jimnoneill/paper-to-field-training huggingface dataset:
E-pharmacophore-based virtual screening to identify GSK-3β inhibitors

Glycogen synthase kinase-3β (GSK-3β) is a serine/threonine kinase which has attracted significant attention during recent years in drug design studies. The deregulation of GSK-3β increased the loss of hippocampal neurons by triggering apoptosis-mediating production of neurofibrillary tangles and alleviates memory deficits in Alzheimer's disease (AD). Given its role in the formation of neurofibrillary tangles leading to AD, it has been a major therapeutic target for intervention in AD, hence was targeted in the present study. Twenty crystal structures were refined to generate pharmacophore models based on energy involvement in binding co-crystal ligands. Four common e-pharmacophore models were optimized from the 20 pharmacophore models. Shape-based screening of four e-pharmacophore models against nine established small molecule databases using Phase v3.9 had resulted in 1800 compounds having similar pharmacophore features. Rigid receptor docking (RRD) was performed for 1800 compounds and 20 co-crystal ligands with GSK-3β to generate dock complexes. Interactions of the best scoring lead obtained through RRD were further studied with quantum polarized ligand docking (QPLD), induced fit docking (IFD) and molecular mechanics/generalized Born surface area. Comparing the obtained leads to 20 co-crystal ligands resulted in 18 leads among them, lead1 had the lowest docking score, lower binding free energy and better binding orientation toward GSK-3β. The 50 ns MD simulations run confirmed the stable nature of GSK-3β-lead1 docking complex. The results from RRD, QPLD, IFD and MD simulations confirmed that lead1 might be used as a potent antagonist for GSK-3β.

Topic: Computational Drug Discovery Methods
Subfield: Computational Theory and Mathematics
Field: Computer Science
Domain: Physical Sciences
Reagent test and process development sample evaluation.

&lt;p&gt;Ethidium bromide stained 1.2% agarose TAE electrophoresis image (3 V/cm×90 min) comparing reagent systems used for stream sediment RNA or TNA recovery. Lane M; Marker III (Roche), lanes (1, 5) extraction product from NOAA sediment core, lanes (2, 6) extraction product from New Horizon sediment core, lanes (3, 7) extraction products from the A-horizon surface soil sample, lanes (4, 8) extraction products from the iron cemented clay sample.&lt;/p&gt;

Topic: Genetic and Environmental Crop Studies
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Generic named-entity recognition for indigenous languages of Sarawak (Nersil)

The aim of this research is to create the first Named Entity Recognition (NER) system for the Sarawak Indigenous Languages (SILs), hereinafter is called NERSIL. The main goal of NERSIL is to achieve a good accuracy with regard to the identification and classification of named entities (NEs). The NEs considered in this research are Person, Location, Organisation, Date, Time, Monetary and Percentage. Generally, all these NEs&#13;\ncarry important information about the text itself. Thus, there are targets for extraction. NER approaches can be categorised broadly as rule-based approach, machine learningbased approach, and hybrid approach. Rule-based approach relies on hand-crafted&#13;\nlinguistic grammars. Machine learning-based approach needs a large amount of annotated training data, which is unavailable for SILs. Hybrid approach is the combination of rulebased&#13;\nand machine learning-based approach. NERSIL requires special attention as it is impossible to apply directly from the existing NER approaches. In this thesis, an NER system that is built by extending and modifying the existing NER approaches is presented. There are three main processes: the non-modified ANNIE (A Nearly-New IE system) NER, the adapted ANNIE to SILs, and finally the context investigation. Firstly, the input texts are submitted to an English NER, in this case ANNIE with the assumption that some NEs that appear in English texts will also occur in SIL‟s texts. At that stage, the rules for unrecognised NEs from the rules of recognised NEs are distinguished. Next, the new rules for unrecognised NEs are written and the new&#13;\ngazetteers for SILs are built in order to identify more NEs. However, the first two v processes are not enough to provide a good accuracy in recognising all NEs. Thus, context investigation is needed. Context investigation includes frequency analysis, triggered words filtering, and concordance analysis. The context of a NE (the left or right side of NE) will be investigated.Finally, a NER system designed for SILs will be an advancement of world knowledge. Besides, the design can be improved by incorporating the machine translation, WordNet, and adding more noise filtering (e.g. context filtering, and morphological filtering). With more research and future studies, this NER system will reach a high level of performance like the English NER work on.

Topic: Natural Language Processing Techniques
Subfield: Artificial Intelligence
Field: Computer Science
Domain: Physical Sciences
Wheat farming in the Columbia Basin of Oregon. Part 3, Impact of proposed wheat programs on a specialized wheat-summerfallow farm

Published March 1962. Facts and recommendations in this publication may no longer be valid. Please look for up-to-date information in the OSU Extension Catalog: http://extension.oregonstate.edu/catalog

Topic: Wheat and Barley Genetics and Pathology
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Childhood Intussusception: Ultrasonography Effectiveness in Imaging Modalities for the Diagnosis

Intussusception is a term originated from the Latin intus (within) and suscipere (to receive). A bowel segment (intussusceptum) enters another just distal to it (intussuscipiens) leading to occlusion. The intestine itself can be a 'telescope' (a non-pathological starting point - up to 75%) or some pathology may be the focus point of invagination (pathological lead point). The mesentery of the intussuscepted bowel gets compressed. The intestinal wall becomes widened and the lumen gets obstructed. Peristalsis breaks down and this causes colic abdominal pain and vomiting. Lymphatic and venous occlusions occur and lead to ischemia. Mostly in children the intussusception is ileocaecal, but ileo-ileocolic and ileoileal or colocolic cases can be also seen.

Topic: Gastrointestinal disorders and treatments
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
Effect of Yokukansan on sleep disturbance and neuropathic pain in chronic constriction injury using a rat model

Abstract Patients with chronic pain develop peripheral neuropathy and experience sleep disturbance. Yokukansan is used to treat insomnia and control neuropathic pain. We studied if Yokukansan affects neuropathic pain and sleep disturbance using a rat model of chronic constriction injury (CCI). Male Wistar rats (4-week age) were divided into the following groups ( n = 7, per group): CCI rats fed normal chow (CCI-0); CCI rats fed powdered chow mixed with 1% Yokukansan (CCI-1); CCI rats fed powdered chow mixed with 3% Yokukansan (CCI-3); and sham-operated control rats fed normal chow (SHAM). We examined sleep duration and quality using electroencephalograms and assessed pain using the von Frey and Hargreaves tests. Results were analyzed by one-way analysis of variance and Bonferroni post hoc tests. The CCI-0 group exhibited an increased wake period, decreased non-rapid eye movement (REM) sleep time, and no change in REM sleep time in comparison to the SHAM group. The CCI-1 group exhibited a decreased wake period, increased non-REM sleep time, and no change in REM sleep time compared to the CCI-0 group. The CCI-3 group exhibited increased non-REM sleep time but no changes in wake and REM sleep times compared to the CCI-1 group. The von Frey and Hargreaves test findings revealed an increase in the pain threshold in the CCI-1 group compared to the CCI-0 group. There was no difference in pain threshold between the CCI-1 and CCI-3 groups. In our rat model of CCI, sleep disturbance was reflected. Yokukansan inhibited CCI-induced sleep disturbance.

Topic: Alkaloids: synthesis and pharmacology
Subfield: Pharmacology
Field: Pharmacology, Toxicology and Pharmaceutics
Domain: Life Sciences
Ongoing outbreak of invasive listeriosis due to serotype 1/2a Listeria monocytogenes, Ancona province, Italy, January 2015 to February 2016

In the first seven weeks of 2016, five serotype 1/2a Listeria monocytogenes isolates were collected from patients with invasive listeriosis in Ancona province in Italy. These strains and six 1/2a isolates identified in 2015 in the same area were typed by ERIC-PCR and PFGE. A clonal relationship, documented between the two sets of isolates, suggested a listeriosis outbreak in Ancona that started most probably in 2015. Investigation into the source of infection is still ongoing.

Topic: Listeria monocytogenes in Food Safety
Subfield: Biotechnology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Modeling and parametric optimization of 3D tendon-sheath actuator system for upper limb soft exosuit

This paper presents an analysis of parametric characterization of a motor driven tendon-sheath actuator system for use in upper limb augmentation for applications such as rehabilitation, therapy, and industrial automation. The double tendon sheath system, which uses two sets of cables (agonist and antagonist side) guided through a sheath, is considered to produce smooth and natural-looking movements of the arm. The exoskeleton is equipped with a single motor capable of controlling both the flexion and extension motions. One of the key challenges in the implementation of a double tendon sheath system is the possibility of slack in the tendon, which can impact the overall performance of the system. To address this issue, a robust mathematical model is developed and a comprehensive parametric study is carried out to determine the most effective strategies for overcoming the problem of slack and improving the transmission. The study suggests that incorporating a series spring into the system's tendon leads to a universally applicable design, eliminating the need for individual customization. The results also show that the slack in the tendon can be effectively controlled by changing the pretension, spring constant, and size and geometry of spool mounted on the axle of motor.

Topic: Orthopedic Surgery and Rehabilitation
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
Neurological basis of phonological/articulatory loop.

作業記憶の下位システムである音韻性 (構音性) ループは,言語性の短期記憶 (STM) から発展した概念であり,内容的にはほぼ同一である。心理学領域,神経心理学領域のさまざまな知見から,音韻性ループの細分化の必要性が生じ,Vallerらは入力側の要素として音韻性短期貯蔵庫,出力側の要素として音韻性出力バッファーをそのモデルのなかに加えた。主として伝導失語からなる脳損傷例のdigit spanの結果から,このモデルの神経解剖学的基盤を検討した。音韻性短期貯蔵庫は上側頭回に,音韻性出力バッファーは中心前回に,音韻性ループは両者を結ぶ頭頂葉に,おのおの対応するとの仮説を提示した。今後は,健常者を対象としたPET賦活研究やfunctional MRIによる知見の集積が期待され,これらの研究と病巣研究が互いの欠点を補完しあうことが期待される。

Topic: Motor Control and Adaptation
Subfield: Cognitive Neuroscience
Field: Neuroscience
Domain: Life Sciences
Distributed Fiber Optic Sensing System for Well‐Based Monitoring Water Injection Tests—A Geomechanical Responses Perspective

Abstract In this study, distributed fiber optic sensing (DFOS) based on hybrid Brillouin‐Rayleigh backscattering is examined for the first time in well‐based monitoring distributed profiles of geomechanical deformation induced by water injection. Field water injection tests are conducted under different injection scenarios between an injection well (230 m, IW #2) and 5.5 m away from a fibered monitoring well (300 m, MW #1) by deploying cables behind the casing at Mobara, Japan. Effects of injection rate, pressure, and lithological heterogeneity on the geomechanical deformation are quantitatively monitored via a DFOS approach and indicate that induced strains significantly depend on injection rate and pressure. The results also indicate that DFOS results are reasonably consistent with simultaneous geophysical well logging data and corresponding numerical simulation. The extent of impacted areas and magnitude of near‐wellbore strains are explored to evaluate formation heterogeneity and fluid migration behaviors. The field testing of hybrid DFOS technology is expected to definitely advance elaborate monitoring and wider applications, such as CO 2 geosequestration sites.

Topic: Seismic Waves and Analysis
Subfield: Geophysics
Field: Earth and Planetary Sciences
Domain: Physical Sciences
Venous Small Bowel Infarction: Intraoperative Laser Doppler Flowmetry Discriminates Critical Blood Supply and Spares Bowel Length

Introduction . In mesenteric infarction due to arterial occlusion, laser Doppler flowmetry and spectrometry are known reliable noninvasive methods for measuring microvascular blood flow and oxygen utilisation. Case Presentation . As an innovation we used these methods in a patient with acute extensive mesenteric infarction due to venous occlusion, occurring after radical right hemicolectomy. Aiming to avoid short bowel syndrome, we spared additional 110 cm of small bowel, instead of leaving only 80 centimetres of clinically viable small bowel in situ. The pathological examination showed only 5 mm of vital mucosa to be left distal to the dissection margin. No further interventions were necessary. Conclusion . Laser doppler flowmetry and spectrometry are potentially powerful methods to assist the surgeon’s decision-making in critical venous mesenteric perfusion, thus having an important impact on clinical outcome.

Topic: Abdominal Surgery and Complications
Subfield: Pulmonary and Respiratory Medicine
Field: Medicine
Domain: Health Sciences
Poetry and Fin de Siècle Socialism

Abstract Poetry was a major cultural genre of the so‐called ‘socialist revival’ in late 19th‐century Britain. Poems were sung at meetings and Labour Church services, published in socialist newspapers and periodicals, and gathered together in collections and anthologies. Socialist activists took to verse to make social, political and ideological interventions, and looked back through the literature of the 19th century to construct a democratic canon of verse which seemed to have the ‘Socialist passion for man,’ as one socialist commentator described it, at its heart. In a mixed socialist movement, engaged in heated internal debate over its aims and strategies, discussions about the nature and purpose of socialist poetry fed into wider discussions about the nature and purpose of fin de siècle socialism itself. There has been a burgeoning of scholarly interest in this field in the early 21st century, and this article explores this small but growing body of work, suggesting directions for future research.

Topic: Legal and Social Philosophy
Subfield: Sociology and Political Science
Field: Social Sciences
Domain: Social Sciences
Infectious endarteritis associated with patent ductus arteriosus and vegetation: a challenging diagnosis and treatment

A 42-year-old female presented with intermittent fever for 1 month. On physical examination, a continuous systolic murmur could be heard in the second left intercostal space. Laboratory test results revealed neutrophilic leucocytosis and elevated C-reactive protein levels. Blood cultures suggested positive findings of methicillin-susceptible Staphylococcus aureus, final clinical diagnosis of infective endocarditis based on modified Duke criteria. Transthoracic echocardiography showed patent ductus arteriosus (PDA) and large vegetation with the size of 1.3 × 0.8 cm attached to the pulmonary arterial wall near the orifice of the duct (Panel A). Colour Doppler flow imaging showed the shunt from the aorta to the pulmonary artery (PA), with a velocity of 5.2 m/s and a pressure difference of 108 mmHg (Panel B). Cardiac computed tomography angiography confirmed the presence of a tubular-type PDA associated with a strand-like vegetation located on the PA end of the ductus (Panels C and D). The patient underwent pulmonary angioplasty, resection of the vegetation, and ligation of PDA under cardiopulmonary bypass successfully. Postoperative pathology suggested the PA wall was associated with infective endarteritis (Panels E and F). The postoperative course was uneventful and discharged after 7 days.

Topic: Cardiovascular Conditions and Treatments
Subfield: Radiology, Nuclear Medicine and Imaging
Field: Medicine
Domain: Health Sciences
263 Interaction between stocking and supplementation rates on the performance of steers grazing mixed-grass prairie during winter

Abstract To evaluate the effects of stocking and supplementation rates on steers grazing mixed-grass prairie during winter, 16 pastures (10 to 21 ha each) were selected and treatments were arranged in a 3 x 2 factorial design; the first factor was an stocking rate of 39.4, 33.2, and 29.7 animal-unit-d/ha harvested over 88 d of grazing; the second factor was supplementation at 0.9 or 1.4 kg/d. Steers were fed a 43% CP cottonseed meal-based pellet. Pastures were stocked annually in late January (2009, 2010, and 2011) with British x Continental crossbred beef steers (body weight = 202 ± 6.7 kg; n = 137 steers/yr) at stocking densities described above. Data were analyzed by ANOVA with pasture as the experimental unit and year as a random variable; least-squares means were separated with linear and quadratic contrast. From late-January to mid-March, average daily gain (ADG, kg) did not differ (P = 0.13) among stocking rates, but ADG differed (P = 0.01) between 0.9 and 1.4 kg of supplement/d. From mid-March to late-April and over the entire grazing period, ADG responded to stocking rate and interacted (P &amp;lt; 0.01) with supplementation rate; ADG tended to respond quadratically (P ≤ 0.09) to stocking rate at 0.9 kg/d of supplementation, but with 1.4 kg/d of supplement ADG was not affected (P ≥ 0.18). Body weight gain per hectare tended (P &amp;lt; 0.08) to interact between stocking and supplementation rates. With 0.9 kg/d of supplement the BW gain per hectare increased quadratically (P &amp;lt; 0.01) in response to increasing stocking rate, where supplementation at 1.4 kg/d resulted in BW gain per hectare increasing linearly (P &amp;lt; 0.01). Optimal supplementation rates with high-protein feeds is related to stocking rate. At lower stocking rates, less supplement seems to be most beneficial. At higher stocking rates, more supplement is justified.

Topic: Ruminant Nutrition and Digestive Physiology
Subfield: Agronomy and Crop Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Can You Imagine That: Individual Differences in Visual Mental Imagery

Differences in mental imagery ability between individuals have been reported since Galton in 1880. Despite much progress in the mental imagery field, particularly with the advent of neuroimaging techniques like functional magnetic resonance imaging, the neural bases of mental imagery and why individual differences exist in mental imagery ability are not fully understood. Several subjective and objective methods have been proposed and utilized to investigate the strength of visual mental imagery, and even to predict the content of imagery. Recent evidence has shown that people with opposite extremes of visual mental imagery ability, aphantasia and hyperphantasia, have selective impairments and enhancements of ability to visualize visual elements in imagery. We argue that this heterogeneity is generalizable to the population who have relatively normal imagery ability. Current studies have overgeneralized specific paradigms and stimuli to apply to visual mental imagery ability of all types of stimuli, under the presumption that this ability is homogenous. Future studies would benefit from both increased granularity and expanded scope of paradigms and stimuli used.

Topic: Face Recognition and Perception
Subfield: Cognitive Neuroscience
Field: Neuroscience
Domain: Life Sciences
Voices in <i>Molecular Pharmaceutics</i>: Meet Dr. Nasim Shadmani Who Utilizes Cell Penetrating Peptides and Nanoparticles for Targeting Hard-to-Reach Areas of the Body Including the Brain

ADVERTISEMENT RETURN TO ISSUEPREVEditorialNEXTVoices in Molecular Pharmaceutics: Meet Dr. Nasim Shadmani Who Utilizes Cell Penetrating Peptides and Nanoparticles for Targeting Hard-to-Reach Areas of the Body Including the BrainNasim Shadmani*Nasim ShadmaniZanjan Pharmaceutical Nanotechnology Research Center (ZPNRC), Zanjan University of Medical Sciences, 45139-56184 Zanjan, IranDepartment of Pharmaceutical Nanotechnology, School of Pharmacy, Zanjan University of Medical Sciences, 45139-56184 Zanjan, Iran*Email: [email protected]More by Nasim ShadmaniView Biographyhttps://orcid.org/0000-0003-1951-8240Cite this: Mol. Pharmaceutics 2024, 21, 3, 996–998Publication Date (Web):February 1, 2024Publication History Received18 December 2023Published online1 February 2024Published inissue 4 March 2024https://pubs.acs.org/doi/10.1021/acs.molpharmaceut.3c01212https://doi.org/10.1021/acs.molpharmaceut.3c01212editorialACS PublicationsCopyright © Published 2024 by American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views473Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (2 MB) Get e-AlertscloseSUBJECTS:Central nervous system,Drug delivery,Nanoparticles,Peptides and proteins,Pharmaceuticals Get e-Alerts

Topic: RNA Interference and Gene Delivery
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Microsatellite genotypes of bearded vultures (Gypaetus barbatus)

Multilocus microsatellite genotypes of 236 <em>Gypaetus barbatus </em>individuals. This first column contains the individual sample identity as provided in Supplementary Data 1 and subsequent columns are allele scores in single row format. Alleles are scored according to their molecular size (in base pairs); missing data is given as "0".

Topic: Genetic diversity and population structure
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Primary Hydatid Cyst of the Spleen: Unusual Location

The rarity of splenic hydatid disease may pose a diagnostic challenge for clinicians, especially in non endemic areas.Herein we report the case of a 65-year-old female presenting with moderate fever and heaviness in the left upper abdomen and found to have splenic hydatidosis.Oral albendazole therapy was applied at 10 mg/kg/day in two divided doses one month before surgery.Then splenectomy was performed.Postoperatively, the patient continued on oral albendazole for 6 months.One year later, the patient remains asymptomatic without any longterm complications observed during the follow-up.

Topic: Parasitic infections in humans and animals
Subfield: Pathology and Forensic Medicine
Field: Medicine
Domain: Health Sciences