jimnoneill/paper-to-field-training huggingface dataset:
Medical Countermeasures for Intoxication by Botulinum Neurotoxin

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Systematic research on the mechanism of action of botulinum neurotoxin (BoNT) began with the work of Justinus Kerner, a German medical officer, who provided the first complete description of botulism while investigating outbreaks of foodborne illnesses in southwestern Germany that were linked to consumption of sausages. The seminal work of van Ermengem revealed that foodborne botulism is intoxication, not an infection, and that the toxin is not destroyed by the harsh conditions in the gastrointestinal tract. The gene coding for the first non-clostridial BoNT-like toxin was identified in Weisella oryzae, a Gram-positive non-spore-forming bacterium found in fermented rice. The exquisite selectivity of BoNT led to its use as a precise chemical tool to identify the role of cholinergic systems in synaptic transmission and for elucidating the role of neural activity and acetylcholine (ACh) secretion in mediating the consequences of disuse atrophy. The clinical syndrome of botulism reflects toxin-induced blockade of ACh release from neuromuscular and neuroeffector junctions.
PALEOENVIRONMENT PLAYED KEY ROLE FOR THE ANATOLIAN POPULATIONS OF CYNIPS DIVISA (HYMENOPTERA: CYNIPIDAE)

Field: Agricultural and Biological Sciences (Life Sciences)

Red-pea gall wasp, Cynips divisa, is an oak- dependent species with a wide distribution range in the Western Palearctic. In this study, we aimed to investigate the genetic diversity of the species across Anatolia and reveal possible factors that governed its contemporary phylogeographic pattern. For this purpose, we sequenced 433 base pairs of mitochondrial cytochrome b gene and the entire nuclear ITS2 region of 278 individuals collected from 22 localities. Our sequence data generated 115 cyt b haplotypes and 15 ITS2 alleles. Estimated genetic diversity for the species was well within the limits of other gall wasp species. Phylogenetic analysis pointed to a separation of C. divisa from outgroups around the Pliocene. Diversification estimates of main haplogroups show signals of major lineage divergences through the Quaternary period. Moreover, splits resulted in more shallow structuring during the last 780.000 years appear to play a key role in the geographic distribution of genetic diversity of red-pea gall wasp species in Anatolia. Our current results support the general view that phylogeography of the Anatolian cynipids has been mainly shaped in a period spanning the last few million years due mostly to changing paleoenvironmental conditions of the area.
Characteristics and outcomes of patients with advanced hepatocellular carcinoma treated on phase I trials.

Field: Medicine (Health Sciences)

281 Background: Patients with advanced hepatocellular carcinoma (HCC) have limited effective therapies. With that purpose, we analyzed the outcomes and prognostic factors of such pts treated on phase I trials w an emphasis on locoregional and targeted agents. Methods: We reviewed the records of 100 consecutive pts referred to the Phase I Clinical Trials Program from March 2004 and assessed characteristics, types of clinical trials, progression-free survival (PFS), overall survival (OS) and oncogenic mutations. Results: Of 100 referred pts, 39 were not treated mainly due to poor performance status (n=22). Of 61 treated pts (49 male, 12 female, median age 60yrs), median # of prior therapies was 3 (range, 0-8). There were no treatment-related mortalities. One pt on a sorafenib regimen had g3 hand foot syndrome unresponsive to dose reduction. A 2 nd pt developed a L-sided visual blurriness after 5 days on a sunitinib regimen; CT showed a small R parieto-occipital hemorrhage, possibly related to therapy. Of 61 treated pts, 7 (11%) had stable disease (SD) > 6 months, 4 (7%) partial response (PR), on protocols combining bevacizumab+sorafenib, pazopanib+everolimus, or single-agent novel oral multikinase inhibitor of VEGFR2-TIE2, or hepatic arterial infusion (HAI) of paclitaxel or oxaliplatin w IV bevacizumab. Median PFS on Phase I trials was 2.2 months vs. 4.4 months and 4.1 months for their 1 st - and 2 nd -line FDA-approved therapy (p 0.019). In univariate analysis, the presence of ascites, portal hypertension, cirrhosis, serum sodium, albumin, and poor Royal Marsden Hospital (RMH) prognostic score were associated with shorter PFS and OS (p < 0.05). On multivariate analysis, independent factors of shorter OS were Caucasian race (p = 0.031), cirrhosis (p = 0.016), serum sodium (p = 0.0013), and poor RMH prognostic score (p = 0.0015). Molecular analysis in progress will be updated. Conclusions: Phase I therapy offer a reasonable therapeutic option for patients with advanced HCC. The RMH prognostic score was validated in this population. The SD > 6 months/PR rate of 18% was observed with regimen of multikinase inhibitors with mTOR inhibitors and HAI therapy.
TU‐A‐230A‐01: Monte Carlo II: MC for Source and Machine Characterization

