jimnoneill/paper-to-field-training huggingface dataset:
Simulation-Guided Engineering Enables a Functional Switch in Selinadiene Synthase toward Hydroxylation

Engineering sesquiterpene synthases to form predefined alternative products is a major challenge due to their diversity in cyclization mechanisms and our limited understanding of how amino acid changes affect the steering of these mechanisms. Here, we use a combination of atomistic simulation and site-directed mutagenesis to engineer a selina-4(15),7(11)-diene synthase (SdS) such that its final reactive carbocation is quenched by trapped active site water, resulting in the formation of a complex hydroxylated sesquiterpene (selin-7(11)-en-4-ol). Initially, the SdS G305E variant produced 20% selin-7(11)-en-4-ol. As suggested by modeling of the enzyme-carbocation complex, selin-7(11)-en-4-ol production could be further improved by varying the pH, resulting in selin-7(11)-en-4-ol becoming the major product (48%) at pH 6.0. We incorporated the SdS G305E variant along with genes from the mevalonate pathway into bacterial BL21(DE3) cells and demonstrated the production of selin-7(11)-en-4-ol at a scale of 10 mg/L in batch fermentation. These results highlight opportunities for the simulation-guided engineering of terpene synthases to produce predefined complex hydroxylated sesquiterpenes.

Topic: Plant biochemistry and biosynthesis
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Chemical Analysis and Cytotoxic Evaluation of Asphodelus aestivus Brot. Flowers

Asphodelus species are among many plants used in traditional medicine, they are used by native peoples for various pathologies.Asphodelus aestivus Brot. is one of Asphodelus species which is considered an important wild medicinal plant growing mainly at Mediterranean region.The present study aims to investigate the chemical constituents and cytotoxic evaluation of A. aestivus flowers.Petroleum ether extract was analyzed by GC/MS assay which revealed the characterization of twenty nine compounds, representing 93.13% of total extract.Also, the chromatographic investigation of the hydromethanolic extract led to the isolation of ten phenolics.They were identified as kaempferol (1), kaempferol 3-Oglucoside (2), kaempferol 3,7-di-O-glucoside (3), luteolin 7-O-glucoside ) 4), isoorientin (5), isoorientin 7-O-glucoside (lutonarin) (6), caffeic acid ( 7) emodin ( 8), apigenin 7-O-glucoside (9) and isovitexin-7-O-glucoside (saponarin) (10), from which, five compounds ((2, 3, 6-8) have been isolated for the first time from A. aestivus.Furthermore, LC-ESI-MS chemical profiling managed to detect the minor contents and led to the annotation of thirteen additional metabolites.In addition, the petroleum ether and the hydromethanolic extracts were investigated against four human carcinoma cell lines; HepG2, HCT-116, MCF-7 and A549 at concentration of 100 mg/mL.The results showed moderate % of inhibition against MCF-7 (63.8 and 68.4) followed by HepG2 (52.3 and 65.7), respectively.Both extracts showed weak inhibition (5.7-14.3%) on HCT-116 and A549.To the best of our knowledge, this is considered the first report of the chemical analysis and biological evaluation of A. aestivus flowers.

Topic: Phytochemistry and biological activity of medicinal plants
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Steroid Hormone Runoff\nfrom Agricultural Test Plots\nApplied with Municipal Biosolids

