jimnoneill/paper-to-field-training huggingface dataset:
Antibiotic resistance pattern of community acquired uropathogens at a tertiary care hospital in Jaipur, Rajasthan

Background: Urinary tract infections (UTIs) are amongst the most common infections described in outpatients setting. Objectives : A study was conducted to evaluate the uropathogenic bacterial flora and its antimicrobial susceptibility profile among patients presenting to the out-patient clinics of a tertiary care hospital at Jaipur, Rajasthan. Materials and Methods : 2012 consecutive urine specimens from symptomatic UTI cases attending to the outpatient clinics were processed in the Microbiology lab. Bacterial isolates obtained were identified using biochemical reactions. Antimicrobial susceptibility testing was performed by the Kirby-Bauer disc diffusion method. Extended spectrum beta lactamase (ESBL) production was determined by the double disk approximation test and the Clinical and Laboratory Standards Institute (formerly NCCLS) confirmatory method. Results: Pathogens were isolated from 346 (17.16%) of the 2012 patients who submitted a urine sample. Escherichia coli was the most frequently isolated community acquired uropathogen accounting for 61.84% of the total isolates. ESBL production was observed in 23.83% of E. coli strains and 8.69% of Klebsiella strains. With the exception of Nitrofurantoin, resistance to agents commonly used as empiric oral treatments for UTI was quite high. Conclusion : The study revealed E. coli as the predominant bacterial pathogen for the community acquired UTIs in Jaipur, Rajasthan. An increasing trend in the production ESBLs among UTI pathogens in the community was noted. Nitrofurantoin should be used as empirical therapy for primary, uncomplicated UTIs.

Topic: Urinary Tract Infections Management
Subfield: Epidemiology
Field: Medicine
Domain: Health Sciences
Paul Scherer. Lord John Russell: A Biography. Cranbury, N.J.: Susquehanna University Press. 1999. Pp. 427. $57.50. ISBN 1-57591-021-7.

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Topic: Philosophy, History, and Historiography
Subfield: History
Field: Arts and Humanities
Domain: Social Sciences
Analysis on the termite capturing effects of the underground stations of the termite monitoring bait systems

By installing the underground stations of the two types of the termite monitoring bait systems in Changde region,we analyzed the termite capturing effects of their underground stations. The results showed that the underground station of Sentricon system had good capturing effect on Coptotermes formosanus Shiraki and Macrotermes barneyi Light,while the underground station of Exterra system had good capturing effect on Reticulitermes flaviceps Oshima and Odontotermes formosanus Shiraki. The certain water absorption and midew of the monitoring wood pieces as well as the invasion of a few soil animals to the underground stations have no obvious influences on their termite capturing effects,so both of them have a good potential as the IPM tools in the field termite control

Topic: Insect and Arachnid Ecology and Behavior
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
MultiCBR: Multi-view Contrastive Learning for Bundle Recommendation

Bundle recommendation seeks to recommend a bundle of related items to users to improve both user experience and the profits of platform. Existing bundle recommendation models have progressed from capturing only user-bundle interactions to the modeling of multiple relations among users, bundles and items. CrossCBR, in particular, incorporates cross-view contrastive learning into a two-view preference learning framework, significantly improving SOTA performance. It does, however, have two limitations: 1) the two-view formulation does not fully exploit all the heterogeneous relations among users, bundles and items; and 2) the "early contrast and late fusion" framework is less effective in capturing user preference and difficult to generalize to multiple views. In this paper, we present MultiCBR, a novel Multi-view Contrastive learning framework for Bundle Recommendation. First, we devise a multi-view representation learning framework capable of capturing all the user-bundle, user-item and bundle-item relations, especially better utilizing the bundle-item affiliations to enhance sparse bundles' representations. Second, we innovatively adopt an "early fusion and late contrast" design that first fuses the multi-view representations before performing self-supervised contrastive learning. In comparison to existing approaches, our framework reverses the order of fusion and contrast, introducing the following advantages: 1)our framework is capable of modeling both cross-view and ego-view preferences, allowing us to achieve enhanced user preference modeling; and 2) instead of requiring quadratic number of cross-view contrastive losses, we only require two self-supervised contrastive losses, resulting in minimal extra costs. Experimental results on three public datasets indicate that our method outperforms SOTA methods.

