Efficient Approximate Kernel Based Spike Sequence Classification.

Machine learning (ML) models, such as SVM, for tasks like classification and clustering of sequences, require a definition of distance/similarity between pairs of sequences. Several methods have been proposed to compute the similarity between sequences, such as the exact approach that counts the number of matches between k-mers (sub-sequences of length k) and an approximate approach that estimates pairwise similarity scores. Although exact methods yield better classification performance, they pose high computational costs, limiting their applicability to a small number of sequences. The approximate algorithms are proven to be more scalable and perform comparably to (sometimes better than) the exact methods - they are designed in a "general" way to deal with different types of sequences (e.g., music, protein, etc.). Although general applicability is a desired property of an algorithm, it is not the case in all scenarios. For example, in the current COVID-19 (coronavirus) pandemic, there is a need for an approach that can deal specifically with the coronavirus. To this end, we propose a series of ways to improve the performance of the approximate kernel (using minimizers and information gain) in order to enhance its predictive performance pm coronavirus sequences. More specifically, we improve the quality of the approximate kernel using domain knowledge (computed using information gain) and efficient preprocessing (using minimizers computation) to classify coronavirus spike protein sequences corresponding to different variants (e.g., Alpha, Beta, Gamma). We report results using different classification and clustering algorithms and evaluate their performance using multiple evaluation metrics. Using two datasets, we show that our proposed method helps improve the kernel's performance compared to the baseline and state-of-the-art approaches in the healthcare domain.

In vitro efficacy of polymer coated miltefosine drug against leishmania tropica.

Polymer based nanoparticles for drug delivery is an alternative approach to overcome drug resistance and drug toxicity especially for cutaneous leishmaniasis treatment. The present study shows synthesis and characterization of Miltefosine loaded chitosan nanoparticles (MFS-CNPs). The synthesized MFS-CNPs were experimented to evaluate the in vitro cytotoxicity and efficacy of the synthesized drug loaded nanoparticles by hemolysis assay and 3-(4, 5- dimethylthiazol-2-yl)-2,5-diphenyletetrazolium bromide (MTT) assay. MFS-CNPs were synthesized by ionic gelation method with sodium tripolyphosphate. The characterization of synthesized NPs was performed to observe the surface morphology, encapsulation efficacy, drug loading content, average size, and zeta potential. In vitro MTT assay was performed to calculate half maximal inhibitory concentration value of synthesized nanoparticles against promastigotes and axenic amastigotes of L. tropica. By using Scanning electron microscope, MFS-CNPs displayed spherical shape having a mean size of 70 nm along with high EE (97%), DLC (91%) and negative surface charge (- 28.0 mV). Dynamic light scattering shows the average size of NPs was 91.4 nm. Moreover, less than 5% hemolytic activity was observed in MFS-CNPs as compared to free MFS in different concentrations (100 µg/ml, 125 µg/ml, 150 µg/ml).It was observed that the effect of MFS-CNPs and free MFS on both forms of the parasite was dose and time dependent. However, the cytotoxic effects of MFS-CNPs were more salient than free MFS on both forms of L. tropica. Using MTT assay, free MFS presented low efficacy at higher concentrations (30 µg/ml) with 21.4 ± 1.3 and 20.5 ± 1.4 mean viability rate of the promastigotes and axenic amastigotes, respectively after 72 h incubation. While MFS-CNPs showed strong antileishmanial effects on both forms of L. tropica (11 ± 0.3 and 14 ± 0.8) mean viability rate after 72 h incubation at (30 µg/ml). When analyzed statistically by the software, Graph Pad Prism version 5, the IC50 value of MFS-CNPs (0.0218 ± 0.01 µg/ml) against promastigotes was effective than free MFS (0.3548 ± 0.17 µg/ml). Similarly, MFS-CNPs activity against axenic amastigotes (0.1008 ± 0.02 µg/ml) was potent than free MFS (0.5320 ± 0.21 µg/ml). Hence, MFS-CNPs exhibited significant antileishmanial activity in vitro. In conclusion, MFS-CNPs manifested enhanced in vitro Leishmanicidal and less hemolytic activity; however more studies are needed to support its efficacy in both animal and human cutaneous leishmaniasis.

