Extraction of knowledge graph of Covid-19 through mining of unstructured biomedical corpora

The number of biomedical articles published is increasing rapidly over the years. Currently there are about 30 million articles in PubMed and over 25 million mentions in Medline. Among these fundamentals, Biomedical Named Entity Recognition (BioNER) and Biomedical Relation Extraction (BioRE) are the most essential in analysing the literature. In the biomedical domain, Knowledge Graph is used to visualize the relationships between various entities such as proteins, chemicals and diseases. Scientific publications have increased dramatically as a result of the search for treatments and potential cures for the new Coronavirus, but efficiently analysing, integrating, and utilising related sources of information remains a difficulty. In order to effectively combat the disease during pandemics like COVID-19, literature must be used quickly and effectively. In this paper, we introduced a fully automated framework consists of BERT-BiLSTM, Knowledge graph, and Representation Learning model to extract the top diseases, chemicals, and proteins related to COVID-19 from the literature. The proposed framework uses Named Entity Recognition models for disease recognition, chemical recognition, and protein recognition. Then the system uses the Chemical - Disease Relation Extraction and Chemical - Protein Relation Extraction models. And the system extracts the entities and relations from the CORD-19 dataset using the models. The system then creates a Knowledge Graph for the extracted relations and entities. The system performs Representation Learning on this KG to get the embeddings of all entities and get the top related diseases, chemicals, and proteins with respect to COVID-19.

Recognition of Chemical Entities using Pattern Matching and Functional Group Classification

The two main challenges in chemical entity recognition are: (i) New chemical compounds are constantly being synthesized infinitely. (ii) High ambiguity in chemical representation in which a chemical entity is being described by different nomenclatures. Therefore, the identification and maintenance of chemical terminologies is a tough task. Since most of the existing text mining methods followed the term-based approaches, the problems of polysemy and synonymy came into the picture. So, a Named Entity Recognition (NER) system based on pattern matching in chemical domain is developed to extract the chemical entities from chemical documents. The Tf-idf and PMI association measures are used to filter out the non-chemical terms. The F-score of 92.19% is achieved for chemical NER. This proposed method is compared with the baseline method and other existing approaches. As the final step, the filtered chemical entities are classified into sixteen functional groups. The classification is done using SVM One against All multiclass classification approach and achieved the accuracy of 87%. One-way ANOVA is used to test the quality of pattern matching method with the other existing chemical NER methods.

9-(2,4-Difluorophenyl)-3,3,6,6-tetramethyl-3,4,5,6,7,9-hexahydro-2H-xanthene-1,8-dione

In the title compound, C₂₃H₂₄F₂O₃, the central pyran ring has a flat-boat conformation, whereas the two fused cyclo­hexenone rings adopt envelope conformations, with the C atom bearing the dimethyl substituent being the flap atom in each case. The pyran ring mean plane and the di­fluoro­phenyl ring are almost normal to each other, making a dihedral angle of 87.55 (4)°. In the crystal, mol­ecules are linked by pairs of C—H⋯O hydrogen bonds, forming inversion dimers with an R₂²(8) ring motif. The F atom at position 2 on the di­fluoro­phenyl ring is disordered over the 2- and 6-positions, and has a refined occupancy ratio of 0.932 (3):0.068 (3).

2-(4-Fluoro-phen-yl)-1-(3-meth-oxy-phen-yl)-4,5-dimethyl-1H-imidazole

In the title compound, C18H17FN2O, the imidazole ring makes dihedral angles of 68.81 (6) and 25.20 (8)° with the meth-oxy-phenyl and fluoro-phenyl rings, respectively. The dihedral angle between the meth-oxy-phenyl and fluoro-phenyl ring is 71.89 (6)°. In the crystal, mol-ecules are linked into inversion dimers with an R 2 (2)(8) graph-set motif by pairs of weak C-H⋯F inter-actions.

2,4-Bis(4-fluoro-phen-yl)-1,5-dimethyl-3-aza-bicyclo-[3.3.1]nonan-9-one

The asymmetric unit of the title compound, C₂₂H₂₃F₂NO, contains two independent mol­ecules, A and B. The bicyclic system adopts a twin-chair conformation in both mol­ecules. The dihedral angles between the fluoro­phenyl rings are 55.27 (8) and 56.37 (7)° in mol­ecules A and B, respectively. The NH groups are not involved in hydrogen bonding due to the steric hindrance of fluoro­phenyl groups. The crystal structure features weak C—H⋯O inter­actions.

1-(3-Methoxyphenyl)-4,5-dimethyl-2-phenyl-1H-imidazole

In the title compound, C₁₈H₁₈N₂O, the imidazole ring makes dihedral angles of 68.26 (7) and 22.45 (9)° with the meth­oxy­phenyl and phenyl rings, respectively. The dihedral angle between the meth­oxy­phenyl and phenyl ring is 71.86 (7)°. In the crystal, weak inter­molecular C—H⋯O and C—H⋯N hydrogen bonds link the mol­ecules into columns propagated in [101].

2,4-Bis(furan-2-yl)-1,5-dimethyl-3-aza-bicyclo-[3.3.1]nonan-9-one

In the title compound, C18H21NO3, the bicyclic ring system adopts a twin-chair conformation. The two methyl groups attached to the bicycle are in an equatorial orientation for both rings. One of the furan rings is disordered over two orientations with an occupancy ratio of 0.686 (6):0.314 (6). In the crystal, very long N-H⋯O hydrogen bonds connect the mol-ecules into a chain perpendicular to the ac plane.

Propan-2-yl r-4-(4-fluoro-phen-yl)-3-hy-droxy-c-6-methyl-2-phenyl-4,5-dihydro-2H-indazole-t-5-carboxyl-ate

In the title compound, C₂₄H₂₃FN₂O₃, the cyclo­hexene ring adopts a screw-boat conformation. The fluorobenzene ring attached to the cyclo­hexene ring and the phenyl ring attached to the indazole moiety are inclined to one another by 57.77 (13)°. In the crystal, mol­ecules are linked by O—H⋯N and C—H⋯O hydrogen bonds, forming chains with C(5) and C(10) graph-set motifs. There are also C—H⋯π inter­actions present. The isopropoxycarbonyl group undergoes considerable thermal motion.

16α,17α-Ep-oxy-17β-(1H-imidazol-1-yl)androst-4-en-3-one monohydrate

In the title compound, C(22)H(28)N(2)O(2)·H(2)O, rings B and C adopt chair conformations. Ring A adopts an envelope conformation, with the non-fused C atom adjacent to the fused C atom bearing a methyl group as the flap atom. Ring D also adopts an envelope conformation, with the fused C atom not bearing a methyl group as the flap atom. The water mol-ecule links the mol-ecules via O-H⋯O and O-H⋯N hydrogen bonds, forming zigzag chains which run parallel to the c axis. Weak C-H⋯O inter-actions also occur.

c-5-Hydroxy-r-2,c-4-bis(methoxycarbonyl)-t-5-methyl-t-3-(3-nitrophenyl)cyclohexanone

In the title compound, C₁₇H₁₉NO₈ [systematic name = dimethyl 4-hydroxy-4-methyl-2-(3-nitrophenyl)-6-oxocyclohexane-1,3-dicarboxylate], the cyclo­hexa­none ring exhibits a chair conformation. The meth­oxy­carbonyl groups are oriented in opposite directions with respect to the cyclo­hexa­none ring. In the crystal, O—H⋯O hydrogen bonds links the mol­ecules into chains running parallel to the a axis. These chains are connected by weak C—H⋯O hydrogen bonds, forming sheets parallel to the ab plane.

Growth and characterization of thiosemicarbazide hydrochloride: a semiorganic NLO material

Thiosemicarbazide hydrochloride (TSCHCL) was synthesized by mixing thiosemicarbazide and hydrochloride in 1:1 molar ratio in double distilled water. Single crystals of TSCHCL were grown by slow evaporation at room temperature and were characterized by single crystal X-ray diffraction study to determine the molecular structure and by FT-IR, (1)H and (13)C NMR spectral analyses to confirm the synthesized compound. Thermogravimetric and differential thermal analyses reveal the thermal stability of the crystal. The transmission spectrum of TSCHCL showed that the crystal is transparent in the wavelength range 380-1100 nm. High resolution X-ray diffractometry (HRXRD) was employed to evaluate the perfection of the grown crystal. Mechanical properties of the grown crystal were studied using Vickers microhardness test. Second harmonic generation efficiency of the powdered TSCHCL was tested using Nd:YAG laser and is ∼1.5 times that of potassium dihydrogen orthophosphate.

Diiodidobis(triphenylphosphine oxide)cadmium

In the title compound, [CdI₂{(C₆H₅)₃PO}₂], the Cd^II atom is ligated by two I atoms and two O atoms from two triphenyl­phosphine oxide ligands in a disorted tetra­hedral arrangement. While the O—Cd—I angles vary from 106.67 (7) to 111.23 (7)°, the O—Cd—O angle is 88.60 (10)° and the I—Cd—I angle angle is 125.47 (2)°. The crystal structure is stabilized by van der Waals forces only.

trans-Bis(dimethyl sulfoxide-κO)bis(thiosemicarbazide-κ2N1,S)cadmium dipicrate dihydrate

In the cation of the title compound, [Cd(CH₅N₃S)₂(C₂H₆OS)₂](C₆H₂N₃O₇)₂·2H₂O, the Cd^II atom is located on an inversion center. It is hexa­coordinated in an octahedral fashion by two thio­semicarbazide mol­ecules, which coordinate in a bidentate manner via the S and N atoms, and to the O atom of two dimethyl sufoxide (DMSO) mol­ecules. The charges are equilibrated by two picrate anions and the complex crystallizes as a dihydrate. In the crystal, these units are linked by a number of O—H⋯O and N—H⋯S hydrogen bonds and weak C—H⋯O inter­actions, forming a three-dimensional network.

Design, synthesis, growth and characterization of 4-methoxy-4'-dimethylamino-benzylidene aniline (MDMABA): a novel third order nonlinear optical material

Synthesis, growth, X-ray crystal structure and characterization of a novel third order nonlinear optical material, 4-methoxy-4'-dimethylamino-benzylidene aniline (MDMABA), are reported for the first time. The asymmetric unit of MDMABA compound contains two crystallographically independent molecules (A and B), and they exist in the E-configuration. The structural perfection of the grown crystal is analyzed by high-resolution X-ray diffraction rocking curve analysis. The functional groups present in MDMABA are investigated by FTIR and FT-Raman spectral analyses. The placement of the protons is determined using HNMR spectrum. The range and percentage of optical transmission were ascertained by recording UV-vis-NIR spectrum. Thermal and mechanical properties are reported. Dielectric study shows that the dielectric constant of the crystal varies with frequency and temperature. The third order nonlinear optical absorption coefficient of the MDMABA crystal is determined by the Z-scan technique.

A follow-up study of children with posterior urethral valve

There are not many studies on long term follow up of children following surgery for posterior urethral valve in India. This study was done to assess the growth and renal function of children who had completed five years after surgery for posterior urethral valve at our hospital. Thirty children were included in this study. They were assessed retrospectively for the age and pattern of presentation, time of surgery and outcome. Outcomes measured were stunting, renal failure (GFR, tubular functions) and bladder functions. Fifty per cent of children were symptomatic five years after surgery with enuresis, dribbling, polyuria and recurrent urinary tract infection (UTI). GFR was <60 ml/m/1.73 m(2) in 33%. Growth failure, according to the World Health Organization (WHO) definition, was present in one-third of children. A low GFR was associated with growth failure. Poor bladder function evidenced by history of dribbling and significant residual urine was seen in one-third of patients. Residual hydronephrosis was seen in 74%. The most common presenting symptoms of PUV were poor urinary stream followed by recurrent UTI, poor weight gain, renal failure and abdominal mass. Eighty per cent of the study population had undergone surgery in infancy. Five years after surgery, 50% children were symptomatic; 30% had stunting. 33% had a GFR <60 ml/m/1.73 m(2) and a significantly greater degree of stunting than those with GFR >60 ml/m/1.73 m(2). Sonologically normal kidneys on follow-up were associated with a GFR above 60 ml/m/1.73 m(2). Poor bladder function was present in 30% of the children. Univariate analysis showed that statistically significant risk factors for decline in GFR in this study are oligohydramnios and surgery beyond the neonatal period.

Chlamydomonas reinhardtii, a model system for functional validation of abiotic stress responsive genes

Stress tolerance is a multigenic character and there are many stress responsive genes, which are stress specific. Although many of these have been cloned, their functional significance remains fragmentary. Hence it is important to identify the relevant stress genes involved in altering the metabolism for adaptation. Overexpression is one of the several approaches and Chlamydomonas is a suitable system to study the functional relevance of stress genes. Stress responses can only be assessed on prior exposure to sublethal induction stress. In this study the acclimation response of Chlamydomonas was assessed for different abiotic stresses using physiological screens like chlorophyll stability, membrane damage, cell viability, accumulation of free radicals, survival and recovery growth. We demonstrate that Chlamydomonas responds to diverse stresses and is a potential system to study the relevance of stress genes. The relevance of choline oxidase A (codA), a key enzyme in glycinebetaine biosynthesis, was examined by developing transformants expressing codA gene from Arthrobacter globiformis. Southern positive transformants showed enhanced accumulation of glycinebetaine. The transformants also showed enhanced growth under salinity, high light coupled with methylviologen-induced oxidative stress, high temperature and cold stress. However the transgenics were not tolerant to PEG-mediated simulated osmotic stress, LiCl, menadione and UV stress. Increased cell survival and decreased chlorophyll degradation in transformants under acclimated conditions further confirmed the relevance of codA in imparting stress tolerance. Our results indicated that the relevance of stress responsive genes can be efficiently validated for diverse abiotic stresses using Chlamydomonas system.

A systematic study to determine the extent of gene silencing in Nicotiana benthamiana and other Solanaceae species when heterologous gene sequences are used for virus-induced gene silencing

Virus-induced gene silencing (VIGS) is a rapid and robust method for determining and studying the function of plant genes or expressed sequence tags (ESTs). However, only a few plant species are amenable to VIGS. There is a need for a systematic study to identify VIGS-efficient plant species and to determine the extent of homology required between the heterologous genes and their endogenous orthologs for silencing. Two approaches were used. First, the extent of phytoene desaturase (PDS) gene silencing was studied in various Solanaceous plant species using Nicotiana benthamiana NbPDS sequences. In the second approach, PDS sequences from a wide range of plant species were used to silence the PDS gene in N. benthamiana. The results showed that tobacco rattle virus (TRV)-mediated VIGS can be performed in a wide range of Solanaceous plant species and that heterologous gene sequences from far-related plant species can be used to silence their respective orthologs in the VIGS-efficient plant N. benthamiana. A correlation was not always found between gene silencing efficiency and percentage homology of the heterologous gene sequence with the endogenous gene sequence. It was concluded that a 21-nucleotide stretch of 100% identity between the heterologous and endogenous gene sequences is not absolutely required for gene silencing.

Polarization-rich continuous wave direct imaging: modeling and visualization

We report a study and comparison of continuous-wave, optical polarization difference imaging (PDI) and polarization modulation imaging (PMI) for imaging through scattering media. The problem is cast in the framework of a theoretical estimation, and the comparison is based on three visualization parameters, namely, the magnitude, the degree, and the orientation of the polarization. We show that PDI is superior in estimating the first two parameters in active imaging under specific conditions, while the PMI is suitable for passive imaging and is the only way to estimate polarization orientation. We also propose new schemes for rendering polarization information as a color image and for applying the newly introduced polarization-orientation imaging for segmentation. Simulation and experimental results verify the theoretical conclusions.

3-(4-Chlorobenzoyl)-7-(N,N-dimethylamino)-1-phenylindolizine and 3-(2,4-dichlorobenzoyl)-7-(N,N-dimethylamino)-1-phenylindolizine

In both of the title compounds, C(23)H(19)ClN(2)O, (I), and C(23)H(18)Cl(2)N(2)O, (II), the molecular packing is influenced by weak intermolecular C-H.O and C-H.pi interactions, but despite the chemical similarity of the compounds, the packing in (II) is entirely different from that observed in (I).

16-(4-Cyanobenzylidene)-17-oxoandrost-5-en-3beta-ol

In the title compound, 4-(3beta-hydroxy-17-oxoandrost-5-en-16-ylidenemethyl)benzonitrile, C(27)H(31)NO(2), rings A and C of the steroid nucleus are in chair conformations. The central six-membered ring B is in an 8beta,9alpha-half-chair conformation, while the five-membered ring D adopts a 13beta,14alpha-half-chair conformation. The cyanobenzylidene moiety has an E configuration with respect to the carbonyl group at position C17. The dihedral angle between the planes of the steroid nucleus and the cyanobenzylidene moiety is 22.61 (15) degrees. Intermolecular O-H.N hydrogen bonds formed between the hydroxyl group of the steroid and the N atom of the cyanobenzylidene moiety of symmetry-related molecules link the steroid molecules into chains which run parallel to the b axis.

16-(4-Cyanobenzylidene)-3 beta-pyrrolidinoandrost-5-en-17 beta-ol monohydrate

In the title compound, C(31)H(40)N(2)O x H(2)O, the outer two six-membered rings are in chair conformations, while the central ring is in an 8 beta,9 alpha-half-chair conformation. The five-membered ring adopts a 13 beta-envelope conformation and the cyanobenzylidene moiety has an E configuration with respect to the hydroxyl group at position 17. The steroid nuclei are linked by intermolecular O[bond]H...O and O[bond]H...N hydrogen bonds to form a molecular network. The molecular packing has an interesting feature, with the steroids aligned parallel to the b axis, forming a closed loop through hydrogen bonds linked via water molecules.