Field: Medicine (Health Sciences)

Monte Carlo algorithms have the ability to accurately model dose distributions for arbitrarily complex treatment delivery scenarios and changing patient geometries. These properties make Monte Carlo ideal for clinical planning, or for benchmarking clinical planning systems. Building on the discussion of the role of Monte Carlo in treatment head simulation (from the first course), this second Monte Carlo course will focus on patient planning applications. The goal of the course is to familiarize clinical medical physicists with the use of Monte Carlo in treatment planning, including advanced treatment techniques such as IMRT and motion compensated 4D treatment, and to discuss how Monte Carlo‐based planning differs from planning with conventional algorithms. We will demonstrate the various approaches used in modeling beam modifying devices, such as the multi‐leaf collimator (MLC), including methods to effectively model the dosimetric consequences of the detailed the MLC geometry. We will review methods used to reduce Monte Carlo‐based clinical dose calculation time, such as variance reduction techniques, and discuss how factors specific to the MC method, such as statistical uncertainties, impact dose distributions and clinical decision making. We will illustrate how a properly benchmarked Monte Carlo algorithm can play a unique role in the modeling of complex delivery procedures, such as IMRT and how Monte Carlo fluence prediction can be combined with analytic dose algorithms to estimate patient dose. Finally, we will show how Monte Carlo can include organ motion in 4D dose calculations without an increase in computation time. In addition to illustrating the role of Monte Carlo in complex treatment planning, a focus of this course will also be to review some of the practical issues associated with the implementation, verification and clinical use of Monte Carlo‐based dose calculation algorithms. Educational Objectives: 1. To familiarize clinical physicists with some of the issues associated with implementation and experimental verification of Monte Carlo‐based dose algorithms in the clinical setting. 2. To understand the factors specific to Monte Carlo‐based dose algorithms, such variance reduction techniques and statistical uncertainties. 3. To become familiar with the various approaches used in Monte Carlo‐based modeling of the MLC and the tradeoffs associated with these methods. 4. To recognize the potential clinical outcome benefits of Monte Carlo‐based dose distributions. 5. To understand the use, benefits and limitations of the Monte Carlo method for IMRT optimization and QA. 6. To become familiar with the role of the Monte Carlo method in motion compensated (4D) treatment planning.
Isolation of Cyanide Hydratase Mutants from Gloeocerospora Sorghi at alkaline pH

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Cyanide is both a useful and dangerous chemical compound that serves as a crucial component in multiple industrial processes, including metal mining. The leaching process that utilizes cyanide ions to help separate target metals and increase mining yield is an industrial standard for chemical leaching. However, this method of ore extraction results in toxic cyanide waste that requires dangerous, costly, and potentially environmentally damaging remediation systems to degrade. As cyanide is a naturally occurring substance, several organisms contain enzymes capable of oxidizing cyanide into less toxic compounds. Despite the effectiveness of these proteins, they lack stability and functionality at the alkaline pH levels industrial cyanide is stored at. This project attempts to optimize the screening and mutagenesis methods in hopes of a isolating an alkaline tolerant mutant of cyanide hydratase, an enzyme originally found in the fungus Gloeocercospora sorghi. This approach incorporates random mutagenesis of the target fungal gene using error-prone polymerase chain reaction and an in vivo picric acid assay that tests the activity of the mutant enzymes at target conditions. Experimentation was used to determine the ideal conditions for a screening method by testing the activity of the wild-type positive control at different reaction conditions. The final, optimized screening conditions for the high throughput assay combined a 50 μL aliquot of cell culture grown overnight in a 96 well plate with a 50 μL of 0.1 M CAPS buffered to pH 10.5. As screening continues, these conditions can be used to identify a viable, alkaline tolerant mutant. If such a mutant is identified, the molecule would be a strong bioremediation candidate for the metal mining industry and could lead to more efficient and environmentally friendly degradation of cyanide waste.
Feature Detection and Classification in Financial News