Bioflavonoid-Induced Apoptosis and DNA Damage in Amastigotes and Promastigotes of Leishmania donovani: Deciphering the Mode of Action.

Natural products from plants contain many interesting biomolecules. Among them, quercetin (Q), gallic acid (GA), and rutin (R) all have well-reported antileishmanial activity; however, their exact mechanisms of action are still not known. The current study is a step forward towards unveil the possible modes of action of these compounds against Leishmania donovani (the causative agent of visceral leishmaniasis). The selected compounds were checked for their mechanisms of action against L. donovani using different biological assays including apoptosis and necrosis evaluation, effects on genetic material (DNA), quantitative testing of nitric oxide production, ultrastructural modification via transmission electron microscopy, and real-time PCR analysis. The results confirmed that these compounds are active against L. donovani, with IC50 values of 84.65 µg/mL, 86 µg/mL, and 98 µg/mL for Q, GA, and R, respectively. These compounds increased nitric oxide production and caused apoptosis and DNA damage, which led to changes in the treated cells' ultrastructural behavior and finally to the death of L. donovani. These compounds also suppressed essential enzymes like trypanothione reductase and trypanothione synthetase, which are critical for leishmanial survival. The selected compounds have high antileishmanial potentials, and thus in-vivo testing and further screening are highly recommended.

Antibacterial, Antihemolytic, Cytotoxic, Anticancer, and Antileishmanial Effects of Ajuga bracteosa Transgenic Plants.

Herbal and traditional medicines can play a pivotal role in combating cancer and neglected tropical diseases. Ajuga bracteosa, family Lamiaceae, is an important medicinal plant. The genetic transformation of A. bracteosa with rol genes of Agrobacterium rhizogenes further enhances its metabolic content. This study aimed at undertaking the molecular, phytochemical, and in vitro biological analysis of A. bracteosa extracts. We transformed the A. bracteosa plant with rol genes and raised the regenerants from the hairy roots. Transgenic integration and expression of rolB were confirmed by conventional polymerase chain reaction (PCR) and qPCR analysis. The methanol: chloroform crude extracts of wild-type plants and transgenic regenerants were screened for in vitro antibacterial, antihemolytic, cytotoxic, anticancer, and leishmanial activity. Among all plants, transgenic line 3 (ABRL3) showed the highest expression of the rolB gene. Fourier transform infra-red (FTIR) analysis confirmed the enhanced number of functional groups of active compounds in all transgenic lines. Moreover, ABRL3 exhibited the highest antibacterial activity, minimum hemolytic activity (CC50 = 7293.05 ± 7 µg/mL) and maximum antileishmanial activity (IC50 of 56.16 ± 2 µg/mL). ABRL1 demonstrated the most prominent brine shrimp cytotoxicity (LD5039.6 ± 4 µg/mL). ABRL3 was most effective against various human cancer cell lines with an IC50 of 57.1 ± 2.2 µg/mL, 46.2 ± 1.1 µg/mL, 72.4 ± 1.3 µg/mL, 73.3 ± 2.1 µg/mL, 98.7 ± 1.6 µg/mL, and 97.1 ± 2.5 µg/mL against HepG2, LM3, A549, HT29, MCF-7, and MDA-MB-231, respectively. Overall, these transgenic extracts may offer a cheaper therapeutic source than the more expensive synthetic drugs.

Evaluating fertility and growth rate potential of indigenous sheep breeds submitted to heat stress under different management systems.

