow within specific water bugs (Naucoridae), which then transmit M ulcerans to mice through their bites. PCR evidence suggests that the mycobacterium is present in water, biofilms of aquatic plants, detritus, invertebrates, and fish; however, systematic ecological studies that would provide a more comprehensive understanding of M ulcerans distribution in the environment have been lacking. Several hypotheses are explored in relation .
α4 but Not α3 and α7 Nicotinic Acetylcholine Receptor Subunits Are Lost from the Temporal Cortex in Alzheimer's Disease

Abstract : Neuronal nicotinic acetylcholine receptors labelled with tritiated agonists are reduced in the cerebral cortex in Alzheimer's disease (AD), but to date it has not been demonstrated which nicotinic receptor subunits contribute to this deficit. In the present study, autopsy tissue from the temporal cortex of 14 AD cases and 15 age‐matched control subjects was compared using immunoblotting with antibodies against recombinant peptides specific for α3, α4, and α7 subunits, in conjunction with [3H]epibatidine binding. Antibodies to α3, α4, and α7 produced one major band on western blots at 59, 51, and 57 kDa, respectively. [3H]Epibatidine binding and α4‐like immunoreactivity (using antibodies against the extracellular domain and cytoplasmic loop of the α4 subunit) were reduced in AD cases compared with control subjects (p <0.02) and with a subgroup of control subjects (n = 9) who did not smoke prior to death (p <0.05) for the former two parameters. [3H]Epibatidine binding and cytoplasmic α4‐like immunoreactivity were significantly elevated in a subgroup of control subjects (n = 4) known to have smoked prior to death (p <0.05). There were no significant changes in α3‐ or α7‐like immunoreactivity associated with AD or tobacco use. The selective involvement of α4 has implications for understanding the role of nicotinic receptors in AD and potential therapeutic targets.