Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of two family AA9 LPMOs from Aspergillus tamarii with distinct activities on xyloglucan reveals structural differences linked to cleavage specificity

Aspergillus tamarii grows abundantly in naturally composting waste fibers of the textile industry and has a great potential in biomass decomposition. Amongst the key (hemi)cellulose-active enzymes in the secretomes of biomass-degrading fungi are the lytic polysaccharide monooxygenases (LPMOs). By catalyzing oxidative cleavage of glycoside bonds, LPMOs promote the activity of other lignocellulose-degrading enzymes. Here, we analyzed the catalytic potential of two of the seven AA9-type LPMOs that were detected in recently published transcriptome data for A. tamarii, namely AtAA9A and AtAA9B. Analysis of products generated from cellulose revealed that AtAA9A is a C4-oxidizing enzyme, whereas AtAA9B yielded a mixture of C1- and C4-oxidized products. AtAA9A was also active on cellopentaose and cellohexaose. Both enzymes also cleaved the β-(1→4)-glucan backbone of tamarind xyloglucan, but with different cleavage patterns. AtAA9A cleaved the xyloglucan backbone only next to unsubstituted glucosyl units, whereas AtAA9B yielded product profiles indicating that it can cleave the xyloglucan backbone irrespective of substitutions. Building on these new results and on the expanding catalog of xyloglucan- and oligosaccharide-active AA9 LPMOs, we discuss possible structural properties that could underlie the observed functional differences. The results corroborate evidence that filamentous fungi have evolved AA9 LPMOs with distinct substrate specificities and regioselectivities, which likely have complementary functions during biomass degradation.
Hyperglycemia Induced Osmotic Disequilibrium, Oxidative Stress and Cell Death in Type II Diabetes Patients.

High unutilized glucose in the body in diabetes along with increased level of Na+ and urea cause altered osmotic equilibrium in the vascular bed contributing altered cellular microenvironment which may further affect membrane function. As plasma membrane is a dynamic structure, it is responsive to chemical exposure. Any chemical exposure may trigger alteration in membrane function and subsequently down-hill reactions. We are therefore studying the role of high glucose concentration in membrane alteration, altered cellular function and cell death in diabetic patients. In our present study we have recruited newly diagnosed 30 type II diabetes mellitus patients, chosen from diabetic clinic, Howrah Zila Hospital, Howrah, West Bengal and 31 age and sex matched healthy control without any history of diabetes from same socio economic background. Significantly high glycemic index (studied by serum glucose level and glycated haemoglobin level), high blood osmolality, osmotic fragility and oxidative stress have been noted in every diabetic participant in comparison to non-diabetic individual of our study population. A significant cell membrane alteration (p<0.05) with altered serum free sialic acid concentration has been noted in diabetic patients. Degree of membrane deformity, frequency of nonviable WBC, frequency of apoptotic cells and length of comet tail all are significantly higher (p<0.01) in diabetic persons in comparison to normal non-diabetic counterpart of the population. Diabetes is an altered homeostatic state which contributes to cellular dis
Genomic Sequence and Pre-Clinical Safety Assessment of Bifidobacterium longum CECT 7347, a Probiotic able to Reduce the Toxicity and Inflammatory Potential of Gliadin-Derived Peptides

Bifidobacteria are common inhabitants of human gut and play a significant role in establishing a well-balanced intestinal microbiota. The strain Bifidobacterium longum CECT 7347 (ES1) has been demonstrated to ameliorate damage caused by gluten in celiac disease (CD), both In vitro and in a murine model. Studies suggest that administering this B. longum strain to supplement the gluten-free diet could provide an additional strategy, thereby improving the health status of patients. Here, we report an in-depth study of this strain, adopting a multidisciplinary strategy to demonstrate its safety according to FAO/WHO criteria for probiotic selection. Whole genome sequencing using a massive sequencing approach on the 454 platforms and annotation showed neither relevant virulence nor potential antibiotic resistance genes. It has been demonstrated that values of lactic acid isomer production, bile salt deconjugation and formation of biogenic amines, considered as specifi c traits to be evaluated according to FAO/ WHO, were very similar to levels previously reported in other Bifidobacteria. It has not shown acquired antibiotic resistance In vitro. Moreover, acute ingestion studies in immunocompetent and immunosuppressed BALB/c mouse models did not cause either mortality or morbidity in any group, and did not lead to signifi cant Bifi dobacterial organ translocation, even in the immunosuppressed group. Altogether, these results confi rm the safety status of the strain B. longum CECT 7347. The safety of strain CECT 7347, together with its previously reported functional role in ameliorating gluten- related damage in CD, would indicate it is a probiotic strain.
How Is the Presence of Company Related to Thwarted Belongingness in Real Time? Taking a Closer Look at the Conceptualization of the Construct of the Interpersonal Theory of Suicide