Topic: Recommender Systems and Techniques
Subfield: Information Systems
Field: Computer Science
Domain: Physical Sciences
Antioxidant, antimicrobial and phytotoxic activities of Rhaponticum acaule DC. essential oil

The in-vitro antioxidant activity of Rhaponticum acaule essential oil (RaEO) was evaluated using beta-carotene/linoleic acid bleaching, chelating activity, and lipid peroxidation inhibition (TBARS) assays. The antimicrobial activity of RaEO was assessed by disc diffusion and microdilution methods against 8 bacteria and 4 yeast. Finally, the allelopathic activity of RaEO on the seed germination and the shoot and root elongation of lettuce (Lactuca sativa L.) seedlings were investigated. According to our results, the RaEO exhibited significant antioxidant activity, similar to those of standards (BHT and ascorbic acid) with IC50 values of 0.042 and 0.045 mg/mL obtained by beta-carotene bleaching and TBARS assays, respectively. On the other hand, despite its interesting ferrous chelating activity, RaEO possesses moderate IC50 value (0.35 mg/mL) as compared with that of EDTA (0.015 mg/mL). RaEO exhibited a strong antimicrobial activity against all the tested microorganisms, with IZ, MIC and MBC values being in the range of 7.67 +/- 0.58 to 13.33 +/- 0.58 mm, 1.25 to 5.00 and 5.00 to 10.00 mg/mL, respectively. The results reveled also that RaEO inhibited the shoot and root growth of Lactuca sativa L. seedlings. Our data suggested that the RaEO had pharmaceutical benefits and could be used as a potential natural herbicide resource.

Topic: Essential Oils and Antimicrobial Activity
Subfield: Food Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Supplementary Table 1 from Exposure to a Histone Deacetylase Inhibitor Has Detrimental Effects on Human Lymphocyte Viability and Function

&lt;p&gt;PDF file - 26KB, Antibody Cocktails for Phosphoproteomic at single cell level.&lt;/p&gt;

Topic: Ubiquitin and proteasome pathways
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Clonidine-induced coronary vasodilatation in isolated guinea pig heart is not mediated by endothelial alpha2 adrenoceptors.

Functional role of endothelial alpha(2)-adrenoceptor in coronary circulation remains unclear. Clonidine, an agonist of alpha(2)-adrenoceptors, was reported to induce coronary vasodilatation via stimulation of endothelial alpha(2)-adrenoceptors or coronary vasoconstriction involving vascular smooth muscle alpha(2)-adrenoceptors. Moreover, H(2) receptor-dependent responses to clonidine were described. Here, we reassess the contribution of endothelial alpha(2)-adrenoceptor and H(2) receptors to coronary flow and contractility responses induced by clonidine in the isolated guinea pig heart. We found that clonidine (10(-9) - 10(-6) M) produced concentration-dependent coronary vasoconstriction without a significant change in contractility. This response was inhibited by the alpha(1)/alpha(2)-adrenoceptor antagonist - phentolamine (10(-5) M) and the selective alpha(2)-adrenoceptor antagonist yohimbine (10(-6) M), but it was not changed by the selective alpha(1)-adrenoceptor antagonist prazosin (10(-6) M). In the presence of nitric oxide synthase inhibitor, L-NAME (10(-4) M) the clonidine-induced vasoconstriction was potentiated. Clonidine at high concentrations of 10(-5) - 3 x 10(-5) M produced coronary vasodilatation, and an increase in myocardial contractility. These responses were abolished by a selective H(2)-receptor antagonist, ranitidine (10(-5) M), but not by phentolamine (10(-5) M). We conclude that in the isolated guinea pig heart, clonidine-induced vasoconstriction is mediated by activation of smooth muscle alpha(2)-adrenoceptors whereas clonidine-induced coronary vasodilatation is mediated by activation of vascular H(2) histaminergic receptors. Accordingly, endothelial alpha(2)-adrenoceptors does not seem to play a major role in coronary flow response induced by clonidine.