The potential presence of steroid hormones in runoff\nfrom sites\nwhere biosolids have been used as agricultural fertilizers is an environmental\nconcern. A study was conducted to assess the potential for runoff\nof seventeen different hormones and two sterols, including androgens,\nestrogens, and progestogens from agricultural test plots. The field\ncontaining the test plots had been applied with biosolids for the\nfirst time immediately prior to this study. Target compounds were\nisolated by solid-phase extraction (water samples) and pressurized\nsolvent extraction (solid samples), derivatized, and analyzed by gas\nchromatography–tandem mass spectrometry. Runoff samples collected\nprior to biosolids application had low concentrations of two hormones\n(estrone &lt;0.8 to 2.23 ng L&lt;sup&gt;–1&lt;/sup&gt; and androstenedione\n&lt;0.8 to 1.54 ng L&lt;sup&gt;–1&lt;/sup&gt;) and cholesterol (22.5 ±\n3.8 μg L&lt;sup&gt;–1&lt;/sup&gt;). In contrast, significantly higher\nconcentrations of multiple estrogens (&lt;0.8 to 25.0 ng L&lt;sup&gt;–1&lt;/sup&gt;), androgens (&lt;2 to 216 ng L&lt;sup&gt;–1&lt;/sup&gt;), and progesterone\n(&lt;8 to 98.9 ng L&lt;sup&gt;–1&lt;/sup&gt;) were observed in runoff samples\ntaken 1, 8, and 35 days after biosolids application. A significant\npositive correlation was observed between antecedent rainfall amount\nand hormone mass loads (runoff). Hormones in runoff were primarily\npresent in the dissolved phase (&lt;0.7-μm GF filter), and,\nto a lesser extent bound to the suspended-particle phase. Overall,\nthese results indicate that rainfall can mobilize hormones from biosolids-amended\nagricultural fields, directly to surface waters or redistributed to\nterrestrial sites away from the point of application via runoff. Although\nconcentrations decrease over time, 35 days is insufficient for complete\ndegradation of hormones in soil at this site.

Topic: Pharmaceutical and Antibiotic Environmental Impacts
Subfield: Pollution
Field: Environmental Science
Domain: Physical Sciences
Effects of reaction time performance on single-unit activity in the central auditory pathway of the rhesus macaque

The activity of single units at various locations in the central auditory pathway of rhesus macaques was recorded during the monkeys' performance and nonperformance in an auditory reaction time task. Evoked unit responses during performance were compared with those observed during passive delivery of identical stimuli. Single units were recorded from the cochlear nucleus, superior olivary complex, lateral lemniscus, inferior colliculus, medial geniculate nucleus, and auditory cortex. Significant effects of task performance on unit discharge patterns were observed at all levels of the central auditory pathway: Spontaneous discharge rates in the more peripheral auditory nuclei tended to be higher during performance. Evoked discharge that occurred relatively late during a stimulus presentation (greater than 75 msec after stimulus onset) was increased during performance, compared with the nonperformance condition, in nuclei above the cochlear nucleus. The initial latency of evoked discharge was increased during performance for subcortical nuclei but was decreased for units in auditory cortex. These results suggest that the effects of performance may be mediated by a tonic increase in the excitability of auditory units which operates primarily at peripheral auditory stations, and a descending, stimulus-evoked increase in excitability which primarily influences the cells of higher auditory nuclei. At the cortical level, these changes lead to increased signal-to-noise ratio of the evoked response during performance in the auditory task.

Topic: Neural dynamics and brain function
Subfield: Cognitive Neuroscience
Field: Neuroscience
Domain: Life Sciences
Jaina Temple in Stereoscopic Relief

The article presents an 3-D image of the Jaina Vimala Vasahī, or Ādinātha temple, (1032 CE) at Dilvāḍā on Mount Ābū, an anaglyphic rendering of the 1902 stereoview card by James Ricalton (1844-1929).

Topic: Hermeneutics and Narrative Identity
Subfield: Philosophy
Field: Arts and Humanities
Domain: Social Sciences
Multilevel analysis of predictors of multiple indicators of childhood vaccination in Nigeria

Substantial inequalities exist in childhood vaccination coverage levels. To increase vaccine uptake, factors that predict vaccination coverage in children should be identified and addressed.Using data from the 2018 Nigeria Demographic and Health Survey and geospatial data sets, we fitted Bayesian multilevel binomial and multinomial logistic regression models to analyse independent predictors of three vaccination outcomes: receipt of the first dose of Pentavalent vaccine (containing diphtheria-tetanus-pertussis, Hemophilus influenzae type B and Hepatitis B vaccines) (PENTA1) (n = 6059) and receipt of the third dose having received the first (PENTA3/1) (n = 3937) in children aged 12-23 months, and receipt of measles vaccine (MV) (n = 11839) among children aged 12-35 months.Factors associated with vaccination were broadly similar for documented versus recall evidence of vaccination. Based on any evidence of vaccination, we found that health card/document ownership, receipt of vitamin A and maternal educational level were significantly associated with each outcome. Although the coverage of each vaccine dose was higher in urban than rural areas, urban residence was not significant in multivariable analyses that included travel time. Indicators relating to socio-economic status, as well as ethnic group, skilled birth attendance, lower travel time to the nearest health facility and problems seeking health care were significantly associated with both PENTA1 and MV. Maternal religion was related to PENTA1 and PENTA3/1 and maternal age related to MV and PENTA3/1; other significant variables were associated with one outcome each. Substantial residual community level variances in different strata were observed in the fitted models for each outcome.Our analysis has highlighted socio-demographic and health care access factors that affect not only beginning but completing the vaccination series in Nigeria. Other factors not measured by the DHS such as health service quality and community attitudes should also be investigated and addressed to tackle inequities in coverage.

Topic: Vaccine Coverage and Hesitancy
Subfield: Health
Field: Social Sciences
Domain: Social Sciences
CCDC 787271: Experimental Crystal Structure Determination

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Topic: Crystallization and Solubility Studies
Subfield: Materials Chemistry
Field: Materials Science
Domain: Physical Sciences
The Struggle Between Norms and the International Organisation: A Case Study of India in the Shanghai Cooperation Organisation (SCO)

The primary aim of this paper is to investigate the objective of India's joining the Shanghai Cooperation Organisation (SCO).The significance of this research lies in finding the correlation between the norms adopted by the organisation and the real reason for a country's joining that organisation.Similarly, special attention has been paid to the concept of international organisations as norm disseminators.The paper first discusses the normative theory of international relations and tries to bridge it with international organisations (IOs).Additionally, the paper assesses the role played by norms in driving international organisations or vice versa.The main argument is that India has adopted a cooperation and competition approach to the SCO, considering its bitter relations with China and Pakistan.This is a qualitative study that considers primary and secondary sources to connect the theoretical understanding with the empirical study.

Topic: International Development and Aid
Subfield: Development
Field: Social Sciences
Domain: Social Sciences
Gram stain and Giemsa stain as a rapid diagnostic tool for diagnosis of vaginal infections” in Western Nepal

Abstract:&#x0D; Introduction: Infective vaginitis accounts for about 90% of all the cases of vaginal discharge in the women of reproductive age group. This includes triad of bacterial vaginosis, candidiasis and trichomoniasis.&#x0D; Method: The study was carried out in Lumbini Medical College and Teaching Hospital, Palpa, Nepal for a time period of 4 months. Total 125 high vaginal swabs from posterior fornix of vagina were collected from November 2014 to February 2015 in the department of Obstetrics and Gynecology, in the patients complaining of vaginal discharge. PH of the vaginal discharge was also determined by using litmus paper. Gram’s and Giemsa stain of vaginal swab smear were done to diagnose Bacterial vaginosis, Candidiasis and Trichomoniasis. Age, parity and pregnancy status of the patients were noted.&#x0D; Result: Out of 125 patient, bacterial vaginosis was found in 16% and candidiasis in 37%.Candidiasis and bacterial vaginosis were observed in child bearing sexually active women. Surprisingly bacterial vaginosis was not observed in pregnant women. Trichomoniasis infection was present in one case (0.8%) while severe invasive Candidiasis was observed in one woman.&#x0D; Conclusion: A definitive diagnosis can easily be made by Gram’s and Giemsa stain and microscopic examination of high vaginal swab. This may help in specific treatment and prevent associated morbidity and recurrence.&#x0D; Key words: Bacterial vaginosis, candidiasis, high vaginal swab, Gram’s stain, Giemsa stain.&#x0D; &#x0D; &#x0D;

Topic: Reproductive tract infections research
Subfield: Microbiology
Field: Immunology and Microbiology
Domain: Life Sciences
CCDC 841962: Experimental Crystal Structure Determination

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Topic: Crystallization and Solubility Studies
Subfield: Materials Chemistry
Field: Materials Science
Domain: Physical Sciences
Body Composition Indices in Women With Well-Controlled Type 1 Diabetes

Changes associated with weight gain in intensive insulin therapy are similar to those seen in insulin resistance syndrome (1). However, the effect of abdominal adiposity in type 1 diabetes has been scarcely documented, especially in women. We conducted a pilot study to document the relationships between daily insulin dose, A1C, body composition, and lipid profile in 16 young (aged 28.1 ± 8.9 years) well-controlled (A1C 6.9 ± 0.7%) type 1 diabetic women.

BMI, waist …

Topic: Diabetes Management and Research
Subfield: Endocrinology, Diabetes and Metabolism
Field: Medicine
Domain: Health Sciences
BEYOND "WHAT WORKS" IN REDUCING CRIME: THE DEVELOPMENT OF A MUNICIPAL COMMUNITY SAFETY STRATEGY IN BRITISH COLUMBIA

Crime is a complex phenomenon and the prevention of it is equally complex. A nation’s ability to reduce crime is fundamental in the quality of life citizen’s experience and public safety is recognized as part of the sustainable development of communities. Crime prevention is understood as the most efficient way to bring about long lasting and sustainable decreases in crime. Canadian municipalities have continued to revisit issues of public safety and have responded by developing public safety plans. This dissertation is a case study of one municipal safety plan in British Columbia. Specifically it examines the formation, development and publication of the City of Surrey’s Crime Reduction Strategy in 2007. Through examination of this case study, it becomes clear at least one municipality is developing plans that move beyond traditional reactionary approaches to crime. Municipalities are well positioned to benefit from advances in crime prevention thought and research. However, a number of substantial challenges remain. In the absence of internationally implemented standards and norms, there are natural ongoing threats to crime prevention (such as tertiary drift and social development creep). Without clear statutory guidance, more statistically valid and reliable information about crime at the neighbourhood level, a firm commitment to documentation and dissemination of information, and a measurable understanding of the relationship between social development and crime prevention, progress in crime prevention at the municipal level should not be assumed.

Topic: Crime Patterns and Interventions
Subfield: Sociology and Political Science
Field: Social Sciences
Domain: Social Sciences
Effects of Different concentration of Copper on Performance, Immunity, Blood biochemical and Carcass traits in Broiler Japanese Quails

Abstract The effects of dietary supplemental copper sources and concentrations on broiler Japanese quail growth performance, immunological response, blood biochemistry and carcass quality were investigated in this study. Two copper sources (copper sulphate - CuS, copper methionine - CuM) were used in this experiment, each at five different dietary dosages of 5, 10, 15, 100, and 150 mg/kg. 280 (10 x 4 x 7) day old quail chicks were randomly assigned to ten feed treatments for a period of up to five weeks. Each treatment had four replications, each with seven chicks. CuM (100 mg Cu/kg diet) supplemented diets had significantly (P &lt; 0.01) higher body weight gain and a better feed conversion ratio (FCR) than CuS supplemented diets, according to the findings. At 150 mg CuM/kg diet, the cell mediated immune response (foot web index to PHAP) was significantly higher (P &lt; 0.01) than at other dietary doses of Cu. With copper sulphate (CuS) supplemented diets, the humoral immunological response (HA titre to SRBC) was significantly (P &lt; 0.01) lower than with copper methionine supplemented diets. At 5, 10, and 15mg Cu/kg diet the humoral immunological response (HA titre to SRBC) was significantly (P &lt; 0.01) lower than at 100 and 150mg Cu/kg diet. Bursa weight was significantly higher (P &lt; 0.01) in the 10 and 15mg Cu/kg meals with copper methionine source than in the 5, 10, 15, and 150 mg Cu/kg diets with copper sulphate supplementation. CuM source resulted in significantly (P &lt; 0.01) larger bursa and spleen weight than CuS source. Serum cholesterol levels were significantly (P &lt; 0.01) lower on the 100 and 150 mg CuM/kg diets compared on the 5,10, and 15mg Cu/kg diets. Various carcass quality parameters including as pre-slaughter live weight, shrinkage loss, blood loss, feather loss, dressed weight, and eviscerated weight were not substantially (P &gt; 0.05) different due to either the main effect or the interaction between copper concentrations and sources. Similarly, the weight of organs such as giblets and liver percent did not alter significantly (P &gt; 0.05) due to either the main effect or the interaction between copper concentrations and sources. At 5 mg Cu/kg diet, there was a significantly higher percent gizzard weight (P0.05) than at other dietary Cu doses. The percent of heart weight recorded at 5mg Cu/kg diet was significantly greater (P &lt; 0.05) than those recorded at other dietary Cu concentrations. Thus it may be concluded that dietary supplementation of copper methionine as a source of Cu @ 100mg Cu/kg diet to broiler Japanese quails was more effective in improving growth performance, immunological response, carcass quality features, and serum cholesterol reduction.

Topic: Animal Nutrition and Physiology
Subfield: Animal Science and Zoology
Field: Agricultural and Biological Sciences
Domain: Life Sciences
SOCIAL AND CULTURAL FOUNDATIONS OF EARTHQUAKE-BASED DISASTER RISK PERCEPTION: A FIELD STUDY IN BANDIRMA

Disaster risk management focuses on strategies to understand, reduce, and transfer risks, enhancing preparedness, response, and recovery efforts at both local and national levels. In Turkey, public perceptions of earthquake risk, particularly following the 1999 Marmara earthquake, which still poses a significant threat, have shaped disaster response efforts and policies over the years. However, the 2023 Maraş-Antakya earthquake revealed persistent preparedness gaps, indicating the need for continuous improvement. This mixed-method study, conducted in the Bandırma district of Balıkesir province with 467 questionnaires and 20 in-depth interviews, aims to examine the perceptions and awareness of residents regarding earthquake-related disasters, understand the social and cultural foundations of disaster awareness, and contribute to efforts to increase sensitivity and reduce disaster impacts. The study sheds light on the need for disaster management policies that promote both individual and collective preparedness at personal and institutional levels, combining cultural, educational, and structural strategies with participatory urban planning to strengthen resilience.

Topic: Disaster Management and Resilience
Subfield: Sociology and Political Science
Field: Social Sciences
Domain: Social Sciences
Molecular chaperones and stress-inducible protein-sorting factors coordinate the spatiotemporal distribution of protein aggregates

Acute stress causes a rapid redistribution of protein quality control components and aggregation-prone proteins to diverse subcellular compartments. How these remarkable changes come about is not well understood. Using a phenotypic reporter for a synthetic yeast prion, we identified two protein-sorting factors of the Hook family, termed Btn2 and Cur1, as key regulators of spatial protein quality control in Saccharomyces cerevisiae. Btn2 and Cur1 are undetectable under normal growth conditions but accumulate in stressed cells due to increased gene expression and reduced proteasomal turnover. Newly synthesized Btn2 can associate with the small heat shock protein Hsp42 to promote the sorting of misfolded proteins to a peripheral protein deposition site. Alternatively, Btn2 can bind to the chaperone Sis1 to facilitate the targeting of misfolded proteins to a juxtanuclear compartment. Protein redistribution by Btn2 is accompanied by a gradual depletion of Sis1 from the cytosol, which is mediated by the sorting factor Cur1. On the basis of these findings, we propose a dynamic model that explains the subcellular distribution of misfolded proteins as a function of the cytosolic concentrations of molecular chaperones and protein-sorting factors. Our model suggests that protein aggregation is not a haphazard process but rather an orchestrated cellular response that adjusts the flux of misfolded proteins to the capacities of the protein quality control system.

Topic: Prion Diseases and Protein Misfolding
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Trade Integration and Business Cycle Synchronization in the Euro Area: The Case of Southern European Countries

This paper examines synchronization in the euro area and the role of intra-EMU trade from 1981 to 2011, focusing in particular on southern European countries.The results indicate that the intensification of synchronisation that occurred in the nineties across almost all countries could partially be explained by the increase in trade, which has been strengthened since the start of the run-up to the EMU.For southern European economies, the results are mixed.We find also that trade imbalances have grown over time, becoming more evident in the common currency period.Furthermore, we document a positive and significant relationship between intra-EMU trade linkages and cyclical correlations.

Topic: Global Financial Crisis and Policies
Subfield: Finance
Field: Economics, Econometrics and Finance
Domain: Social Sciences