CORAL: Monte Carlo based global QSAR modelling of Bruton tyrosine kinase inhibitors using hybrid descriptors

Global QSAR modelling was performed to predict the pIC₅₀ values of 233 diverse heterocyclic compounds as BTK inhibitors with the Monte Carlo algorithm of CORAL software using the DCW hybrid descriptors extracted from SMILES notations of molecules. The dataset of 233 BTK inhibitors was randomly split into training, invisible training, calibration and validation sets. The index of ideality of correlation was also applied to build and judge the predictability of the QSAR models. Eight global QSAR models based on the hybrid optimal descriptor using two target functions, i.e. TF₁ (W_IIC = 0) and TF₂ (W_IIC = 0.2) have been constructed. The statistical parameters of QSAR models computed by TF₂ are more reliable and robust and were used to predict the pIC₅₀ values. The model constructed for split 4 via TF₂ is regarded as the best model and the numerical values of r²_Train, r²_Valid, Q²_Train and Q²_Valid are equal to 0.7981, 0.7429, 0.7898 and 0.6784, respectively. By internal and external validation techniques, the predictability and reliability of the designed models have been assessed. The structural attributes responsible for the increase and decrease of pIC₅₀ of BTK inhibitors were also identified.

Morphometry and morphological analysis of carotico-clinoid foramen: an anatomical study with clinical implications

BACKGROUND

The dural fold between anterior and middle clinoid processes on mineralisation leads to the formation of caroticoclinoid foramen (CCF). Different morphology of this foramen presents with different clinical features. The present study reports the frequency of CCF in the population of Bihar, while providing an account of assimilated information from previous literature regarding the association of caroticoclinoid ligament ossification with age and human genetics.

MATERIALS AND METHODS

The study was conducted on 100 adult dry human skulls of unknown age and sex, and 50 lateral view radiographs of the head.

RESULTS

Of the 100 dry skull bones, 9 presented with different forms of CCF. Bilateral complete foramina were noticed in 2 (2%) skull bones, while the incomplete foramina were observed bilaterally in 3 (3%) and unilaterally in 4 (4%) skulls. The lateral view radiograph data (n = 50) presented with a bilateral foramen in one subject and unilateral complete CCF in two different subjects. On measurements of the diameters of the complete CCF the mean values observed were 4.06 mm and 4.51 mm on the right side, while that on the left side were 5.15 mm and 4.14 mm. For the incomplete foramina, the mean values for the vertical diameter were 4.48 mm on the right and 4.19 mm on the left side, respectively.

CONCLUSIONS

The frequency of CCF in the present study population of Bihar was much lesser than that of previously studied populations. However, the variation in frequency of different morphological types of CCF was observed to be the same across populations. The variations in CCF's metric data could help in predicting the morphological changes it causes to the clinoidal segment of the internal carotid artery, as well as in distinguishing its varieties.

Trends in packaging material for food products: historical background, current scenario, and future prospects

The commercial demand for food products and dietary supplements has increased drastically in the last few decades. The packed food products and nutritional supplements have made a profound impact on the modern human lifestyle. Since ancient times, storage and long-term use of food products remain a significant challenge for humans. There are different parameters for the evaluation of food products and dietary supplements broadly categorized as quality control and quality assurance. On an average million tons of food, materials get spoiled daily worldwide due to lack of storage and transportation point out packaging systems inequalities. To ensure the quality of packed food products and nutritional supplements among available measures, packaging remained an important event and had been refined from time to time to provide a standard. Over a period, the packaging industry has evolved using modern technology from the conventional methods of new generation packaging, including glass, wood, and paper to most new biodegradable materials. The ancient pattern of packaging; manual packaging has been taken over by an automated system of packing, resulting in enhanced output with minimal chance of damage to valuable products for humanity. The article will emphasize new insights into current packaging system not only provide the quality of these products but also in aiming new heights beyond conventional technologies and consumer opinions. In the present study, we have given more emphasis on novel methods of packaging, the packaging materials, quality of packed products, and their impacts of food products on the environment.

First molecular modelling report on tri-substituted pyrazolines as phosphodiesterase 5 (PDE5) inhibitors through classical and machine learning based multi-QSAR analysis

Phosphodiesterase 5 (PDE5) falls under a broad category of metallohydrolase enzymes responsible for the catalysis of the phosphodiesterase bond, and thus it can terminate the action of cyclic guanosine monophosphate (cGMP). Overexpression of this enzyme leads to development of a number of pathological conditions. Thus, targeting the enzyme to develop inhibitors could be useful for the treatment of erectile dysfunction as well as pulmonary hypertension. In the current study, several molecular modelling techniques were utilized including Bayesian classification, single tree and forest tree recursive partitioning, and genetic function approximation to identify crucial structural fingerprints important for optimization of tri-substituted pyrazoline derivatives as PDE5 inhibitors. Later, various machine learning models were also developed that could be utilized to predict and screen PDE5 inhibitors in the future.

Morphological and Transcriptional Responses to CRISPRi Knockdown of Essential Genes in Escherichia coli

CRISPR interference (CRISPRi) has facilitated the study of essential genes in diverse organisms using both high-throughput and targeted approaches. Despite the promise of this technique, no comprehensive arrayed CRISPRi library targeting essential genes exists for the model bacterium Escherichia coli, or for any Gram-negative species. Here, we built and characterized such a library. Each of the ∼500 strains in our E. coli library contains an inducible, chromosomally integrated single guide RNA (sgRNA) targeting an essential (or selected nonessential) gene and can be mated with a pseudo-Hfr donor strain carrying a dcas9 cassette to create a CRISPRi knockdown strain. Using this system, we built an arrayed library of CRISPRi strains and performed population and single-cell growth and morphology measurements as well as targeted follow-up experiments. These studies found that inhibiting translation causes an extended lag phase, identified new modulators of cell morphology, and revealed that the morphogene mreB is subject to transcriptional feedback regulation, which is critical for the maintenance of morphology. Our findings highlight canonical and noncanonical roles for essential genes in numerous aspects of cellular homeostasis. IMPORTANCE Essential genes make up only ∼5 to 10% of the genetic complement in most organisms but occupy much of their protein synthesis and account for almost all antibiotic targets. Despite the importance of essential genes, their intractability has, until recently, hampered efforts to study them. CRISPRi has facilitated the study of essential genes by allowing inducible and titratable depletion. However, all large-scale CRISPRi studies in Gram-negative bacteria thus far have used plasmids to express CRISPRi components and have been constructed in pools, limiting their utility for targeted assays and complicating the determination of antibiotic effects. Here, we use a modular method to construct an arrayed library of chromosomally integrated CRISPRi strains targeting the essential genes of the model bacterium Escherichia coli. This library enables targeted studies of essential gene depletions and high-throughput determination of antibiotic targets and facilitates studies targeting the outer membrane, an essential component that serves as the major barrier to antibiotics.

Prediction of power conversion efficiency of phenothiazine-based dye-sensitized solar cells using Monte Carlo method with index of ideality of correlation

Simplified molecular-input line-entry system (SMILES) notation and inbuilt Monte Carlo algorithm of CORAL software were employed to construct generative and prediction QSPR models for the analysis of the power conversion efficiency (PCE) of 215 phenothiazine derivatives. The dataset was divided into four splits and each split was further divided into four sets. A hybrid descriptor, a combination of SMILES and hydrogen suppressed graph (HSG), was employed to build reliable and robust QSPR models. The role of the index of ideality of correlation (IIC) was also studied in depth. We performed a comparative study to predict PCE using two target functions (TF₁ without IIC and TF₂ with IIC). Eight QSPR models were developed and the models developed with TF₂ was shown robust and reliable. The QSPR model generated from split 4 was considered a leading model. The different statistical benchmarks were computed for the lead model and these were rtraining set2=0.7784; rinvisible training set2=0.7955; rcalibration set2=0.7738; rvalidation set2=0.7506; Qtraining set2=0.7691; Qinvisible training set2=0.7850; Qcalibration set2=0.7501;  Qvalidation set2=0.7085; IIC_{training set} = 0.8590; IIC_{invisible training set} = 0.8297; IIC_{calibration set} = 0.8796; IIC_{validation set} = 0.8293, etc. The promoters of increase and decrease of endpoint PCE were also extracted.

Immunotherapy for Alzheimer's Disease: Current Scenario and Future Perspectives

Alzheimer's disease (AD) is a global health concern owing to its complexity, which often poses a great challenge to the development of therapeutic approaches. No single theory has yet accounted for the various risk factors leading to the pathological and clinical manifestations of dementia-type AD. Therefore, treatment options targeting various molecules involved in the pathogenesis of the disease have been unsuccessful. However, the exploration of various immunotherapeutic avenues revitalizes hope after decades of disappointment. The hallmark of a good immunotherapeutic candidate is not only to remove amyloid plaques but also to slow cognitive decline. In line with this, both active and passive immunotherapy have shown success and limitations. Recent approval of aducanumab for the treatment of AD demonstrates how close passive immunotherapy is to being successful. However, several major bottlenecks still need to be resolved. This review outlines recent successes and challenges in the pursuit of an AD vaccine.

Study of Change in Physico-Chemical Parameters by Treatment of Sludge from Common Effluent Treatment Plant (CETP) with Earthworms

One of the most vital problems of environmental protection concern is that of solid waste disposal. This problem continues to grow with the growth of population and the development of industries. The Common Effluent Treatment Plant (CETP) already establishes itself as a service to society at large, contributing towards a cleaner environment. However, the inappropriate disposal of CETP’s hazardous sludge can cause serious environmental problems. The sludge if sent for landfilling may cause groundwater contamination, changing the soil fertility parameters as well. The research presented here is carried out to explore the ability of an epigeic earthworm Eudrilus eugeniae to transform the sludge produced from CETP into a value-added product i.e., vermicompost. In this study, six samples of feed mixture were used with different ratios of CETP sludge, cow dung, and sawdust. Physico-chemical parameters such as pH, Electrical Conductivity (EC), Volatile Solids (VS), Total Nitrogen (TN), Nitrate Nitrogen (NO3--N), Ammonium Nitrogen (NH4+-N) were characterized to analyze the quality of the compost formed. All these parameters are in the agreement with recommended standards of mature compost. The result shows that vermicomposting technique when used, epigeic earthworm Eudrilus eugeniae can work as a favorable alternative solution for the disposal of CETP sludge.

Combining tumor deposits with the number of lymph node metastases to improve the prognostic accuracy in stage III colon cancer: a post hoc analysis of the CALGB/SWOG 80702 phase III study (Alliance)☆

BACKGROUND

In colon cancer, tumor deposits (TD) are considered in assigning prognosis and staging only in the absence of lymph node metastasis (i.e. stage III pN1c tumors). We aimed to evaluate the prognostic value of the presence and the number of TD in patients with stage III, node-positive colon cancer.

PATIENTS AND METHODS

All participants from the CALGB/SWOG 80702 phase III trial were included in this post hoc analysis. Pathology reports were reviewed for the presence and the number of TD, lymphovascular and perineural invasion. Associations with disease-free survival (DFS) and overall survival (OS) were evaluated by multivariable Cox models adjusting for sex, treatment arm, T-stage, N-stage, lymphovascular invasion, perineural invasion and lymph node ratio.

RESULTS

Overall, 2028 patients were included with 524 (26%) TD-positive and 1504 (74%) TD-negative tumors. Of the TD-positive patients, 80 (15.4%) were node negative (i.e. pN1c), 239 (46.1%) were pN1a/b (<4 positive lymph nodes) and 200 (38.5%) were pN2 (≥4 positive lymph nodes). The presence of TD was associated with poorer DFS [adjusted hazard ratio (aHR) = 1.63, 95% CI 1.33-1.98] and OS (aHR = 1.59, 95% CI 1.24-2.04). The negative effect of TD was observed for both pN1a/b and pN2 groups. Among TD-positive patients, the number of TD had a linear negative effect on DFS and OS. Combining TD and the number of lymph node metastases, 104 of 1470 (7.1%) pN1 patients were re-staged as pN2, with worse outcomes than patients confirmed as pN1 (3-year DFS rate: 65.4% versus 80.5%, P = 0.0003; 5-year OS rate: 87.9% versus 69.1%, P = <0.0001). DFS was not different between patients re-staged as pN2 and those initially staged as pN2 (3-year DFS rate: 65.4% versus 62.3%, P = 0.4895).

CONCLUSION

Combining the number of TD and the number of lymph node metastases improved the prognostication accuracy of tumor-node-metastasis (TNM) staging.

Constraints on Cosmic Strings Using Data from the Third Advanced LIGO-Virgo Observing Run

We search for gravitational-wave signals produced by cosmic strings in the Advanced LIGO and Virgo full O3 dataset. Search results are presented for gravitational waves produced by cosmic string loop features such as cusps, kinks, and, for the first time, kink-kink collisions. A template-based search for short-duration transient signals does not yield a detection. We also use the stochastic gravitational-wave background energy density upper limits derived from the O3 data to constrain the cosmic string tension Gμ as a function of the number of kinks, or the number of cusps, for two cosmic string loop distribution models. Additionally, we develop and test a third model that interpolates between these two models. Our results improve upon the previous LIGO-Virgo constraints on Gμ by 1 to 2 orders of magnitude depending on the model that is tested. In particular, for the one-loop distribution model, we set the most competitive constraints to date: Gμ≲4×10^{-15}. In the case of cosmic strings formed at the end of inflation in the context of grand unified theories, these results challenge simple inflationary models.

Constraints on Cosmic Strings Using Data from the Third Advanced LIGO-Virgo Observing Run

We search for gravitational-wave signals produced by cosmic strings in the Advanced LIGO and Virgo full O3 dataset. Search results are presented for gravitational waves produced by cosmic string loop features such as cusps, kinks, and, for the first time, kink-kink collisions. A template-based search for short-duration transient signals does not yield a detection. We also use the stochastic gravitational-wave background energy density upper limits derived from the O3 data to constrain the cosmic string tension Gμ as a function of the number of kinks, or the number of cusps, for two cosmic string loop distribution models. Additionally, we develop and test a third model that interpolates between these two models. Our results improve upon the previous LIGO-Virgo constraints on Gμ by 1 to 2 orders of magnitude depending on the model that is tested. In particular, for the one-loop distribution model, we set the most competitive constraints to date: Gμ≲4×10^{-15}. In the case of cosmic strings formed at the end of inflation in the context of grand unified theories, these results challenge simple inflationary models.

Cloning, characterisation and expression of the SERPINB14 gene, and association of promoter polymorphisms with egg quality traits in layer chicken

1. Ovalbumin (SERPINB14) is the most abundant protein present in egg white contributing about 54% of the total egg protein. In this study, the objectives were to clone and characterise the coding sequence of the SERPINB14 gene, to explore its expression profile, identify polymorphisms in the promoter of the gene and explore any association with egg quality traits in White Leghorn chickens.2. SNPs and mRNA expression of SERPINB14 in White Leghorn chicken lines were detected by PCR-single strand conformation polymorphism (SSCP) along with sequencing and qPCR. The open reading frame (ORF) was cloned in an expression plasmid vector and sequenced.3. The ORF of this gene was 1161 bp encoding a peptide of 386 amino acids. There were three SNPs observed in the coding region of the gene, one of which was of the mis-sense type, having c562G>A transition which resulted in substitution of alanine to threonine at position 188 in the protein sequence. In both the lines, an increase in expression of the gene was observed after onset of egg production with peak expression at the 40^th week of age compared to before onset of lay. The SERPINB14 gene was expressed in the magnum, but not in ovary and infundibulum, tissues of each White Leghorn line. The promoter region of the gene showed SNPs with three haplotypes; H1, H2, and H3. The haplo groups were associated with the egg weight and age at sexual maturity in the IWI line and Haugh unit and albumin index in the IWK line.4. It was concluded that the ORF of SERPINB14 gene in White Leghorn chicken lines is polymorphic. The promoter region of the gene is also polymorphic and has significant (P < 0.05) association with Haugh unit and egg weight in IWK and IWI chicken lines, respectively.

The perspectives of biomarker-based electrochemical immunosensors, artificial intelligence and the Internet of Medical Things toward COVID-19 diagnosis and management

The World Health Organization (WHO) has declared the COVID-19 an international health emergency due to the severity of infection progression, which became more severe due to its continuous spread globally and the unavailability of appropriate therapy and diagnostics systems. Thus, there is a need for efficient devices to detect SARS-CoV-2 infection at an early stage. Nowadays, the reverse transcription polymerase chain reaction (RT-PCR) technique is being applied for detecting this virus around the globe; however, factors such as stringent expertise, long diagnostic times, invasive and painful screening, and high costs have restricted the use of RT-PCR methods for rapid diagnostics. Therefore, the development of cost-effective, portable, sensitive, prompt and selective sensing systems to detect SARS-CoV-2 in biofluids at fM/pM/nM concentrations would be a breakthrough in diagnostics. Immunosensors that show increased specificity and sensitivity are considerably fast and do not imply costly reagents or instruments, reducing the cost for COVID-19 detection. The current developments in immunosensors perhaps signify the most significant opportunity for a rapid assay to detect COVID-19, without the need of highly skilled professionals and specialized tools to interpret results. Artificial intelligence (AI) and the Internet of Medical Things (IoMT) can also be equipped with this immunosensing approach to investigate useful networking through database management, sharing, and analytics to prevent and manage COVID-19. Herein, we represent the collective concepts of biomarker-based immunosensors along with AI and IoMT as smart sensing strategies with bioinformatics approach to monitor non-invasive early stage SARS-CoV-2 development, with fast point-of-care (POC) diagnostics as the crucial goal. This approach should be implemented quickly and verified practicality for clinical samples before being set in the present times for mass-diagnostic research.

Linear lesions in dermatology: a clinicoaetiopathological study

BACKGROUND

Linear lesions are fairly common in our daily practice. However, the appearance of these lesions can vary, thus complicating the diagnosis.

AIMS

To study the various clinical presentations, the demographic profile of patients and the clinicopathological correlations of dermatoses presenting with a linear distribution.

METHODS

We conducted an institution-based, cross-sectional, descriptive study of 281 consecutive patients with linear lesions attending dermatology clinics. MedCalc software (V11.6) was used for statistical analysis.

RESULTS

Patients were divided into eight groups: lesions along the lines of Blaschko (n = 136), lesions along blood vessels (n = 3), lesions along lymphatics (n = 3), Koebner phenomenon (n = 24), autoinoculation (n = 24), external factors (n = 45), infestations (n = 2) and 'other' (n = 44). The mean age at presentation was 24.50 ± 18.82 years and the male/female ratio was 1.32 : 1. The commonest symptom was itching/burning (56.94% of patients), while the commonest site was the arm (44.48%); followed by the leg (30.60%), trunk and abdomen (22.42%), head and neck (19.20%), and genitalia (0.35%). Apart from the common cases, there was a wide gamut of rare conditions (e.g. angiokeratoma circumscriptum naeviforme, porokeratotic eccrine ostial and dermal duct naevus, Blaschko-linear syringocystadenoma papilliferum, progressive cribriform and zosteriform hyperpigmentation, unilateral naevoid acanthosis nigricans, fixed drug eruption, discoid lupus erythematosus).

CONCLUSION

Linear lesions act as diagnostic clues to many dermatological conditions, therefore, the importance of meticulous examination in clinical dermatology cannot be overemphasized.

A strategy to enhance the photocatalytic efficiency of α-Fe2O3

The photocatalytic dye degradation of pure α-Fe₂O₃ and different concentration of Co doped α-Fe₂O₃ is explored. Facile hydrothermal method were employed to prepare pristine, 2% and 4% Co-Fe₂O₃ nanoparticles. Further, synthesized product confirmation studies were employed from X-ray diffraction, UV-vis spectrometry, Fourier-transform infrared, Raman, scanning electron microscope and transmission electron microscope studies. The rhombohedral nanoparticles developed were enhanced photocatalytic action. Photocatalytic dye degradation studies were analyzed for prepared three samples and the photocatalytic efficacy of the obtained photocatalysts was compared experimentally. Methylene blue dye was degraded under UV-light irradiation with 364 nm. The results showed that 4% Co doped α-Fe₂O₃ sample exhibited better dye degradation with 92% efficiency. The 4% doping of cobalt ions enhanced the photocatalytic property of Fe₂O₃ and is a good candidate for methylene blue dye degradation above 90%. In addition, strategy for photocatalytic efficiency enhancement was proposed.