Topic: Nitric Oxide and Endothelin Effects
Subfield: Physiology
Field: Medicine
Domain: Health Sciences
Genomics to select treatment for patients (pts) with metastatic cancer: Final analysis of Molecular Tumor Board (MTB) evaluations in the ROME trial.

3157 Background: The ROME trial (NCT04591431) investigates the efficacy of a tailored treatment (TT), driven by extensive genomic tests and Molecular Tumor Board (MTB) evaluation, compared to standard treatment (SoC) in patients (pts) with refractory metastatic cancer. Here we report the prevalence of actionable variants identified and the personalized treatment received by the patients enrolled. Methods: A centralized extensive NGS test (FoundationOne CDx and Liquid CDx) was performed on both tissue and blood samples. Pts with at least one potentially targetable alteration matched to the available drugs were discussed at the MTB. MTB evaluation criteria were: genomic variant type, tumor mutational burden (TMB), VAF, availability of preclinical or clinical data of efficacy and patients’ clinical characteristics. COSMIC, ClinVar, OncoKB and VarSome datasets were used to evaluate the clinical actionability of genomic alterations. MTB indications were: randomization to TT vs SoC, screening failure (SF), or indication to other trial/access to the drug. Results: From November 2020 to August 2023, 1794 pts were screened. A total of 127 weekly MTB meetings were conducted and 899 cases were discussed (7 cases/meeting on average). After MTB discussion, a targetable genomic alteration was identified in 425 pts, who received an indication to be randomized. MTB assigned ICIs to 190 pts (155 to ipilimumab plus nivolumab; 8 to nivolumab) due to high (≥10 mut/mb) TMB. 234 pts had indications to target therapy: 86 pts (37%) to PI3K/AKT/mTOR inhibitors(i), 59 (25%) anti-HER2 agents, 34 (15%) FGFRi, 31 (13%) BRAF/MEKi, 7 (3%) PARPi, 5 (2%) CDK4/6i, 4 (2%) ALKi, 2 (&gt;1%) NTRKi, 2 (&gt;1%) RETi, 2 (&gt;1%) Hedgehog-i, 1 (&gt;1%) JAKi, 1 (&gt;1%) MEKi. 27 pts had indication to ICIs plus target therapy combinations. Additionally, 150 pts with potentially hereditary variants were addressed to genetic counselling and germline testing. Finally, according to the genomic evaluation, 63 pts were referred by MTB to other clinical trial even if considered SF for the ROME trial, 34 patients received from the MTB a modification of the initially proposed standard therapy and 4 had both suggestions. Overall, 652 pts (36%) received an indication following NGS test and MTB evaluation. Conclusions: Our study provides evidence that MTB discussion of comprehensive genomic profiling data identifies a personalized treatment in a large (36%) fraction of patients, thus outperforming the traditional histological approach. Clinical trial information: NCT04591431 .

Topic: Cancer Genomics and Diagnostics
Subfield: Cancer Research
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
349-OR: Reduction of RNA-Editing Enzyme ADAR1 in Human Islets Triggers an Interferon Response and Impairs Beta-Cell Function

Introduction &amp; Objective: It is thought that viral infection triggers islet inflammation, an interferon signature, and autoimmunity resulting in type 1 diabetes. Despite extensive research, an inciting virus has not been identified. We hypothesized that impaired RNA editing and accumulation of double-stranded RNA in beta cells triggers an interferon response, causing islet inflammation, autoimmunity, and beta cell destruction. While RNA editing regulated by adenosine deaminases acting on RNA (ADAR) has been studied in some organs and in cancer, little is known about the role of ADAR in human islets. Method: To elucidate the role of ADAR1 in human islets, we first studied ADAR expression and distribution in human pancreas across postnatal developmental timeline (1 day, 4 months, 2, 6, 10, 35 years). Then we transduced human pseudoislets with a shRNA for ADAR and examined their function and gene expression. The transduced pseudoislets were also transplanted into NSG mice. Insulin secretion was measured and grafts were studied. Results: We found that ADAR1 expression at all ages was greater in endocrine cells than acinar cells. Using the shRNA approach, ADAR mRNA levels were reduced by 70% (n=11 donors). After 7-day culture, expression of dsRNA sensors, IFNB1, IRF7, IRF9, and interferon-stimulated genes was increased while INS and MAFA expression was reduced in ADAR knockdown islets without changes in insulin secretion. However, 3 weeks post transplantation, glucose/arginine-stimulated human insulin secretion was significantly decreased in mice with the ADAR shRNA graft compared with scrambled shRNA control graft (0.117 vs 0.300 ng/mL, p=0.0001, n=3 donors). Analysis of pseudoislet grafts 4 weeks after transplantation showed marked accumulation of mouse CD45+ cells around ADAR-knockdown islet grafts. Conclusion: Interruption of RNA editing in human islets activates the interferon signaling pathway leading to islet inflammation and beta cell dysfunction. Disclosure C. Dai: None. A.K. Singh: None. R. Brantley: None. A. Bradley: None. R. Jenkins: None. D.C. Saunders: None. M. Brissova: None. E. Levanon: Advisory Panel; ADARX, Exsilio. A. Klochendler: None. Y. Dor: None. A.C. Powers: None.

Topic: RNA regulation and disease
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Three-dimensional reconstruction of the 30S ribosomal subunit from randomly oriented particles

The small (30S) subunit of prokaryotic ribosomes can assume any of a wide range of tilt positions on the specimen support. Correspondence analysis should make it possible to order views appearing in the electron micrograph according to the angle of tilt. 231 individual windowed images from two micrographs showing negatively stained 30S subunits from E. coli ribosomes were subjected to multireference alignment. Correspondence analysis yielded six morphologically significant factors of variance. The second of these related to variations in stain concentrations, which are irrelevant at the level of gross morphology. The coordinates for each image in five-dimensional space (relating to factors 1,3,4,5, and 6) were subjected to a nonlinear mapping algorithm, which calculated an optimal two-dimensional map. The resulting distribution (Fig 1) consisted of two clusters, one of rightfacing, the other of left-facing views. Subaverages along the outer margin of the cluster on the left showed the particle in a range of typical views.

Topic: Molecular Biology Techniques and Applications
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Factors influencing placental and fetal development in the mare: important considerations for the selection of embryo recipients

In mammals the placenta is the vehicle for nutritional and gaseous exchange between the maternal and fetal circulations during pregnancy. The allantochorionic placenta of equids is classified as non–deciduate, non–invasive, epitheliochorial and diffuse and, as such, equine placentation demands fetomaternal interdigitation over the entire endometrial surface to optimise fetal development in utero . Any shortcomings are reflected by slower growth and delayed maturation of the fetus. This requirement for an unabbreviated area of placental attachment is emphasised by the inability of mares to carry twin conceptuses to term due to simple competition between the two placentae for the limited area of endometrium which results in progressive starvation of one or both fetuses (Jeffcott and Whitwell, 1973). In addition, age–related chronic degenerative changes in the mare's endometrium (endometrosis) may compromise the uterine environment during pregnancy and Bracher et al . (1996) showed a close relationship between the health of the endometrium, the normality of structure and the density of the microcotyledons on the surface of the allantochorion, and fetal weight.

Topic: Reproductive Physiology in Livestock
Subfield: Agronomy and Crop Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Technology and market opportunities in fiber cement composites for small scale enterprises in Nigeria

Solving problems of unemployment and developing new materials for buildings requires moving beyond the traditional approaches to more economical, environmentally benign performance models and design properties. New approaches should develop models based on the literature and a full understanding of the root causes of failure, derived from careful failure analysis. One of the main drivers of the development efforts in fibre based composites is the trend towards greater environmental awareness and the health hazards associated with the utilization of asbestos fibres. The key to effectively developing marketable fibre cement composites for use as building materials that can be used for construction of safe and affordable structures is to identify the research and development and market needs for such products. This paper looks into the empirical production and market opportunities in terms of product performance accruable to locally manufactured fibre cement ceiling boards.KEY WORDS: Fibre Cement Boards, Production, Market Needs, Product Performance

Topic: BIM and Construction Integration
Subfield: Building and Construction
Field: Engineering
Domain: Physical Sciences
Deposition of a Sorbent into a Recession on a Solid Support To Provide a New, Mechanically Robust Solid-Phase Microextraction Device

To date, solid-phase microextraction (SPME) fibers used for in vivo bioanalysis can be too fragile and flexible, which limits suitability for direct tissue sampling. As a result, these devices often require a sheathing needle to prepuncture robust sample matrixes and protect the extraction phase from mechanical damage. To address this limitation, a new SPME device is herein presented which incorporates an extraction phase recessed into the body of a solid needle. This device requires no additional support or shielding during puncture events through protective tissue. The presented device was thoroughly tested, being fired at 90 m·s<sup>-1</sup> through fish scales, forced through vial septa, and employed in a targeted study of polyunsaturated fatty acids in salmon where the protective outer skin was repetitively punctured during sampling. Finally, the recessed SPME device was applied to an on-site application for the tissue analysis of wild muskellunge. With this advancement, rapid, minimally invasive, and easily executed in vivo SPME is now possible opening the door to near endless sampling opportunities.

Topic: Analytical chemistry methods development
Subfield: Analytical Chemistry
Field: Chemistry
Domain: Physical Sciences
Inconsistent outcome reporting in large neonatal trials: a systematic review

Objective Inconsistent outcome selection and reporting in clinical trials are important sources of research waste; it is not known how common this problem is in neonatal trials. Our objective was to determine whether large clinical trials involving infants receiving neonatal care report a consistent set of outcomes, how composite outcomes are used and whether parents or former patients were involved in outcome selection. Design A literature search of CENTRAL, CINAHL, EMBASE and MEDLINE was conducted; randomised trials published between 1 July 2012 and 1 July 2017 and involving at least 100 infants in each arm were included. Outcomes and outcome measures were extracted and categorised by physiological system; reported former patient and parent involvement in outcome selection was extracted. Results Seventy-six trials involving 43 126 infants were identified; 216 different outcomes with 889 different outcome measures were reported. Outcome reporting covered all physiological systems but was variable between individual trials: only 67/76 (88%) of trials reported survival and 639 outcome measures were only reported in a single trial. Thirty-three composite outcomes were used in 41 trials. No trials reported former patient or parent involvement in outcome selection. Conclusions Inconsistent outcome reporting and a lack of parent and former patient involvement in outcome selection in neonatal clinical trials limits the ability of such trials to answer clinically meaningful questions. Developing and implementing a core outcome set for future neonatal trials, with input from all stakeholders, should address these issues.

Topic: Neonatal Respiratory Health Research
Subfield: Pulmonary and Respiratory Medicine
Field: Medicine
Domain: Health Sciences
Quantification Tests for Carbohydrate Detection

Quantification of carbohydrates by the anthrone method is a colourimetric assay. In this method, first, the complex carbohydrates are hydrolysed in a highly acidic medium, resulting in monosaccharides. Thereafter, these monosaccharides are dehydrated to form 5-hydroxymethylfurfural (5-HMF) or 2-furfural (2-F), followed by reacting with anthrone reagent. This reaction produces a blue-green complex which is colourimetrically determined. In DNSA method 3,5-dinitrosalicylic acid (DNSA), a yellow colour reagent reacts with reducing sugar’s carbonyl group and forms orangered colour compound 3-Amino-5-nitrosalicylic acid (ANSA). The quantity of carbohydrate present in a sample is determined by Beer-Lambert’s law. Apart from these techniques Folin-Wu, Hexokinase, Phenol-Sulphuric acid, Somogvi-Nelson, and GOPOD method are discussed in this chapter in detail.

Topic: Amino Acid Enzymes and Metabolism
Subfield: Biochemistry
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences