Insights into renal and urological complications of inflammatory bowel disease.

Inflammatory bowel disease (IBD) is a chronic condition characterized by immune-mediated inflammation in the gastrointestinal tract, which follows a relapsing and remitting course. Apart from affecting the gastrointestinal tract, IBD also has extra-intestinal manifestations (EIMs). While the etiology of extraintestinal manifestation remains unclear, it is theorized to be based on immunological responses influenced by genetic factors. Renal involvement is one of the EIMs observed in ulcerative colitis and Crohn's disease. The renal manifestations in IBD patients encompass a range of conditions including nephrolithiasis, amyloidosis, tubulointerstitial nephritis, glomerulonephritis (GN), obstructive pathologies, and chronic kidney disease (CKD). The incidence of CKD in IBD patients varies from 5%-15%. The decline in renal function can stem from various factors such as direct inflammatory damage to the kidneys leading to glomerular or tubular injury, or from complications like recurrent stones, amyloidosis, or GN. Additionally, nephrotoxic medications used in treating IBD, such as TNF-α inhibitors, calcineurin inhibitors, and aminosalicylates, can exacerbate the decline in renal function. Currently, there is a lack of consensus regarding these patients' screening and renal function monitoring. This review aims to assess the existing literature on the different renal complications among individuals with IBD, shedding light on their pathophysiology and management.

Microbially derived surfactants: an ecofriendly, innovative, and effective approach for managing environmental contaminants.

The natural environment is often contaminated with hydrophobic pollutants such as long-chain hydrocarbons, petrochemicals, oil spills, pesticides, and heavy metals. Hydrophobic pollutants with a toxic nature, slow degradation rates, and low solubility pose serious threats to the environment and human health. Decontamination based on conventional chemical surfactants has been found to be toxic, thereby limiting its application in pharmaceutical and cosmetic industries. In contrast, biosurfactants synthesized by various microbial species have been considered superior to chemical counterparts due to their non-toxic and economical nature. Some biosurfactants can withstand a wide range of fluctuations in temperature and pH. Recently, biosurfactants have emerged as innovative biomolecules not only for solubilization but also for the biodegradation of environmental pollutants such as heavy metals, pesticides, petroleum hydrocarbons, and oil spills. Biosurfactants have been well documented to function as emulsifiers, dispersion stabilizers, and wetting agents. The amphiphilic nature of biosurfactants has the potential to enhance the solubility of hydrophobic pollutants such as petroleum hydrocarbons and oil spills by reducing interfacial surface tension after distribution in two immiscible surfaces. However, the remediation of contaminants using biosurfactants is affected considerably by temperature, pH, media composition, stirring rate, and microorganisms selected for biosurfactant production. The present review has briefly discussed the current advancements in microbially synthesized biosurfactants, factors affecting production, and their application in the remediation of environmental contaminants of a hydrophobic nature. In addition, the latest aspect of the circular bioeconomy is discussed in terms of generating biosurfactants from waste and the global economic aspects of biosurfactant production.

Millets: a nutritional powerhouse for ensuring food security.

MAIN CONCLUSION: Millets are important food source to ensure global food and nutritional security and are associated with health benefits. Millets have emerged as a nutritional powerhouse with the potential to address food security challenges worldwide. These ancient grains, which come in various forms, including finger millet, proso millet, and pearl millet, among others, are essential to a balanced diet, since they provide a wide range of nutritional advantages. Millets have a well-rounded nutritional profile with a high protein, dietary fiber, vitamin, and mineral content for optimal health and wellness. In addition to their nutritional advantages, millets exhibit remarkable adaptability and durability to various agroecological conditions, making them a valuable resource for smallholder farmers functioning in resource-poor regions. Promoting the growth and use of millet can lead to several benefits that researchers and development experts may discover, including improved nutrition, increased food security, and sustainable agricultural methods. Therefore, millets are food crops, that are climate smart, nutritional, and food secured to feed the increasing global population, and everyone could have a healthier, more resilient future.

An Improved Chromosome-scale Genome Assembly and Population Genetics resource for Populus tremula.

Aspen (Populus tremula L.) is a keystone species and a model system for forest tree genomics. We present an updated resource comprising a chromosome-scale assembly, population genetics and genomics data. Using the resource, we explore the genetic basis of natural variation in leaf size and shape, traits with complex genetic architecture. We generated the genome assembly using long-read sequencing, optical and high-density genetic maps. We conducted whole-genome resequencing of the Umeå Aspen (UmAsp) collection. Using the assembly and re-sequencing data from the UmAsp, Swedish Aspen (SwAsp) and Scottish Aspen (ScotAsp) collections we performed genome-wide association analyses (GWAS) using Single Nucleotide Polymorphisms (SNPs) for 26 leaf physiognomy phenotypes. We conducted Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq), identified genomic regions of accessible chromatin, and subset SNPs to these regions, improving the GWAS detection rate. We identified candidate long non-coding RNAs in leaf samples, quantified their expression in an updated co-expression network, and used this to explore the functions of candidate genes identified from the GWAS. A GWAS found SNP associations for seven traits. The associated SNPs were in or near genes annotated with developmental functions, which represent candidates for further study. Of particular interest was a ~177-kbp region harbouring associations with several leaf phenotypes in ScotAsp. We have incorporated the assembly, population genetics, genomics, and GWAS data into the PlantGenIE.org web resource, including updating existing genomics data to the new genome version, to enable easy exploration and visualisation. We provide all raw and processed data to facilitate reuse in future studies.

Biogenic synthesis of silver nanoparticle by Cytobacillus firmus isolated from the river sediment with potential antimicrobial properties against Edwardsiella tarda.

The aquatic environment, independent of their host, is more favorable to pathogenic bacteria than the terrestrial environment. Consequently, pathogenic bacteria can reach very high densities around aquatic animals and can cause high mortality. The conventional approach, such as antibiotics, has minimal effectiveness. Additionally, due to the emergence of (multiple) resistance, their use is under intense scientific and public scrutiny. Hence, there is a need for the development of alternative control techniques, with an emphasis on prevention, which is likely to be more cost-effective. In this study, a potential bacterial strain Cytobacillus firmus was isolated from polluted river sediment and characterized using a comprehensive range of techniques including biochemical, 16S rRNA sequencing and antibiogram assay. The pathogenicity of the bacteria was tested in vivo on Labeo rohita fingerlings found as non-pathogenic. Further, the bacteria were found to synthesize silver nanoparticles (AgNPs) using AgNO3 as a substrate. The obtained AgNPs were characterized by various methods, including UV-vis spectroscopy, FTIR (Fourier-transform infrared spectroscopy), and Transmission Emission Microscopy (TEM). The study found that the AgNPs were 20 nm in size on average. The antimicrobial activity of synthesized AgNPs was examined against the model freshwater pathogenic bacteria, Edwardsiella tarda and both the MIC (Minimum Inhibitory Concentration) and MBC (Minimum Bactericidal Concentration) were 0.156 µM, while biofilm inhibition activity was also observed at 0.156 µM. The AgNPs showed no haemolytic activity at 0.313 µM. Our findings suggest that C. firmus mediated bacteriogenic AgNPs modulate the activity of common pathogenic bacteria E. tarda. The thoroughness of our research process gives us confidence in the potential of applying AgNPs in aquaculture as a considerable strategy to control the E. tarda infection.

In silico and in vitro evaluation of the immunogenic potential of Leishmania donovani ascorbate peroxidase and its derived peptides.

The control and eradication of any infectious disease is only possible with a potential vaccine, which has not been accomplished for human visceral leishmaniasis (VL). The lack of vaccines may increase the risk of VL outbreaks periodically in endemic zones. Identifying a reliable vaccine candidate for Leishmania is a major challenge. Here, we considered Leishmania donovani ascorbate peroxidase (LdAPx) for its in vitro evaluation with the hope of future vaccine candidates for VL. LdAPx was selected based on its unique presence in Leishmania and virulence in VL pathogenesis. Initially, we found antibodies against recombinant LdAPx (rLdAPx) in the serum of VL patients. Therefore, using bioinformatics, we predicted and selected ten (MHC class I and II) peptides. These peptides, evaluated in vitro with PBMCs from healthy, active VL, and treated VL individuals induced PBMC proliferation, IFN-γ secretion, and Nitric Oxide (NO) production, indicating host-protective immune responses. Among them, three peptides (PEP6, PEP8, and PEP9) consistently elicited a Th1-type immune response in PBMCs. Treated VL individuals showed a stronger Th1 response compared to active VL patients and healthy subjects, highlighting these peptides' potential as vaccine candidates. Further studies are on the way toward evaluating the LdAPx-derived peptides or sub-unit vaccine in animal models against the L. donovani challenge.

Synthesis of 3-Methyleneisoindolin-1-ones via Rhodium(III)-Catalyzed C-H/N-H Activation and Annulation of N-Methoxybenzamides with Potassium Vinyltrifluoroborate.

Isoindolinones are vital heterocyclic compounds in medicinal chemistry, notable for their diverse bioactivities. Significant attention has been devoted to their preparation; however, existing methods are unsuitable for constructing unsubstituted 3-methyleneisoindolin-1-ones. Herein, we present a rhodium(III)-catalyzed method for synthesizing unsubstituted 3-methyleneisoindolin-1-ones via C-H/N-H activation and annulation of N-methoxybenzamides with potassium (ethenyl)trifluoroborate. This approach offers mild reaction conditions, high regioselectivity, and efficient yields. Interestingly, sterically demanding or heterocyclic N-methoxyaromaticamides resulted in the formation of 2-vinyl(hetero)aromatic amides instead of 3-methyleneisoindolin-1-ones. Mechanistic insights suggest a rhodacycle intermediate pathway, highlighting the method's potential for developing new bioactive isoindolinone derivatives.

Beyond the Liver: A Unique Case of Pyogenic Liver Abscess Caused by Peptostreptococcus micros Penetrating the Chest Wall.

Liver abscesses are uncommon pyogenic infections with diverse microbiology, often involving enteric gram-negative bacilli such as Escherichia coli and Klebsiella pneumoniae. Standard management includes antibiotic therapy and abscess drainage. We present a case of a 37-year-old male with chronic right upper quadrant abdominal pain, who was found to have an enlarging liver mass infiltrating the chest wall and right-side chest ribs, ultimately diagnosed as a large pyogenic liver abscess (PLA) extending into the chest wall. Notably, the abscess was attributed to Peptostreptococcus micros, a rarely isolated pathogen in liver abscesses. Despite initial unsuccessful percutaneous drainage, surgical intervention proved necessary for definitive treatment. This case underscores the diagnostic challenge posed by uncommon pathogens in liver abscesses and emphasizes the effectiveness of surgical drainage in managing refractory cases.

Trends of autoimmune liver disease inpatient hospitalization and mortality from 2011 to 2017: A United States nationwide analysis.

BACKGROUND: Autoimmune liver diseases (AiLD) encompass a variety of disorders that target either the liver cells (autoimmune hepatitis, AIH) or the bile ducts [(primary biliary cholangitis (PBC), and primary sclerosing cholangitis (PSC)]. These conditions can progress to chronic liver disease (CLD), which is characterized by fibrosis, cirrhosis, and hepatocellular carcinoma. Recent studies have indicated a rise in hospitalizations and associated costs for CLD in the US, but information regarding inpatient admissions specifically for AiLD remains limited. AIM: To examine the trends and mortality of inpatient hospitalization of AiLD from 2011 to 2017. METHODS: This study is a retrospective analysis utilizing the National Inpatient Sample (NIS) databases. All subjects admitted between 2011 and 2017 with a diagnosis of AiLD (AIH, PBC, PSC) were identified using the International Classification of Diseases (ICD-9) and ICD-10 codes. primary AiLD admission was defined if the first admission code was one of the AiLD codes. secondary AiLD admission was defined as having the AiLD diagnosis anywhere in the admission diagnosis (25 diagnoses). Subjects aged 21 years and older were included. The national estimates of hospitalization were derived using sample weights provided by NIS. χ 2 tests for categorical data were used. The primary trend characteristics were in-hospital mortality, hospital charges, and length of stay. RESULTS: From 2011 to 2017, hospitalization rates witnessed a significant decline, dropping from 83263 admissions to 74850 admissions (P < 0.05). The patients hospitalized were predominantly elderly (median 53% for age > 65), mostly female (median 59%) (P < 0.05), and primarily Caucasians (median 68%) (P < 0.05). Medicare was the major insurance (median 56%), followed by private payer (median 27%) (P < 0.05). The South was the top geographical distribution for these admissions (median 33%) (P < 0.05), with most admissions taking place in big teaching institutions (median 63%) (P < 0.05). Total charges for admissions rose from 66031 in 2011 to 78987 in 2017 (P < 0.05), while the inpatient mortality rate had a median of 4.9% (P < 0.05), rising from 4.67% in 2011 to 5.43% in 2017. The median length of stay remained relatively stable, changing from 6.94 days (SD = 0.07) in 2011 to 6.51 days (SD = 0.06) in 2017 (P < 0.05). Acute renal failure emerged as the most common risk factor associated with an increased death rate, affecting nearly 68% of patients (P < 0.05). CONCLUSION: AiLD-inpatient hospitalization showed a decrease in overall trends over the studied years, however there is a significant increase in financial burden on healthcare with increasing in-hospital costs along with increase in mortality of hospitalized patient with AiLD.

Computational modeling and uncertainty prediction of hyperelastic constitutive responses of damaged brain tissue under different temperature and strain rates.

The effect of strain rate and temperature on the hyperelastic material stress-strain characteristics of the damaged porcine brain tissue is evaluated in this present work. The desired constitutive responses are obtained using the commercially available finite element (FE) tool ABAQUS, utilizing 8-noded brick elements. The model's accuracy has been verified by comparing the results from the previously published literature. Further, the stress-strain behavior of the brain tissue is evaluated by varying the damages at various strain rates and temperatures (13, 20, 27, and 37°C) under compression test. Additionally, the sensitivity analysis of the model is computed to check the effect of input parameters, that is, the temperature, strain rate, and damages on the material properties (shear modulus). The modeling and discussion sections enumerate the inclusive features and model capabilities.

Ellagic acid mitigates heat-induced testicular detriment in a mouse model.

Heat stress has been shown to have a detrimental impact on testicular activity and spermatogenesis. Ellagic acid is a plant-derived organic compound that has a variety of biological functions. Thus, it is believed that ellagic acid may improve heat-stressed testicular dysfunction. There has been no research on the impact of ellagic acid on heat-stressed testicular dysfunction. The mice were divided into 4 groups. The first group was the normal control group (CN), and the second received heat stress (HS) by submerging the lower body for 15 min in a water bath with a thermostatically controlled temperature kept at 43°C (HS), and the third and fourth groups were subjected to heat-stress similar to group two and given two different dosages of ellagic acid (5 mg/kg (EH5) and 50 mg/kg (EH50) for 14 days. Ellagic acid at a dose of 50 mg/kg improved the level of circulating testosterone (increased 3ßHSD) and decreases the oxidative stress. The testicular and epididymal architecture along with sperm parameters also showed improvement. Ellagic acid treatment significantly increases the germ cell proliferation (GCNA, BrdU staining) and Bcl2 expression and decreases active caspase 3 expression. Heat stress downregulated the expression of AR, ER-α and ER-ß, and treatment with ellagic acid increased the expression of ER-α and ER-ß markers in the 50 mg/kg treatment group. Thus, our finding suggests that ellagic acid ameliorates heat-induced testicular impairment through modulating testosterone synthesis, germ cell proliferation, and oxidative stress. These effects could be manifested by regulating androgen and estrogen receptors. However, the two doses showed differential effects of some parameters, which require further investigation.

Bi-SeqCNN: A Novel Light-weight Bi-directional CNN Architecture for Protein Function Prediction.

Deep learning approaches, such as convolution neural networks (CNNs) and deep recurrent neural networks (RNNs), have been the backbone for predicting protein function, with promising state-of-the-art (SOTA) results. RNNs with an in-built ability (i) focus on past information, (ii) collect both short-and-long range dependency information, and (iii) bi-directional processing offers a strong sequential processing mechanism. CNNs, however, are confined to focusing on short-term information from both the past and the future, although they offer parallelism. Therefore, a novel bi-directional CNN that strictly complies with the sequential processing mechanism of RNNs is introduced and is used for developing a protein function prediction framework, Bi-SeqCNN. This is a sub-sequence-based framework. Further, Bi-SeqCNN + is an ensemble approach to better the prediction results. To our knowledge, this is the first time bi-directional CNNs are employed for general temporal data analysis and not just for protein sequences. The proposed architecture produces improvements up to +5.5% over contemporary SOTA methods on three benchmark protein sequence datasets. Moreover, it is substantially lighter and attain these results with (0.50-0.70 times) fewer parameters than the SOTA methods.

Lemmel Syndrome: Unveiling the Underrecognized Pancreatobiliary Diagnosis, Management Strategies, and Future Directions.

Lemmel syndrome, a rare condition, is characterized by biliary obstruction caused by a periampullary diverticulum (a pouch-like outgrowth of the duodenum near the ampulla of Vater). In our case, a 76-year-old male patient presented with epigastric pain and exhibited a cholestatic pattern on liver function tests. Imaging revealed dilated pancreatic and common bile ducts due to compression by a periampullary diverticulum (double duct sign: simultaneous dilation of the common bile duct and pancreatic duct). Upper endoscopy showed one medium-sized periampullary diverticulum. This case emphasizes the diagnostic process and the importance of considering Lemmel syndrome in differential diagnosis in elderly patients with biliary obstruction. We discuss the prevalence, diagnostic considerations, including imaging modalities, and treatment options, emphasizing the need for further research.

Sperm-Specific CatSper is Not Conserved in All Vertebrates and May Not be the Only Progesterone-Responsive Ion Channel Present in Sperm.

Progesterone (P4) acts as a key conserved signalling molecule in vertebrate reproduction. P4 is especially important for mature sperm physiology and subsequent reproductive success. "CatSpermasome", a multi-unit molecular complex, has been suggested to be the main if not the only P4-responsive atypical Ca2+-ion channel present in mature sperm. Altogether, here we analyse the protein sequences of CatSper1-4 from more than 500 vertebrates ranging from early fishes to humans. CatSper1 becomes longer in mammals due to sequence gain mainly at the N-terminus. Overall the conservation of full-length CatSper1-4 as well as the individual TM regions remain low. The lipid-water-interface residues (i.e. a 5 amino acid stretch sequence present on both sides of each TM region) also remain highly diverged. No specific patterns of amino acid distributions were observed. The total frequency of positively charged, negatively charged or their ratios do not follow in any specific pattern. Similarly, the frequency of total hydrophobic, total hydrophilic residues or even their ratios remain random and do not follow any specific pattern. We noted that the CatSper1-4 genes are missing in amphibians and the CatSper1 gene is missing in birds. The high variability of CatSper1-4 and gene-loss in certain clades indicate that the "CatSpermasome" is not the only P4-responsive ion channel. Data indicate that the molecular evolution of CatSper is mostly guided by diverse hydrophobic ligands rather than only P4. The comparative data also suggest possibilities of other Ca2+-channel/s in vertebrate sperm that can also respond to P4.

Comparative metagenomic analysis from Sundarbans ecosystems advances our understanding of microbial communities and their functional roles.

The Sundarbans mangrove, located at the mouth of the Ganges and Brahmaputra Rivers, is the world's largest tidal mangrove forest. These mangroves are also one of the most striking sources of microbial diversity, essential in productivity, conservation, nutrient cycling, and rehabilitation. Hence, the main objective of this study was to use metagenome analysis and provide detailed insight into microbial communities and their functional roles in the Sundarbans mangrove ecosystem. A comparative analysis was also done with a non-mangrove region of the Sundarbans ecosystem to assess the capability of the environmental parameters to explain the variation in microbial community composition. The study found several dominant bacteria, viz., Alphaproteobacteria, Actinomycetota, Bacilli, Clostridia, Desulfobacterota, Gammaproteobacteria, and Nitrospira, from the mangrove region. The mangrove sampling site reports several salt-tolerant bacteria like Alkalibacillus haloalkaliphilus, Halomonas anticariensis, and Salinivibrio socompensis. We found some probiotic species, viz., Bacillus clausii, Lactobacillus curvatus, Vibrio mediterranei and Vibrio fluvialis, from the Sundarbans mangrove. Nitrifying bacteria in Sundarbans soils were Nitrococcus mobilis, Nitrosococcus oceani, Nitrosomonas halophila, Nitrospirade fluvii, and others. Methanogenic archaea, viz., Methanoculleus marisnigri, Methanobrevibacter gottschalkii, and Methanolacinia petrolearia, were highly abundant in the mangroves as compared to the non-mangrove soils. The identified methanotrophic bacterial species, viz., Methylobacter tundripaludum, Methylococcus capsulatus, Methylophaga thiooxydans, and Methylosarcina lacus are expected to play a significant role in the degradation of methane in mangrove soil. Among the bioremediation bacterial species identified, Pseudomonas alcaligenes, Pseudomonas mendocina, Paracoccus denitrificans, and Shewanella putrefaciens play a significant role in the remediation of environmental pollution. Overall, our study shows for the first time that the Sundarbans, the largest mangrove ecosystem in the world, has a wide range of methanogenic archaea, methanotrophs, pathogenic, salt-tolerant, probiotic, nitrifying, and bioremediation bacteria.

Electrocatalytic Performance of 2D Monolayer WSeTe Janus Transition Metal Dichalcogenide for Highly Efficient H2 Evolution Reaction.

Nowadays, the development of clean and green energy sources is the priority interest of research due to increasing global energy demand and extensive usage of fossil fuels, which create pollutants. Hydrogen has the highest energy density by weight among all chemical fuels. For the commercial-scale production of hydrogen, water electrolysis is the best method, which requires an efficient, cost-effective, and earth-abundant electrocatalyst. Recent studies have shown that the 2D Janus transition metal dichalcogenides (JTMDs) are promising materials for use as electrocatalysts and are highly effective for electrocatalytic H2 evolution reaction (HER). Here, we report a 2D monolayer WSeTe JTMD, which is highly effective toward HER. We have studied the electronic properties of 2D monolayer WSeTe JTMD using the periodic hybrid DFT-D method, and a direct electronic band gap of 2.39 eV was obtained. We have explored the HER pathways, mechanisms, and intermediates, including various transition state (TS) structures (Volmer TS, i.e., H*-migration TS, Heyrovsky TS, and Tafel TS) using a molecular cluster model of the subject JTMD noted as W10Se9Te12. The present calculations reveal that the 2D monolayer WSeTe JTMD is a potential electrocatalyst for HER. It has the lowest energy barriers for all the TSs among other TMDs. It has been shown that the Heyrovsky energy barrier (= 8.72 kcal mol-1) in the case of the Volmer-Heyrovsky mechanism is larger than the Tafel energy barrier (= 3.27 kcal mol-1) in the Volmer-Tafel mechanism. Hence, our present study suggests that the formation of H2 is energetically more favorable via the Volmer-Tafel mechanism. This study helps to shed light on the rational design of 2D single-layer JTMD, which is highly effective toward HER, and we expect that the present work can be further extended to other JTMDs to find out the improved electrocatalytic performance.

Prefoldins are novel regulators of the unfolded protein response in artemisinin resistant Plasmodium falciparum malaria.

Emerging Artemisinin (ART) resistance in Plasmodium falciparum (Pf) poses challenges for the discovery of novel drugs to tackle ART-resistant parasites. Concentrated efforts toward the ART resistance mechanism indicated a strong molecular link of ART resistance with upregulated expression of unfolded protein response pathways involving Prefoldins (PFDs). However, a complete characterization of PFDs as molecular players taking part in ART resistance mechanism, and discovery of small molecule inhibitors to block this process have not been identified to date. Here, we functionally characterized all Pf Prefoldin subunits (PFD1-6) and established a causative role played by PFDs in ART resistance by demonstrating their expression in intra-erythrocytic parasites along with their interactions with Kelch13 protein through immunoprecipitation coupled MS/MS analysis. Systematic biophysical interaction analysis between all subunits of PFDs revealed their potential to form a complex. The role of PFDs in ART resistance was confirmed in orthologous yeast PFD6 mutants, where PfPFD6 expression in yeast mutants reverted phenotype to ART resistance. We identified an FDA-approved drug "Biperiden" that restricts the formation of Prefoldin complex and inhibits its interaction with its key parasite protein substrates, MSP-1 and α-tubulin-I. Moreover, Biperiden treatment inhibits the parasite growth in ART-sensitive Pf3D7 and resistant Pf3D7k13R539T strains. Ring survival assays that are clinically relevant to analyze ART resistance in Pf3D7k13R539T parasites demonstrate the potency of BPD to inhibit the growth of survivor parasites. Overall, our study provides the first evidence of the role of PfPFDs in ART resistance mechanisms and opens new avenues for the management of resistant parasites.

CrossPredGO: A Novel Light-weight Cross-modal Multi-attention Framework for Protein Function Prediction.

Proteins are represented in various ways, each contributing differently to protein-related tasks. Here, information from each representation (protein sequence, 3D structure, and interaction data) is combined for an efficient protein function prediction task. Recently, uni-modal has produced promising results with state-of-the-art attention mechanisms that learn the relative importance of features, whereas multi-modal approaches have produced promising results by simply concatenating obtained features using a computational approach from different representations which leads to an increase in the overall trainable parameters. In this paper, we propose a novel, light-weight cross-modal multi-attention (CrMoMulAtt) mechanism that captures the relative contribution of each modality with a lower number of trainable parameters. The proposed mechanism shows a higher contribution from PPI and a lower contribution from structure data. The results obtained from the proposed CrossPredGO mechanism demonstrate an increment in Fmax in the range of +(3.29 to 7.20)% with at most 31% lower trainable parameters compared with DeepGO and MultiPredGO.

Morin hydrate ameliorates Di-2-ethylhexyl phthalate (DEHP) induced hepatotoxicity in a mouse model via TNF-α and NF-κß signaling.

Di-(2-ethylhexyl) phthalic acid (DEHP) pollutes the environment, and posing a significant risk to human and animal health. Consequently, a successful preventative strategy against DEHP-induced liver toxicity needs to be investigated. Morin hydrate (MH), a flavanol compound, possesses toxic preventive attributes against various environmental pollutants. However, the effects of MH have not been investigated against DEHP-induced liver toxicity. Female Swiss albino mice were divided into four groups: control, DEHP (orally administered with 500 mg/kg, DEHP plus MH 10 mg/kg, and DEHP plus MH 100 mg/kg for 14 days. The results showed that the MH treatment ameliorated the DEHP-induced liver dysfunctions by decreasing the alanine transaminase (ALT), aspartate aminotransferase (AST), total bilirubin, liver histoarchitecture, fibrosis, and markers of oxidative stress. Furthermore, DEHP increased apoptosis, increased active caspase 3 and decreased B cell lymphoma-2 (Bcl-2) expression. However, the MH treatment showed a differential effect on these proteins; a lower dose increased, and a higher dose decreased the expression. Thus, a lower dose of MH could be involved in the disposal of damaged hepatocytes. Expression of Estrogen receptors alpha (ERα) also showed a similar trend with active caspase 3. Furthermore, the expression of Tumor necrosis factor alpha (TNF-α) and Nuclear factor-κß (NF-κß) were up-regulated by DEHP treatment, and MH treatment down-regulated the expression of these two inflammatory markers. Since this down-regulation of TNF-α and NF-κß coincides with improved liver functions against DEHP-induced toxicity, it can be concluded that MH-mediated liver function involves the singling of TNF-α and NF-κß.

Reinventing shake flask fermentation: The breathable flask.

Cultivating cells in shake flasks is a routine operation that is largely unchanged since its inception. A glass or plastic Erlenmeyer vessel with the primary gas exchange taking place across various porous plugs is used with media volumes typically ranging from 100 mL to 2 L. Oxygen limitation and carbon dioxide accumulation in the vessel is a major concern for studies involving shake flask cultures. In this study, we enhance mass transfer in a conventional shake flask by replacing the body wall with a permeable membrane. Naturally occurring concentration gradient across the permeable membrane walls facilitates the movement of oxygen and carbon dioxide between the flask and the external environment. The modified flask called the breathable flask, has shown a 40% improvement in mass transfer coefficient (kLa) determined using the static diffusion method. The prokaryotic cell culture studies performed with Escherichia coli showed an improvement of 28%-66% in biomass and 41%-56% in recombinant product yield. The eukaryotic cell culture study performed with Pichia pastoris expressing proinsulin exhibited a 40% improvement in biomass and 115% improvement in protein yield. The study demonstrates a novel approach to addressing the mass transfer limitations in conventional shake flask cultures. The proposed flask amplifies its value by providing a membrane-diffusion-based sensing platform for the integration of low-cost, noninvasive sensing capabilities for real-time monitoring of critical cell culture parameters like dissolved oxygen and dissolved carbon dioxide.