jimnoneill/paper-to-field-training huggingface dataset:
Druglike molecule datasets for drug discovery

<strong>Background</strong><br> Trnasformer-based AI models have shown outstanding performance in identifying druggable candidate molecules. In most cases, models are trained on a massive amount of database of molecular information to capture the latent meaning of a given molecule. However, the desirable properties of candidate molecules include the feasibility of synthesizing them, low toxicity, and high druggability. In this study, we injected prior knowledge of the desirable properties of molecules during the training process. <strong>Methods</strong><br> Using the PubChem database (100 M), we filtered druglike molecules based on the quantity of drug-likeliness (QED) score and the Pfizer rule. With this dataset of drug-like molecules, we trained both the molecular representation model (chemBERTa) and the molecular generation models (MolGPT). The molecular representation model was evaluated by fine-tuning the results on the MoleculeNet benchmark datasets, and the molecular generation model was evaluated based on the generated samples (10 K). <strong>Results</strong><br> Training with druglike molecules enabled the generation of molecules with desirable properties without any conditioning. Although the molecular representation learning model was not remarkable, however, its performance in predicting clinical toxicology exceeded that of conventional molecular representation models. <strong>Conclusion</strong><br> By training based on a dataset of druglike molecules, our approach enables molecular representation models to predict clinical toxicity more precisely. Furthermore, it enables the molecule generation model to generate molecules with desirable druglike properties without any conditional generation procedures.<br> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- import pickle with open("druglike_molecules_QED.pkl", "rb") as f: data = pickle.load(f)

Topic: Computational Drug Discovery Methods
Subfield: Computational Theory and Mathematics
Field: Computer Science
Domain: Physical Sciences
Silver‐complexation liquid chromatography for fast, high‐resolution separations of triacylglycerols

A high‐speed, high‐resolution approach to silvercomplexation chromatography of triacylglycerols in vegetable fats and cocoa butter equivalents is described. Trisaturated and major isomeric unsaturated species with up to five double bonds are eluted within 12 min. A simple change of solvent composition enables elution of species with up to nine double bonds within the same time‐frame. Throughput is three samples/hr (70 samples/24 hr with an automatic system). Short‐term reproducibility of analytical data for the system gives standard deviations similar to those obtained in practice for high‐resolution capillary gas chromatography of triacylglycerols, and quantitative accuracy is good. Details of column preparation, solvent gradient and system operation are given.

Topic: Food Chemistry and Fat Analysis
Subfield: Food Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Domain Coexistence in Two-Dimensional Optical Patterns

We give evidence of coexisting transverse patterns of different symmetry in an optical beam circulating in a loop which contains a nonlinear medium. The symmetry of the patterns is controlled by the azimuthal rotation introduced in the feedback loop (nonlocality), while the competition is ruled by the input intensity which determines the distance from threshold (nonlinearity). Domains corresponding to patterns with different wave vectors (either different wavelength or different orientation) coexist, nucleating and moving. This gives rise to a complex spatiotemporal dynamics which is characterized by means of suitable collective indicators.

Topic: Nonlinear Dynamics and Pattern Formation
Subfield: Computer Networks and Communications
Field: Computer Science
Domain: Physical Sciences
Recognition delay and recognition rate of knee motor intention recognized by electromyogram and continuous hidden Markov model

A motor rehabilitation robot applied patient's intention can enhance the rehabilitation efficacy. Continuous hidden Markov models of knee flexion and extension are trained using autoregressive model coefficients of knee flexor and extensor electromyograms. The patient's intention of knee movement are recognized by the trained continuous hidden Markov models and the user's knee flexor and extensor electromyograms. The suggested method was applied to a knee joint rehabilitation robot for identifying the suggested classification method in real time. A nondisabled healthy subject wore the robot, and its knee joint was extended when the subject's intention was recognized as `Extension.' The robot's knee joint was bended when the subject's intention was recognized as `Flexion'. If the user's intention wasn't recognized as `Extension' nor `Flexion', the robot's knee joint was remained stationary. The robot had followed properly the subject's knee joint motor intention. As a result of hidden Markov model classification, the robot reflects the subject's intensions with the recognition delay shorter than 200 msec and the recognition rate of 94.23 %. The results show the suggested method has good potential as a bio-signal classification method for a motor rehabilitation robot.