(1) Background: The role of thwarted belongingness (TB) in predicting suicidal ideation, as originally assumed by the Interpersonal Theory of Suicide, is repeatedly challenged by empirical findings. This could be due to an inadequate conceptualization of the construct of TB that is assumed to be influenced by intrapersonal and interpersonal factors. (2) Methods: We examined the associations of TB with intrapersonal variables related to depression, and with interpersonal variables related to an individual’s actual social environment. We analyzed data from an ecological momentary assessment study in psychiatric inpatients with depressive disorders. N = 73 participants rated momentary TB, depressive affect and status of company up to 10 times per day, over a period of six days, on smartphones. (3) Results: TB was lower when assessed while participants were in company compared to when they were alone, and the more desired the company was, the less TB was experienced. Individuals who had a partnership experienced less momentary TB. Furthermore, higher levels of momentary depressive affect, as well as more stable levels of depression, were related to higher levels of TB, and the relation between the presence of company and TB was weaker for more depressed persons. (4) Conclusions: Our findings can be seen as evidence that both intrapersonal and interpersonal factors relate to TB, and thus support the conceptualization of TB as proposed by the Interpersonal Theory of Suicide.
Methods for Model Calibration under High Uncertainty: Modeling Cholera in Bangladesh

Background. Published data on a disease do not always correspond directly to the parameters needed to simulate natural history. Several calibration methods have been applied to computer-based disease models to extract needed parameters that make a model’s output consistent with available data. Objective. To assess 3 calibration methods and evaluate their performance in a real-world application. Methods. We calibrated a model of cholera natural history in Bangladesh, where a lack of active surveillance biases available data. We built a cohort state-transition cholera natural history model that includes case hospitalization to reflect the passive surveillance data-generating process. We applied 3 calibration techniques: incremental mixture importance sampling, sampling importance resampling, and random search with rejection sampling. We adapted these techniques to the context of wide prior uncertainty and many degrees of freedom. We evaluated the resulting posterior parameter distributions using a range of metrics and compared predicted cholera burden estimates. Results. All 3 calibration techniques produced posterior distributions with a higher likelihood and better fit to calibration targets as compared with prior distributions. Incremental mixture importance sampling resulted in the highest likelihood and largest number of unique parameter sets to better inform joint parameter uncertainty. Compared with naïve uncalibrated parameter sets, calibrated models of cholera in Bangladesh project substantially more cases, many of which are not detected by passive surveillance, and fewer deaths. Limitations. Calibration cannot completely overcome poor data quality, which can leave some parameters less well informed than others. Calibration techniques may perform differently under different circumstances. Conclusions. Incremental mixture importance sampling, when adapted to the context of high uncertainty, performs well. By accounting for biases in data, calibration can improve model projections of disease burden.
Antimicrobial Activity of Piper ribesoides Root Extract Against Staphylococcus aureus

The methanol extract of Piper ribesoides Wall, was evaluated for potential antimicrobial activity against Staphylococcus aureus (Rosenbach). The methanol extract of P. ribesoides root was effective on S. aureus. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values of the methanol extract of P. ribesoides were 3.125 mg/ml and 6.250 mg/ ml, respectively. Apart from the antibacterial effects, imaging using scanning electron microscopy (SEM) was done to determine the major alterations in the microstructure of the S. aureus. The main abnormalities noted via SEM studies were alterations in morphology and complete collapse of the bacterial cells after 36 h of exposure to the extract. The effect of the extract on the growth profile of the bacteria was also examined. The extract changed the normal growth profile of S. aureus, thus confirming the bactericidal effect of the extract on S. aureus.
Studies on Boronic Acid-modified Nucleotides for Diagnostic Applications and Development of Fluorescent Chemoprobes for Molecules of Biological Importance