Field: Computer Science (Physical Sciences)

The thesis concerns the detection of composite features in news articles as well as their significance for the classification's performance. The considered documents are related to the monetary policy conducted by the Federal Reserve. One principal goal of this work is to quantify embedded information in financial texts by using phrase structure grammar trees in combination with statistical measures and domain knowledge. Thereby, each document is represented as a combination of linguistic features and feature-values. Furthermore, the work examines the correlations between the determined features and an equity market index by modelling the index volatilities as functions of key announcements. A design is targeted, which should enable the temporal tracking of information alterations. Essential aspects of the thesis are the identification, the extraction, and the representation of domain-specific features and their conditional feature-values.
Multiple Periodicity in a Predator–Prey Model with Prey Refuge

Field: Mathematics (Physical Sciences)

We consider a delayed prey–predator model incorporating a refuge with a non-monotone functional response. It is supposed that prey can live in the predatory region and prey refuge, respectively. Based on Mawhin’s coincidence degree and nontrivial estimation techniques for a priori bounds of unknown solutions to the operator equation Lv=λNv, we prove the existence of multiple periodic solutions. Finally, an example demonstrates the feasibility of our main results.
I. Pathogenic variation in fungi and bacteria and mycorrhizal compatibility: Pathogenic variation in Verticillium albo‐atrum isolates from hop (Humulus lupulus)

Field: Agricultural and Biological Sciences (Life Sciences)

ABSTRACT Non‐lethal (M strain) ‘fluctuating’ wilt was first identified in hops in 1924. Lethal (V strain) ‘progressive’ wilt appeared in the 1930s and spread rapidly through Kent, destroying all commercial varieties. By 1965 the disease was largely controlled by use of new resistant cultivars, accompanied by restricted nitrogen fertilisers, non‐cultivation (with weed control by overall herbicides), and high standards of field hygiene. Between 1968 and 1971 severe wilt developed in previously highly resistant clones, used as ‘controls’ in routine field resistance tests. Verticillium isolates from the two farms supplying the natural inoculum for these tests during 1968–71 were more virulent than previously encountered V strains, some causing severe wilt in all resistant cultivars. Subsequent surveys supported by pathogenicity tests against resistant cultivars indicated the existence of two ‘super virulent’ strains on eight farms in Kent. The appearance of mild (M) strains in the 1920s, virulent (VI) strains in the 1930s, and ‘super‐virulent’ (V2 and V3) strains in the 1960s follow 400 years of apparent freedom from wilt. This suggests that the initial breakage of resistance barriers was critical and subsequent variations in an apparently complex, polygenically controlled resistance system are rapidly being matched by the pathogen.
Characterizations of piezoelectric thick films made by screen printing

Field: Materials Science (Physical Sciences)

Screen printing provides a cost effective, high productivity and flexible method to achieve lead zirconate titanate (PZT) thick films for many sensor and actuator applications. PZT thick films with thickness of 5μm to 100μm can be easily obtained from screen printing and the thick film effectively fill the technological gap between thin film and bulk ceramics. However, screen printed thick films usually have poor densification due to high porosity resulting in inferior ferroelectric, dielectric and piezoelectric properties. To improve the density of the thick film, glass frit addition or sol infiltration to the thick film has been incorporated with the screen printing method. Nevertheless, inorganic binder like glass reduces the ferroelectric and piezoelectric properties of PZT thick films due to its low dielectric permittivity while spin coating sol-gel only managed to infiltrate the top part of the thick film therefore still leaving voids between powders. In this report, binder-less PZT composite thick film up to 50 μm on alumina substrate will be fabricated through the mixture of modified PZT powder of different sizes achieved through ball milling technique. Only organic vehicle is used to form the thixotropic paste for screen printing and no binder is added. Different composition of the PZT powder and processing techniques were explored to achieve thick films with satisfactory densification. Microstructures of the fabricated thick film will be evaluated using Scanning Electron Microscope. Thick films with dense microstructure will then be characterized and evaluated on their ferroelectric, dielectric and piezoelectric properties.
Physical activity and nutrition guidelines to help with the fight against COVID-19

Field: Health Professions (Health Sciences)

As the world is witnessing the epidemic of coronavirus disease 2019, emerging genetics and clinical pieces of evidence suggest a similar immunopathology to those of severe acute respiratory syndrome and Middle East respiratory syndrome. Staying at home to prevent the spread of the virus and consequently being largely inactive is associated with unintended consequences. These can actually enhance the infection risk and exacerbate poor health conditions including impaired immune function. Physical activity is a feasible way of improving health, particularly physical and mental health in a time of social isolation. However, people with certain health conditions in these circumstances may need a special physical activity programme in addition to any exercise they may already be performing via online programmes. This review aims to provide practical guidelines during the COVID-19 quarantine period. We suggest performing aerobic, resistance training, respiratory muscle training and yoga in the healthy, and in those with upper respiratory tract illness, patients with lower respiratory tract illness should be restricted to respiratory muscle training and yoga. In addition, vitamins D and C, omega-3 fatty acids, and regular consumption of fruit and vegetables might be considered as nutritional aids to support the immune system in those affected by COVID-19.
A note on choice and detect probabilities in the presence of choice bias

Field: Neuroscience (Life Sciences)

Recently we have presented the analytical relationship between choice probabilities, noise correlations and read-out weights in the classical feedforward decision-making framework (Haefner et al. 2013). The derivation assumed that behavioral reports are distributed evenly between the two possible choices. This assumption is often violated in empirical data - especially when computing so-called grand CPs combining data across stimulus conditions. Here, we extend our analytical results to situations when subjects show clear biases towards one choice over the other, e.g. in non-zero signal conditions. Importantly, this also extends our results from discrimination tasks to detection tasks and detect probabilities for which much empirical data is available. We find that CPs and DPs depend monotonously on the fraction, p, of choices assigned to the more likely option: CPs and DPs are smallest for p equal to 0.5 and increase as p increases, i.e. as the data deviates from the ideal, zero-signal, unbiased scenario. While this deviation is small, our results suggest a) an empirical test for the feedforward framework and b) a way in which to correct choice probability and detect probability measurements before combining different stimulus conditions to increase signal/noise.
The Stability of a Natural Convection Flow above a Point Heat Source

Field: Engineering (Physical Sciences)

Linear stability theory is applied to laminar natural convection plumes arising from a point heat source for Prandtl numbers of 2 and 0.7 (air). The axisymmetric steady plume which has a boundary-layer structure is used as the basic flow. The stability equations which include the effect of velocity-temperature disturbance coupling are numerically solved for both axisymmetric and non-axisymmetric disturbances. The axisymmetric mode is found to be stable. The non-axisymmetric mode n =1 is found to be unstable but n =2 stable, where n is the azimuthal wave-number of the non-axisymmetric disturbance.
The Cotton Wool Child

Field: Social Sciences (Social Sciences)

Risk and challenge are fundamental components of child development and wellbeing. Yet, concerns for danger, injury, and the threat of modern societies have led to the increase in regulation and provision intending to ensure secure, risk-free environments. Nevertheless, the confrontation of risk does not only lie in adults’ experience but is a lifelong skill that may be fostered from early childhood through risk literacy. The aim of this chapter is to explore the position of risk in children’s contemporary lives by drawing on the controversy between the cotton wool child and the ‘risk expert’ (Adams, 2006), risk literate child. It is proposed that besides safeguarding, there should be invested interest in supporting children to develop their own risk awareness and understanding of risk. Such implications signpost the importance of setting the foundations for risk literate children as present and future citizens in a sustainable, multimodal world.
STUDI HABITAT DAN SUMBER PAKAN LEBAH KELULUT DI KAWASAN CAGAR ALAM GUNUNG NYIUT DESA PISAK KABUPATEN BENGKAYANG

Field: Agricultural and Biological Sciences (Life Sciences)

Kelulut Bees is a stingless bee that produces honey, in the area of Gunung Nyiut Nature Reserve Kelulut Bees lives naturally with nests on tree trunks. It is not yet known how the habitat and sources of feed so that it is necessary to do research on the study of habitat and feed sources of Kelulut Bees. This study aims to obtain information about the condition of habitat and feed sources of Kelulut Bees. The method used was a survey with double plots which purposively placed, then identified the condition of habitat and feed sources. Types of hornet bees found were: Heterotrigona itama, Tetragonula laeviceps, Geniotrigona thoracica, Trigona carbonaria and Trigona drescheri. The bees nesting place were in living trees is (52%), dead trees (20%) and soil (28%). Daily mean temperature, air humidity and light intensity were 28.81 °C, 83.06%, and 583.76%. Soil type is PMK with pH 4.4, soil temperature 26.6 C °, soil moisture 26%. Altitude ± 360 masl. Tree analysis was dominated by Xanthophyllum amoenum 36.38%, Lepisanthes tetraphylla 38.01%, Syzgium chloranthum 45.8%, and Bellucia pentamera seedlings 51.58%. The feed sources at the observation sites were dominated by the family Myrtaceae and Dipterocarpaceae, while outside the plots the feed source was dominated by Cocos nucifera L, Durio zibethinus, Nephelium lappaceum L, Syzygium aqueum.Keywords : Feed source, Gunung Nyiut, habitat, kelulut bees, Nature Reserve.
Additional file 5 of Optimal dose of perineural dexmedetomidine to prolong analgesia after brachial plexus blockade: a systematic review and Meta-analysis of 57 randomized clinical trials

Field: Medicine (Health Sciences)

Additional file 5. Sensitivity analysis by eliminating two notable outliers respectively. Abbreviations: DEX, dexmedetomidine; LA, local anesthetic; CI, confidence interval.
Strukturen der mittleren Ringverbindungen. IV. 1, 6‐trans‐Diaminocyclodecan‐dihydrochlorid, trikline Modifikation

Field: Chemistry (Physical Sciences)

Abstract 1,6‐ trans ‐diaminocyclodecane dihydrochloride crystallizes in triclinic and monoclinic modifications. The structure of the triclinic form with a = 9,02; b = 6,19; c = 6,20 Å; α = 96,7°; β = 99,3°; γ = 108,1°; space group P 1 ; Z = 1, has been determined by analysis of the (001) and (010) projections and the conformation of the cyclodecane ring thereby established. Although the molecule, and its environment, is crystallographically only centrosymmetric, the carbon skeleton does not deviate significantly from the higher 2/m (C 2h ) symmetry. Of the torsion angles around the ring, 8 are close to 60° (syn‐skew) the remaining 2 being 156° (nearly anti‐planar). Some stereochemical implications of the cyclodecane conformation are briefly mentioned.
Purification and antioxidative function of anthocyanins from fructus rhodomyrti

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Background: Fructus rhodomyrti, as a colorful fruit, is rich in anthocyanins and anthocyanins have strong antioxidant capacity.Methods: The purification and antioxidative capacity of anthocyanins from Fructus rhodomyrti (fruit of downy rose myrtle, AFR) were studied and compared to those of black rice (ABR). Results:The result of the thiobarbituric acid reactive substances (TBARS) assay showed that both AFR and ABR effectively prevented the oxidation of thiobarbituric acid and reduced the production of malondialdehyde (MDA).The restriction effect of AFR was slightly weaker than that of ABR, but no significant difference was observed.The antioxidative activities of AFR toward H 2 O 2 and epinephrine were also slightly weaker than those of ABR.Conclusion: Fructus rhodomyrti, which has an abundance of anthocyanins and antioxidation activities comparable to those of black rice, has excellent potential as a health care product and should be further explored.However, considering the ecological restoration function of downy rose myrtle, the use of anthocyanins from black rice was suggested as being more economical, more ecological and more effective.