Topic: Muscle activation and electromyography studies
Subfield: Biomedical Engineering
Field: Engineering
Domain: Physical Sciences
Validity of the Loewenstein Occupational Therapy Cognitive Assessment in People With Intellectual Disabilities

Abstract We examined the psychometric properties (internal consistency, concurrent criterion validity, and known-group validity) of the Loewenstein Occupational Therapy Cognitive Assessment (LOTCA) in people with intellectual disabilities. A total of 111 people with intellectual disabilities and 19 people with no disabilities were included. We used Cronbach's alpha, Spearman's rho, the Kruskal–Wallis test, and one-way analysis of variance for analysis, where appropriate. Results showed good internal consistency on Orientation, Visual Perception, Spatial Perception, Visuomotor Organization, and Thinking Operations subscales (Cronbach's αs = .82, .74, .76, .86, and .80, respectively), but not on the Motor Praxis subscale (α = .48). We found significant correlations between participants’ performance on the Pictorial IQ test and disability level and scores on the LOTCA. The known-group validity of the LOTCA in people with intellectual disabilities was satisfactory. We concluded that the LOTCA is a suitable instrument for measuring cognitive abilities and visual perception in people with intellectual disabilities.

Topic: Cerebral Palsy and Movement Disorders
Subfield: Psychiatry and Mental health
Field: Medicine
Domain: Health Sciences
A Study on Performance Simulation of an Reciprocating Engine for Small Long Endurance Unmanned Aerial Vehicles

Development of an engine with good fuel economy is very important for successful implementation of long endurance miniature UAVs (unmanned aerial vehicles). In the study, a 4-stroke glow-plug engine was modified to a gasoline-fueled spark-ignition engine. Engine tests measuring performance and friction losses were conducted to tune a simulation program for performance prediction. It has been found that excessive friction losses are caused by insufficient lubrication at high speeds. The simulation program predicts that engine power and fuel economy get worse with high altitude due to increasing portion of friction losses. The simulation results suggest quantitative guidelines for further development of a practical engine.

Topic: Engineering Applied Research
Subfield: Civil and Structural Engineering
Field: Engineering
Domain: Physical Sciences
Stimulation of a histone H4 protein kinase in Triton X-100 lysates of rabbit peritoneal neutrophils pretreated with chemotactic factors. Effect of fMet-Leu-Phe and partial characterization of the protein kinase.

Rabbit peritoneal neutrophils were stimulated with either the chemotactic factor, fMet-Leu-Phe (10(-8) M, 10 s) or the protein kinase C activator, phorbol-12-myristate-13-acetate (PMA), (0.1 microgram/ml, 3 min) at 37 degrees C, lysed with Triton X-100 at the indicated times and the histone H4 kinase activity of the lysate measured. The histone H4 protein kinase activity was increased severalfold by fMet-Leu-Phe but not PMA. The inclusion of the potent protein kinase C inhibitor, 1-(5-isoquinoline-sulfonyl)-2-methylpiperazine (50 microM) inhibited little if any of the histone H4 protein kinase activity. The effect of fMet-Leu-Phe was transient, maximum stimulation occurring within 10 s and decaying thereafter. The soluble fraction (extract) of the Triton X-100 lysates from control and fMet-Leu-Phe-treated cells was found to contain both histone H4 protein kinase and calcium-phospholipid-activated protein kinase (protein kinase C) activities. The histone H4 protein kinase activity obtained after fMet-Leu-Phe treatment was very little affected by calcium, phospholipid, and PMA and preferred histone H4 but not H1 or H2A as its substrate. In contrast, the calcium-phospholipid-activated protein kinase activity of the extract preferred histones H1 or H2A as substrates and was strongly inhibited by 1-(5-isoquinoline-sulfonyl)-2-methylpiperazine. The histone H4 protein kinase was partially separated from kinase C by DEAE-cellulose and phenyl-Sepharose 4B chromatography. It phosphorylated mostly serine in histone H4. The results indicate that the chemotactic factor, fMet-Leu-Phe, stimulates a protein kinase with substrate specificity and biochemical properties distinct from calcium-phospholipid-activated protein kinase C.

Topic: Protein Kinase Regulation and GTPase Signaling
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
In Vitro Antibacterial Activity of Alchornea cordifolia and Costus afer Against Some Bacterial Isolates

The antibacterial activity of the fresh and concentrated extracts of Alchornea cordifolia and Costus afer against five bacterial species was demonstrated in vitro. The diameter of the zones of inhibition ranged from 6.7±1.5mm to 39.±2.5mm for the fresh juices. The concentrated leaf and stem pith extracts had an inhibition range of 6.3±0.7mm to 22.0±2.5mm. The fresh stem pith juice of Alchornea cordifolia was the most potent plant part and K. varians (39.3±2.5mm) was the most susceptible isolate with a zone of inhibition, which compared well with the gentamycin control (39.3±0.6mm). Extracts from the concentrated leaves were more potent than the juice from the fresh leaves. A combination of the fresh juices did not result in higher zones of inhibition. The extracts obtained from the concentrated leaves and stem of C. afer did not inhibit any of the bacteria tested. The pattern of response exhibited by the bacteria to the extracts was shown by ANOVA to be significantly different. However, ANOVA showed no significant difference in the activity of the concentrated extracts from the leaves of lchornea cordifolia on K. varians (P&gt;0.05). The stem pith and leaves of A. cordifolia can be exploited for use as antibacterial drugs against the bacteria tested since susceptibility to some of them compared well as to gentamycin. The traditional use of these plants for the treatment of diseases caused by the tested isolates was scientifically verified.

Topic: Diphtheria, Corynebacterium, and Tetanus
Subfield: Endocrinology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Transcavernous Approach for Microsurgical Clipping of Ruptured Right Superior Cerebellar Artery Aneurysm with Cadaveric Stepwise Video Illustration

Abstract Superior cerebellar artery (SCA) aneurysms are rare. The management options are not well defined. There is increasing role of endovascular treatment for all aneurysms, especially for aneurysms of the posterior circulation. However in some situations (wide base, dysmorphic features) coiling is not feasible. The surgical management of these aneurysms has its own distinct complexity and requires careful planning. The classic pterional or subtemporal approaches had its own limitation in proper visualization of the neurovascular anatomy. In this video, we describe the technical nuances of transcavernous sinus approach for microsurgical clipping SCA and A-comm aneurysms. We present the case of a 67-year-old RHF who presented with ruptured right-sided SCA aneurysm. She complained of Headache, confusion, and double vision. On physical examination, she had no focal deficits and was Hunt and Hess grade 3. A brain computed tomography (CT) scan revealed a subarachnoid hemorrhage Fisher's grade 4. A brain CT angiography (CTA) demonstrated an aneurysm at the origin of right SCA. The patient had failed attempt of endovascular coiling and she underwent microsurgical clipping. Stepwise demonstration of the approach with cadaveric anatomical dissection is illustrated. The technique presented here allows for safe clipping of the aneurysm through the cavernous sinus. The approach allows for good exposure of the aneurysm and the surrounding structures. Care is taken to visualize the perforators to avoid any devastating brain stem infarction during the clipping. The transcavernous sinus is a robust approach with good visualization of the neurovascular structures allowing safe aneurysm clipping in this location. The link to the video can be found at: https://youtu.be/oE-HyDASiKM.

Topic: Intracranial Aneurysms: Treatment and Complications
Subfield: Neurology
Field: Medicine
Domain: Health Sciences
Data from Anticancer Activity of a Novel Selective CYP17A1 Inhibitor in Preclinical Models of Castrate-Resistant Prostate Cancer

&lt;div&gt;Abstract&lt;p&gt;VT-464 is a novel, nonsteroidal, small-molecule CYP17A1 inhibitor with 17,20-lyase selectivity. This study evaluates the anticancer activity of VT-464 compared with abiraterone (ABI) in castrate-resistant prostate cancer cell lines and xenograft models that are enzalutamide (ENZ)-responsive (C4-2) or ENZ-resistant (MR49C, MR49F). &lt;i&gt;In vitro&lt;/i&gt;, androgen receptor (AR) transactivation was assessed by probasin luciferase reporter, whereas AR and AR-regulated genes and steroidogenic pathway enzymes were assessed by Western blot and/or qRT-PCR. The MR49F xenograft model was used to compare effects of oral VT-464 treatment to vehicle and abiraterone acetate (AA). Steroid concentrations were measured using LC-MS chromatography. VT-464 demonstrated a greater decrease in AR transactivation compared with ABI in C4-2 and both ENZ-resistant cell lines. At the gene and protein level, VT-464 suppressed the AR axis to a greater extent compared with ABI. Gene transcripts StAR, CYP17A1, HSD17B3, and SRD5A1 increased following treatment with ABI and to a greater extent with VT-464. &lt;i&gt;In vivo&lt;/i&gt;, intratumoral androgen levels were significantly lower after VT-464 or AA treatment compared with vehicle, with the greatest decrease seen with VT-464. Similarly, tumor growth inhibition and PSA decrease trends were greater with VT-464 than with AA. Finally, an AR-antagonist effect of VT-464 independent of CYP17A1 inhibition was observed using luciferase reporter assays, and a direct interaction was confirmed using an AR ligand binding domain biolayer interferometry. These preclinical results suggest greater suppression of the AR axis with VT-464 than ABI that is likely due to both superior selective suppression of androgen synthesis and AR antagonism. &lt;i&gt;Mol Cancer Ther; 14(1); 59–69. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;

Topic: Estrogen and related hormone effects
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Protocol development of irradiated rice calli and subsequent in vitro regeneration

Fine and aromatic rice varieties, such as Kataribhog, hold significant commercial value in Bangladesh, particularly in regions like Dinajpur where Kataribhog is primarily cultivated. Despite its popularity, Kataribhog rice has a low yield (less than 2.50 t/ha) and is prone to lodging. To address these issues, a study was conducted using in vitro culture techniques combined with gamma irradiation (60Co) to improve the variety. Three different media (PT-100G, PT-011G, and PT-100) were used to induce callus, followed by exposure to varying radiation doses (10Gy, 12Gy, and 15Gy). The PT-100G medium found most effective, inducing an embryogenic callus formation rate of 32.93%, while PT-011G and PT-100 showed lower rates 27.87% and 11.11%, respectively. A radiation dose of 10Gy was found optimal, with an 80% survival rate for calli and the best plant regeneration outcomes. Bangladesh J. Nuclear Agric, 38(2): 151-159, 2024

Topic: GABA and Rice Research
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
The future of governing marine living resources in the Polar Regions

The Polar Regions are in their worst time of climate change and increased human pressures. It is also the best time to develop a governance regime that could finally help humanity achieve sustainable management of fisheries. There are hopes and positive signs, but difficulties and problems also exist. This final chapter predicts future governance of Polar marine living resources in the context of technology development, climate change and a shifting geopolitical landscape.

Topic: Arctic and Russian Policy Studies
Subfield: Sociology and Political Science
Field: Social Sciences
Domain: Social Sciences
Artist's Statement

In this artist's statement, originally written for a keynote lecture given at the American Bande Dessinée Society conference held at Miami University (Oxford, Ohio) on 3 November 2012, Clément Baloup recounts his artistic trajectory through comics, moving from his experience as a comics reader to his art work as a professional cartoonist. He speaks about other cartoonists who influenced his work, ranging from Baru to Baudoin, Mazzuchelli to Miller, and Sacco to Spiegelman. He then describes three aspects of his comics about the Vietnamese and their history: the stories that he has created, his research and writing process, and the cartooning techniques involved in making each book.

Topic: Comics and Graphic Narratives
Subfield: Visual Arts and Performing Arts
Field: Arts and Humanities
Domain: Social Sciences
TEXTILE DYE BIOREMEDIATION POTENTIAL OF SOME RHIZOBIAL STRAINS AND THEIR HEAVY-METAL AND HIGH SALINITY TOLERANCE