Post-synthesis DNA modification is a very useful method for DNA functionalization. This is achieved by using a modified NTP, which has a handle for further modifications, replacing the corresponding natural NTP in polymerase-catalyzed DNA synthesis. Subsequently, the handle can be used for further functionalization, preferably through a very fast reaction. Herein we describe polymerase-mediated incorporation of trans-cyclooctene modified thymidine triphosphate (TCO-TTP). Subsequently, the trans-cyclooctene group was reacted with a tetrazine tethered to other functional groups through a very fast click reaction. The utility of this DNA functionalization method was demonstrated with the incorporation of a boronic acid group and a fluorophore. The same approach was also successfully used in modifying a known aptamer for fluorescent labeling applications. Boronic acid modified DNA molecules were further applied in aptamer selection for cancer cell recognition. The second project was focused on developing fluorescent probes/sensors for biothiols. Because of the biological relevance of thiols and sulfides such as cysteine, homocysteine and hydrogen sulfide, their detection has attracted a great deal of research interest. Fluorescent probes are emerging as a new strategy for thiol and hydrogen sulfide analysis due to their high sensitivity, low cost, and ability to detect and image thiols in biological samples. A sulfonyl azide-based fluorescent probe has been developed for the quantitative detection of H2S in aqueous media such as phosphate buffer and bovine serum. In addition, another novel fluorescent probe has been developed for the detection of homocysteine. The fluorescence response is selective for homocysteine over other biologically abundant thiols such as cysteine and glutathione. In addition, a linear calibration curve was also be obtained for quantitative analysis in phosphate buffer and plasma. These selective fluorescent probes could be very useful tool for biothiol tests. INDEX WORDS: Post-synthesis modification, Bioorthogonal reaction, Oligonucleotides, Gasotransmitter, Biothiol detection, Redox reaction STUDIES ON BORONIC ACID-MODIFIED NUCLEOTIDES FOR DIAGNOSTIC APPLICATIONS AND DEVELOPMENT OF FLUORESCENT CHEMOPROBES FOR MOLECULES OF BIOLOGICAL IMPORTANCE
Original Contribution ENHANCED PRODUCTION OF ENTEROCIN FROM ENTEROCOCCUS FAECIUM LR/6 BY STATISTICAL OPTIMIZATION OF THE GROWTH MEDIUM

Statistical screening of media constituents for enhancement of enterocin production from a soil isolate Enterococcus faecium LR/6 has been carried out. Sodium acetate, dipotassium hydrogen phosphate, triammonium citrate and tween-80 were identified as the most important factors for enterocin production in the first step, using Plackett-Burman design. Response surface methodology (RSM) was further applied to study their interaction and to determine their optimum levels. The analysis indicated that the maximum enterocin production was achieved in a TGYE medium supplemented with 11 g/l sodium acetate, 3 g/l dipotassium hydrogen phosphate, 1 g/l triammonium citrate and 1 g/l tween-80 after an incubation period of 18 h. Approximately 2-fold improvement in enterocin production was achieved due to this medium optimization. The results indicated the importance of statistical tools in identifying and optimizing various culture components for enhanced enterocin production from E. faecium LR/6. Such an improved production will facilitate the purification and various applications of enterocin, especially in food biopreservation.
FOUR NEWLY RECORDED TO CHINA SPECIES OF THE GENUS THEMUS MOTSCHULSKY, 1857 (COLEOPTERA: CANTHARIDAE)

Summary. Four species of the subgenus Haplothemus Wittmer, 1973 (Themus cacharensis Champion, 1926, T. lamellatus Wittmer, 1973, T. probsti Wittmer, 1993, and T. reymondi Bourgeois, 1907) are firstly recorded from China. Themus cacharensis is transferred from the nominotypical subgenus to the subgenus Haplothemus.
Detection of common resistance genes of Gram- negative bacteria by DNA microarray assay

To design a DNA microarray for the detection of com mon resistance genes of Gram-negative bacteria, we collected 70 strains of Gram-negative bacilli ( Klebsiella pneumoniae, Escherichia coli, Enterobacter cloacae, Pseudomonas aeruginosa, Acinetobacter baumannii), and the primers and probes were designed and synthesized according to the known res istance genes to prepare the deoxyribonucleic acid (DNA) microarray for the detection of these re sistance genes. Then, hybridization and subsequent scanning were performed. The results of DNA microar ray assay were compared with results from the polymerase chain reaction ( PCR). Results showed that the consistency rate was 100. 00% in the detection of 8 resistance genes (TEM, SHV, CTX-M, D HA, CIT, VIM, KPC and OXA-23). PCR assay revealed the resistance gene IMP in 1 strain of P. aeruginosa, which was absent in the DNA microarray assay. The DNA microarray designed in the present s tudy has clinical value in the detection of common resistance genes of Gram-negative bacteria.
On Clustering and Embedding Manifolds using a Low Rank Neighborhood Approach

Samples from intimate (non-linear) mixtures are generally modeled as being drawn from a smooth manifold. Scenarios where the data contains multiple intimate mixtures with some constituent materials in common can be thought of as manifolds which share a boundary. Two important steps in the processing of such data are (i) to identify (cluster) the different mixture-manifolds present in the data and (ii) to eliminate the non-linearities present the data by mapping each mixture-manifold into some low-dimensional euclidean space (embedding). Manifold clustering and embedding techniques appear to be an ideal tool for this task, but the present state-of-the-art algorithms perform poorly for hyperspectral data, particularly in the embedding task. We propose a novel reconstruction-based algorithm for improved clustering and embedding of mixture-manifolds. The algorithms attempts to reconstruct each target-point as an affine combination of its nearest neighbors with an additional rank penalty on the neighborhood to ensure that only neighbors on the same manifold as the target-point are used in the reconstruction. The reconstruction matrix generated by using this technique is block-diagonal and can be used for clustering (using spectral clustering) and embedding. The improved performance of the algorithms vis-a-vis its competitors is exhibited on a variety of simulated and real mixture datasets.
Sodium‐Ion Batteries Paving the Way for Grid Energy Storage

The recent proliferation of renewable energy generation offers mankind hope, with regard to combatting global climate change. However, reaping the full benefits of these renewable energy sources requires the ability to store and distribute any renewable energy generated in a cost‐effective, safe, and sustainable manner. As such, sodium‐ion batteries (NIBs) have been touted as an attractive storage technology due to their elemental abundance, promising electrochemical performance and environmentally benign nature. Moreover, new developments in sodium battery materials have enabled the adoption of high‐voltage and high‐capacity cathodes free of rare earth elements such as Li, Co, Ni, offering pathways for low‐cost NIBs that match their lithium counterparts in energy density while serving the needs for large‐scale grid energy storage. In this essay, a range of battery chemistries are discussed alongside their respective battery properties while keeping metrics for grid storage in mind. Matters regarding materials and full cell cost, supply chain and environmental sustainability are discussed, with emphasis on the need to eliminate several elements (Li, Ni, Co) from NIBs. Future directions for research are also discussed, along with potential strategies to overcome obstacles in battery safety and sustainable recyclability.
Effects of Fragmentation of Araucarian Vine Forest on Small Mammal Communities

Abstract: Habitat loss and fragmentation are major threats to the survival of forest‐dependent fauna. We examined the abundance of small mammal species in forests, corridors, remnants of araucarian vine forest, and Araucaria cunninghamii plantations and pastures. None of the forest mammal species persisted following conversion of forest to pasture. Plantations supported lowered abundances of a subset of forest species that were mainly habitat generalists with respect to their occurrence in different floristic types of undisturbed native forest. Within plantations, an increased subcanopy cover was associated with a more forest‐like small mammal assemblage. Species' responses to habitat fragmentation varied. The floristic habitat generalists were largely tolerant of habitat fragmentation, their abundance being similar in forests, corridors, and remnants, and were capable of persisting in remnants a few hectares in area. Floristic habitat specialists were vulnerable to habitat fragmentation and thus were abundant in continuous forest, were less abundant in corridors, and were generally absent from remnants. Species that avoid the corridor matrix and are therefore constrained to the corridor may be disadvantaged by the linearity of the habitat, consistent with the predictions of central‐place foraging theory. Although small remnants and corridors provide habitat for some species, those that are more specialized in their use of undisturbed habitat types require the retention or reestablishment of large intact areas.
Continuous Monitoring of in Vztro Oxidation of Human Low Density Lipoprotein

The kinetics of the oxidation of human low densit) lipoprotein (LDL) can be measured continuously by monitoring the change of the 234 nm diene absorption. The time-course shows three consecutive phases. a lag-phase during which the diene absorption increases only weakly. a propagation phase with a rapid increase of the diene absorption and finally a decomposition phase. The increase of the dienes is highly correlated with the increase of MDA or lipid hydroperoxides. The duration of the lag-phase is determined by the endogenous antioxidants contained in LDL (vitamin E. carotenoids. retinylstearate). Water-soluble antioxidants (ascorbic acid. urate) added in micromolar concentrations prolong the lag-phase in a concentration-dependent manner. The determination of the lag-phase is a convenient and objective procedure for determining the susceptibility of LDL from different donors towards oxidation as well as effects of proand antioxidants.
Resistance to -lactams of human and veterinary Salmonella isolates in Egypt and Algeria

Seventy six non-typhoid Salmonella were isolated from both human and poultry in Egypt and Algeria and tested for their antibiotics resistance. The incidence of multiple antibiotics resistance was high. To study �-lactams resistance mechanisms, double disk synergy test (DDST) with and without cloxacilline was used, results revealed the production of extended spectrum �-lactamases (ESBLs) and cephalosporinase in seven and one human Egyptian isolates, respectively. The seven ESBL isolates were identified as Salmonella enterica serotype Poona and their molecular typing by ERIC-PCR revealed unrelated genetic patterns, indicating that these isolates are not clonal. The Cephalosporinase-ESBL- producing isolate was identified as S. enterica serotype Hadar. Polymerase chain reaction (PCR) with specific primers showed the presence of blaTEM and blaSHV genes, respectively, in all and four ESBL producers, and blaAmpC gene was detected in cephalosporinaseproducing isolate. Genetic transfer by conjugation and plasmid profiles analysis showed that these genes and their resistance markers were transferable in association with plasmids of 60 kb for ESBLs and 64 and 3.2 kb for AmpC cephalosporinase.
Cached fungi in non‐native conifer forests and their importance for red squirrels (Sciurus vulgaris L.)

The caching of fungi by red squirrels Sciurus vulgaris was investigated in commercial conifer plantations by walking transects in Kielder Forest, Cumbria and Wauchope Forest, Scotland. In 11 transects, a total of 58 fungal fruiting bodies were observed on branches in trees, consisting of four different species (49 Russula ochroleuca , seven R. metica , one R. vesca , one Colybia maculata ). Fungal stores were found to be short lived and most fruiting bodies cached were gone after 2 weeks. Based on the survey findings we estimate that within an average red squirrel home range there would be a minimum of 42 cached fruiting bodies, constituting a food store of approx. 525–714 kJ.
The Effect of Trade Openness on Carbon Dioxide Emission in Taiwan: A Quantile Mediation Analysis

This paper adopts an innovative method, called a quantile mediation analysis, which combines a quantile regression and mediation analysis to examine the impact of trade openness on carbon dioxide emission whether through economic growth or not from 1990 to 2018 in Taiwan. The result of the traditional ordinary least square approach shows that Taiwan’s trade openness affects carbon dioxide emission through the full mediation effect of economic growth for the period of 1990-2018 and there is no direct relation between trade openness and carbon dioxide emission. Moreover, the results of this innovative analysis indicate that Taiwan’s trade openness also affects carbon dioxide emission through the full mediation effect of economic growth at any distribution of carbon dioxide emission, and there is no direct effect from trade openness to carbon dioxide emission. This result indicates that trade openness only exists an indirect effect through economic growth in Taiwan. This finding supports Antweiler, Copeland and Taylor’s point of view [1].