OBJECTIVE: Sheep farming is an important source of livelihood in the southern Khyber Pakhtun Khwa province of Pakistan where they are reared under extensive system (ES). This system has limitations of improper feeding, rearing, and management which negatively affect their productivity. The present study compares different rearing systems and their stresses on fertility, behavior, and growth rate potential of two sheep breeds of Pakistan. MATERIALS AND METHODS: Eighty ewes were selected; forty each from Damani and Balkhi breeds reared in semi-intensive system (SIS) and ES at Paharpur district, Dera Ismail Khan. Blood samples were collected in triplicate on days 0, 14, and 28 of May, and the molecular and behavioral stress, growth, and fertility rates were recorded. RESULTS: The highest growth and fertility rate were observed in both the breeds in SIS than in ES (p < 0.01). The values of stress indicators (cortisol, heat shock protein (HSP-70)) and behavioral stress parameters were found lower in Damani breed as compared to Balkhi breed in both rearing systems (p < 0.01). All the molecular stress and behavioral stress parameters were negatively associated with metabolic hormones (T3 and T4) (p < 0.01). A positive correlation was observed among all the molecular stress and behavioral stress parameters (p < 0.01). Similarly, T3 and T4 were positively interlinked to one another (p < 0.01). CONCLUSION: It was concluded that both Damani and Balkhi sheep showed lower stress levels and better fertility and growth parameter in SIS than ES system of rearing. Local Damani breed exhibited well tolerant ability and genetic adaptation to the local environment as compared to Balkhi breed.

Frozen-thawed gelatin-induced osteogenic cell sheets of canine adipose-derived mesenchymal stromal cells improved fracture healing in canine model.

We assessed the efficacy of frozen-thawed gelatin-induced osteogenic cell sheet (FT-GCS) compared to that of fresh gelatin-induced osteogenic cell sheet (F-GCS) with adipose-derived mesenchymal stromal cells (Ad-MSCs) used as the control. The bone differentiation capacity of GCS has already been studied. On that basis, the experiment was conducted to determine ease of use of GCS in the clinic. In vitro evaluation of F-GCS showed 3-4 layers with an abundant extracellular matrix (ECM) formation; however, cryopreservation resulted in a reduction of FT-GCS layers to 2-3 layers. Cellular viabilities of F-GCS and FT-GCS did not vary significantly. Moreover, there was no significant difference in mRNA expressions of Runx2, ß-catenin, OPN, and BMP-7 between F-GCS and FT-GCS. In an in vivo experiment, both legs of six dogs with transverse radial fractures were randomly assigned to one of three groups: F-GCS, FT-GCS, or control. Fracture sites were wrapped with the respective cell sheets and fixed with 2.7 mm locking plates and six screws. At 8 weeks after the operations, bone samples were collected and subjected to micro computed tomography and histopathological examination. External volumes of callus as a portion of the total bone volume in control, F-GCS, and FT-GCS groups were 49.6%, 45.3%, and 41.9%, respectively. The histopathological assessment showed that both F-GCS and FT-GCS groups exhibited significantly (p < 0.05) well-organized, mature bone with peripheral cartilage at the fracture site compared to that of the control group. Based on our results, we infer that the cryopreservation process did not significantly affect the osteogenic ability of gelatin-induced cell sheets.

Application of tuned liquid column ball damper (TLCBD) for improved vibration control performance of multi-storey structure.

Tuned liquid column ball damper (TLCBD) is a passive control device used for controlling the building vibrations induced from wind or earthquakes. TLCBD is a modified form of conventional tuned liquid column damper (TLCD). This paper studies the effect of TLCBD on the four-storey steel frame structure. The performance of the TLCBD is also compared with conventional TLCD. The analytical model of both TLCD and TLCBD is presented here. The effectiveness of these analytical models is examined experimentally by series of shaking table tests under different excitation levels including harmonic loadings and seismic excitations. In TLCBD, the vibration is reduced significantly as compared to TLCD by using steel ball as a moving orifice. The difference in diameter of steel ball and tube, containing the liquid column, acts as an orifice which moves with the movement of the ball. This moving orifice phenomenon enhanced the vibration reduction effect by resisting the water motion in the TLCBD. Root mean square (RMS) and peak values of acceleration were calculated for each loading and each storey of uncontrolled and controlled structures. Comparison of the time histories of controlled and uncontrolled structures for different loadings is also reported. Results indicate that the TLCBD is more effective in the earthquake scenarios as compared to the harmonic excitations. The TLCBD controls the vibration of the primary structure significantly in vibration reduction.

Selenium-enriched probiotics improve hepatic protection by regulating pro-inflammatory cytokines and antioxidant capacity in broilers under heat stress conditions.

OBJECTIVE: High ambient temperature in poultry is a challenging and fatal stress among environmental factors. It affects the production quality, damages the liver, and increases mortality in broilers. The present study is focused to explore appropriate utilization of Selenium (Se) as a feed additive in broiler chickens against high temperature. MATERIALS AND METHODS: Day-old male broiler chickens (Ross 308) (n = 200) were grouped according to the supplements used in their basal diets such as: corn-soybean basal diet as control (Con), a basal diet containing sodium selenite, basal diet with probiotics, and a basal diet containing selenium-enriched probiotics (SP). At the end of the experimental period of 42 days, the liver was isolated and was used to determine the antioxidant capacity through a spectrophotometer. Inflammatory and anti-inflammatory cytokines production in the liver was measured through a real-time polymerase chain reaction. RESULTS: Hepatic analyses revealed the decreased level of malondialdehyde, whereas glutathione, glutathione peroxidase (GSH-Px), and superoxide dismutase levels were increased in the SP group. Furthermore, supplementation of SP significantly up-regulated the mRNA expression of glutathione peroxidase 1 (GPx1), GPx4, IL6, and IL10 and down-regulated the expression of pro-inflammatory cytokines. CONCLUSION: It is thus concluded that SP as a potential nutritive supplement may facilitate hepatic protection by suppressing hepatic oxidation, inflammation, and necrosis during the high ambient temperature of summer.

Therapeutic Effects of Intravenous Injection of Fresh and Frozen Thawed HO-1-Overexpressed Ad-MSCs in Dogs with Acute Spinal Cord Injury.

Owing to the antioxidant and anti-inflammatory functions of hemeoxygenase-1 (HO-1), HO-1-expressing canine adipose-derived mesenchymal stem cells (Ad-MSCs) could be efficacious in treating spinal cord injury (SCI). Further, frozen thawed HO-1 Ad-MSCs could be instantly available as an emergency treatment for SCI. We compared the effects of intravenous treatment with freshly cultured HO-1 Ad-MSCs (HO-1 MSCs), only green fluorescent protein-expressing Ad-MSCs (GFP MSCs), and frozen thawed HO-1 Ad-MSCs (FT-HO-1 MSCs) in dogs with acute SCI. For four weeks, dogs were evaluated for improvement in hind limb locomotion using a canine Basso Beattie Bresnahan (cBBB) score. Upon completion of the study, injured spinal cord segments were harvested and used for western blot and histopathological analyses. All cell types had migrated to the injured spinal cord segment. The group that received HO-1 MSCs showed significant improvement in the cBBB score within four weeks. This group also showed significantly higher expression of NF-M and reduced astrogliosis. There was reduced expression of proinflammatory cytokines (IL6, TNF-α, and IL-1ß) and increased expression of anti-inflammatory markers (IL-10, HO-1) in the HO-1 MSC group. Histopathological assessment revealed decreased fibrosis at the epicenter of the lesion and increased myelination in the HO-1 MSC group. Together, these data suggest that HO-1 MSCs could improve hind limb function by increasing the anti-inflammatory reaction, leading to neural sparing. Further, we found similar results between GFP MSCs and FT-HO-1 MSCs, which suggest that FT-HO-1 MSCs could be used as an emergency treatment for SCI.

Improved Healing after the Co-Transplantation of HO-1 and BDNF Overexpressed Mesenchymal Stem Cells in the Subacute Spinal Cord Injury of Dogs.

Abundant expression of proinflammatory cytokines after a spinal cord injury (SCI) creates an inhibitory microenvironment for neuroregeneration. The mesenchymal stem cells help to mitigate the inflammation and improve neural growth and survival. For this purpose, we potentiated the function of adipose-derived mesenchymal stem cells (Ad-MSCs) by transfecting them with brain-derived neurotrophic factor (BDNF) and heme oxygenase-1 (HO-1), through a lentivirus, to produce BDNF overexpressed Ad-MSCs (BDNF-MSCs), and HO-1 overexpressed Ad-MSCs (HO-1-MSCs). Sixteen SCI beagle dogs were randomly assigned into four treatment groups. We injected both HO-1 and BDNF-overexpressed MSCs as a combination group, to selectively control inflammation and induce neuroregeneration in SCI dogs, and compared this with BDNF-MSCs, HO-1-MSCs, and GFP-MSCs injected dogs. The groups were compared in terms of improvement in canine Basso, Beattie, and Bresnahan (cBBB) score during 8 weeks of experimentation. After 8 weeks, spinal cords were harvested and subjected to western blot analysis, immunofluorescent staining, and hematoxylin and eosin (H&E) staining. The combination group showed a significant improvement in hindlimb functions, with a higher BBB score, and a robust increase in neuroregeneration, depicted by a higher expression of Tuj-1, NF-M, and GAP-43 due to a decreased expression of the inflammatory markers interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α), and an increased expression of interleukin-10 (IL-10) ( P ≤ 0.05). H&E staining showed more reduced intraparenchymal fibrosis in the combination group than in other groups ( P ≤ 0.05). It was thus suggested that the cotransplantation of HO-1 and BDNF-MSCs is more effective in promoting the healing of SCI. HO-1-MSCs reduce inflammation, which favors BDNF-induced neuroregeneration in SCI of dogs.

Different Bone Healing Effects of Undifferentiated and Osteogenic Differentiated Mesenchymal Stromal Cell Sheets in Canine Radial Fracture Model.

Cell sheets technology is being available for fracture healing. This study was performed to clarify bone healing mechanism of undifferentiated (UCS) and osteogenic (OCS) differentiated mesenchymal stromal cell (MSC) sheets in the fracture model of dogs. UCS and OCS were harvested at 10 days of culture. Transverse fractures at the radius of six beagle dogs were assigned into three groups (n = 4 in each group) i.e. UCS, OCS and control. The fractures were fixed with a 2.7 mm locking plate and six screws. Cell sheets were wrapped around the fracture site. Bones were harvested 8 weeks after operation, then scanned by micro-computed tomography (micro-CT) and analyzed histopathologically. The micro-CT revealed different aspects of bone regeneration among the groups. The percentages of external callus volume out of total bone volume in control, UCS, and OCS groups were 42.1, 13.0 and 4.9% (p < 0.05) respectively. However, the percentages of limbs having connectivity of gaps were 25, 12.5 and 75% respectively. In histopathological assessments, OCS group showed well organized and mature woven bone with peripheral cartilage at the fracture site, whereas control group showed cartilage formation without bone maturation or ossification at the fracture site. Meanwhile, fracture site was only filled with fibrous connective tissue without endochondral ossification and bone formation in UCS group. It was suggested that the MSC sheets reduced the quantity of external callus, and OCS induced the primary bone healing.

Gelatin positively regulates the immunosuppressive capabilities of adipose-derived mesenchymal stem cells.

This characteristics of adipose-derived mesenchymal stem cells (Ad-MSCs) can be selectively enhanced by altering the culture environment. We evaluated the effects of gelatin on Ad-MSCs when used in combination with culture media. Ad-MSCs were initially cultured in 0%, 0.5%, 1%, 2%, and 4% gelatin in Dulbecco's modified Eagle's medium (DMEM) to evaluate cell proliferation. This expression of inflammatory, antiinflammatory, antioxidant, and osteogenic markers was then assessed by rtPCR in Ad-MSCs cultured in 0.5% gelatin in DMEM (GMSCs), and without gelatin (MSCs), for 5 and 10 days. We found that 0.5% gelatin significantly increased the proliferation rate of Ad-MSCs after 24 h of incubation, up until 72 h. GMSCs had upregulated IL-10, VEGF, and HO-1 after 5 and 10 days of incubation, while IL-6 and TNF-α were upregulated after 5 days and then significantly decreased after 10 days of incubation. The osteogenic factors BMP-7, AXIN, and ß-catenin were significantly upregulated in GMSCs after 5 and 10 days. Notably, there was 5- to 8-fold higher expression of BMP-7 in GMSCs than in MSCs. We conclude that culture medium containing 0.5% gelatin enhances the proliferation rate, induces immunosuppression, and activates BMP-7 and the wnt/AXIN/ß-catenin pathway in Ad-MSCs.