The discharge of untreated textile dye effluents enriched with toxic pollutants including dyes, heavy metals and other hazardous materials may cause negative impacts on the entire ecosystem. The proposed work aimed to isolate, molecularly identify and characterize the native rhizobial strains with textile dye biodegradation potential in relation with their tolerance to high salinity and heavy metals (usually meet in high concentrations in the textile dye effluents). Native rhizobial strains were isolated from various terrestrial ecosystems originated in Danube – Delta Biosphere Reserve. Most of the strains tolerated ≥ 2.0% NaCl. Our data showed that 3 strains (Agrobacterium sp.CR-B19; Rhizobium giardinii CR- B22 and Ensifer sp.CR-B26) were able to tolerate 15 ppm concentration of cadmium (Cd2+), whereas all strains identified as Rhizobium sp. (except R. leguminosarum CR-B10), and Agrobacterium sp. could tolerate 70 ppm of chromium (Cr6+).. Moreover, 3 indigenous strains (Rhizobium giardinii CR-B13; Rhizobium sp.CR-B15 and Agrobacterium sp. CR-B19) tolerated a concentration of 200 ppm of lead (Pb2+). In regard to azo-dye degrading potential, only Rhizobium leguminosarum CR-B10 was able to degrade the Reactive Orange 16 dye (90.18% decolorization) in stationary conditions, at 30°C. Comparatively, Agrobacterium sp. CR - B19 strain removed Reactive Orange 16 (sulphonic azo-dye) (78.92 % decolorization) and Reactive Blue 4 (antraquinonic dye) (12 % decolorization) by adsorbtion. Based on their bioremediation potential, the newly isolated rhizobial strains could be further used (in pure culture or in consortia) to develop a new environmental friendly and cost–effective biotechnology in order to reduce the toxicity of textile dyes effluents.

Topic: Enzyme-mediated dye degradation
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Preference of<i>Rj</i>-soybean cultivars for<i>Bradyrhizobium japonicum</i>for nodulation

Abstract In order to Investigate the correlation between the preference of soybeans (Glycine max L.) for Bradyrhizobium japonicum for nodulation and their Rj-genotypes, rhizobia were isolated from eight cultivars (non-Rj-cultivars: T202, Tol-1, and CNS-J; Rj 2 Rj 3-ones: Hardee, IAC-2, and Bonminori; Rj 4-ones: Hill and Amsoy 71) grown in the field and their compatibilities with Hill and IAC-2 were examined. Sixty-three percent of the nodules of the Rj 2 Rj 3-cultivars were occupied by rhizobia of nodulation-type C, which were compatible with the Rj 2 Rj 3-cultivars but incompatible with the Rj 4-one. Sixty-one percent of the nodules of the Rj 4 cultivars were occupied by isolates of nodulation-type B, which were compatible with the Rj{ni4}-cultivars but incompatible with the Rj 2 Rj 3-one. Non -Rj- cultivars preferred rhizobia of nodulation-type A, which were compatible with both Rj-cultivars. To estimate the effect of planting of Rj-cultivars on the rhizobial population in soils, Rj 2 Rj 3-(IAC-2) and Rj 4-(Hill) cultivars were inoculated with dilutions of supernatants of suspended soils in which theRj 4-cultivar (Fukuyutaka) and non-Rj-one (Akisirome) were planted in the preceding year, and the nodule number was counted. Based on the results, it was shown that the planting of the Rj 4-cultivar increased the population of compatible rhizobia with the Rj 4-cultivar and decreased that of the compatible rhizlbia with the Rj 2 Rj 3-cultivar. Planting of the non-Rj-cultivar did not influence remarkably the rhizobial population in soil. The cultivars IAC-2 (Rj 2 Rj 3), Hill (Rj 4), and Orihime (non-Rj) were planted in the soils used in the above experiment, and the nodulation-types of the isolates from the nodules were identified. Marked preference of IAC-2 for type C rhizobia was observed In the soil planted with the non-Rj-cultivar (87%), while for the type A ones in the soil planted with the Rj 4-cultivar (87%). IAC-2 significantly preferred the type C rhizobia in the soil containing type C rhizobia, but the type A rhizobia when the number of type C rhizobia was very small as in the Fukuyutaka (Rj 4)-cultivated soil. On the basis of these results, it was suggested that the Rj-genes were involved in the inhibition of effective nodulation by certain serogroups of rhizobia as well as in preference for appropriate rhizobia in relation to nodulation and increase of those populations in soil.

Topic: Legume Nitrogen Fixing Symbiosis
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences