jimnoneill/paper-to-field-training huggingface dataset:
Strain diversity in vitamin B1 yield in Saccharomyces cerevisiae

Field: Agricultural and Biological Sciences (Life Sciences)

Yeasts are highly exploited for the production of flavours. Yeast biomass itself is valuable in food applications by being converted to yeast extracts, which are used for their umami flavour as an alternative to glutamate. Yeasts can also produce numerous vitamins. S. cerevisiae produces thiamine (vitamin B1). As awareness over health is gaining more attention, it would be interesting to increase thiamine levels in yeast extracts to use as flavour in (fermented) meat analogues, among other possible substrates. In this study the capability of different strains of S. cerevisiae to produce vitamin B1 is investigated. A screening of different yeast strains, isolated from various food sources, was carried out in Wickerham minimal medium lacking amino acids and thiamine. In this screening intracellular and extracellular thiamine production was measured among the different strains. The screening showed large variation in thiamine production and excretion among the tested strains, ranging in the ppm levels for intracellular thiamine content and ppb for extracellular. Intracellular thiamine levels are shown to be growth stage dependent.
The effect of non-Gaussian statistics on the mass multiplicity of cosmic structures

Field: Physics and Astronomy (Physical Sciences)

The mass function of cosmic structures is computed in the framework of the hierarchical clustering picture for a general statistics of density perturbations. 'Hierarchical' distributions are extensively analyzed; it is found that the multiplicity function preserves the Press-Schechter functional form with enhanced power on large scales compared to the Gaussian case. A class of scale-invariant non-Gaussian statistics, among which are a model due to Peebles and the lognormal distribution, are also analyzed. All these predict a mass function which is a decreasing power law at low mass followed by an exponential decay at high mass; none of them, however, yields a mass function of the Press-Schechter type. The effect of a statistical bias on the origin of condensations is also discussed. The comparison of these theoretical formulae with the observed mass multiplicity of galaxies, groups, and clusters may represent a powerful tool to test the statistics of cosmological perturbations.
Molecular dynamics simulation on the heat transfer at liquid-solid interfaces and enhancement mechanism

Field: Materials Science (Physical Sciences)

To investigate the effect of surface roughness on the heat transfer mechanism, a molecular dynamics model of heat transfer between solid and liquid interfaces was established in this paper. The temperature distribution, heat flux, thermal resistance, and number density distribution of water molecules in the interface are calculated and discussed systematically. The effects of energy parameters between solid and liquid, and the roughness level of the wall on the heat transfer performance were analyzed. The results show that as the energy parameter rises from 0.413 to 1.651 kcal/mol, the heat flux increases from 1.5 × 10 9 to 3.2 × 10 9 Wm −2 , and the thermal resistance at the cold and hot ends of the solid-liquid interface demonstrates a decreasing trend from 18.75 × 10 −9 to 2.50 × 10 −9 Km 2 ·W −1 . It indicates that the interaction between solid and liquid is enhanced, and more water molecules gather near the solid-liquid interface, which promotes energy transfer and thus strengthens the heat transfer between solid and liquid. As the depth of surface roughness varies from 1a to 2.5a, the static contact angle of droplets decreases from 69.06° ± 0.28° to 49.98° ± 0.44°, slightly enhancing the hydrophilicity of the rough wall structure. Thus, compared with the smooth wall, the rough wall structure enables more water molecules to come into contact with the wall, thereby increasing the heat transfer area and consequently enhancing the heat flux and reducing the thermal resistance. With the increase of wall roughness, the cold (hot) thermal resistance further decreases from 19.2 (19.7) × 10 −9 to 4.9 (5.0) × 10 −9 Km 2 ·W −1 .
Soil burial controls organic carbon variability in the deep soil of the Loess Critical Zone

Field: Environmental Science (Physical Sciences)

The Loess Plateau in China has the world's deepest loess deposits, containing a significant amount of organic carbon (OC) in deep soils. However, the factors influencing OC variability in the loess-paleosol profile remain unclear, thereby limiting our understanding of global/regional terrestrial carbon reserves. In this study, we examined a 30–191-m soil profile collected from five borehole sites of the Loess Critical Zone (LCZ) to analyze OC variability in the deep soil based on various proxy parameters. Analytical results indicated a decrease in soil OC concentrations with increasing soil depth, exhibiting significant site-based differences within the 0–30 ​m profile. The estimated soil OC storage ranged from 778–3895 ​Mg ​C ha−1, which mainly depended on the soil depth. Local wavelet spectrum analysis of borehole site 3's OC content showed no cyclical trends across most depths. Environmental factors attributes primarily influence vertical OC distribution at a smaller scale. Soil burial depth, bulk density, and the rubidium/strontium ratio showed negative relationship (p ​< ​0.05 or 0.01) with deep-soil OC concentration, with soil burial depth contributing more significantly to OC content variability than other parameters. Deep soil (> 5 ​m) accounted for > 91% of the total soil OC storage, underscoring the critical role of deep soil in regulating carbon sequestration and cycling. These findings provide valuable insights into the depth-dependent spatial patterns of soil OC, offering a scientific basis for estimating soil OC reserves across the LCZ.
Cyborg Intelligence: Recent Progress and Future Directions

Field: Neuroscience (Life Sciences)

The combination of biological and artificial intelligence is a promising methodology to construct a novel intelligent modality, proposed as cyborg intelligence. The hierarchical conceptual framework is based on the interaction and combination of comparable components of biological cognitive units and computing intelligent units. The authors extend the previous conceptual framework and focus on sensorimotor circuits to explore the representation and integration of sensation. They then present a cognitive computing model for brain-computer integration and design efficient machine-learning algorithms for neural signal decoding. They also propose biological reconstruction methods for sensorimotor circuits to not only restore but enhance functionalities with AI. They develop a series of demonstrating systems to validate the conceptual framework of cyborg intelligence and possibly herald bright prospects and high values in diversified aspects of theoretical research, engineering techniques, and clinical applications. Finally, the authors summarize the latest research trends and challenges, which they believe will further boost new scientific frontiers in cyborg intelligence.
Mechanical circulatory support for high-risk surgical aortic valve and ascending aortic replacement in severe bicuspid aortic valve stenosis: a case series

Field: Medicine (Health Sciences)

Abstract Background Bicuspid aortic valve (BAV) is the most common congenital heart defect (reported incidence of 0.5%–2%) and is commonly associated with proximal aortic dilation. Patients with severe aortic stenosis (AS) of BAV have been shown to have worse pre-operative left ventricular (LV) function as well as a higher incidence of post-operative heart failure hospitalization when compared with analogous patients with tri-leaflet aortic valve disease. While surgical aortic valve replacement (SAVR) may be favoured over transcatheter aortic valve implantation (TAVI) due to anatomical factors or concomitant aortopathy and coronary artery disease, surgical candidacy is often limited by prohibitive operative risk. Case summary We report on three cases of severe AS in BAV with concomitant aortopathy and severe left ventricular dysfunction in whom we proceeded with SAVR with a priori planned venoarterial extracorporeal membrane oxygenation (VA-ECMO) support and inotrope-assisted wean. All patients had severe LV dysfunction (ejection fraction &lt; 25%) at baseline with gradual substantial improvement or normalization after successful SAVR. Discussion These cases demonstrate the utility of planned VA-ECMO with SAVR and aortic root replacement as an integral component of the operative strategy for high surgical risk patients with severe BAV AS not amenable to TAVI. Appropriate pre-operative planning and consent for VA-ECMO as well as a multi-disciplinary approach involving anaesthesia, intensive care, and heart failure cardiology are the key to offering this option as an alternative to palliative medical therapy to a selected group of patients.
Root Distribution and Nitrogen Fixation Activity of Tropical Forage Legume American Jointvetch (Aeschynomene americanaL.) cv. Glenn under Waterlogging Conditions

Field: Agricultural and Biological Sciences (Life Sciences)

We investigated the root distribution and nitrogen fixation activity of American jointvetch ( Aeschynomene americana L.) cv. Glenn, under waterlogging treatment. The plants were grown in pots under three different treatments: no waterlogging (control), 30 days of waterlogging (experiment 1), and 40 days of waterlogging (experiment 2). The plants were subjected to the treatments on day 14 after germination. Root dry matter (DM) weight distribution of waterlogged plants was shallower than controls after day 20 of waterlogging. Throughout the study period, the total root DM weight in waterlogged plants was similar to that in the controls. Enhanced rooting (adventitious roots) and nodule formation at the stem base were observed in waterlogged plants after day 20 of waterlogging. The average DM weight of individual nodules on the region of the stem between the soil surface and water surface of waterlogged plants was similar to that of individual taproot nodules in the controls. Waterlogged plants had slightly greater plant DM weight than the controls after 40 days of treatment. The total nitrogenase activity (TNA) of nodules and nodule DM weight were higher in waterlogged plants than in the controls. Waterlogged American jointvetch had roots with nodules both around the soil surface and in the area between the soil surface and water surface after 20 days of waterlogging, and they maintained high nitrogenase activity and net assimilation rate that resulted in an increased growth rate.
Fabrication of Phospholipid Vesicle-Interacted Calcium Phosphate Films with Sterilization Stability

Field: Materials Science (Physical Sciences)

The development of a calcium phosphate (CP) coating technique on tissue culture poly(styrene) (TCPS) is important in biomedical fields. In this study, the CP hybridized with l-α-phosphatidylcholine phospholipid vesicle (PV) was formed on TCPS as the film state for suggesting the unique CP/PV hybrid films. The film formation was conducted by the following two different processes: (i) the CP deposited on PV was prepared in a simulated body fluid (SBF) and subsequently casted on TCPS to form the films, and (ii) the CP was precipitated in SBF on the pre-prepared PV films on TCPS. These films were denoted as "CP/PV-Bef" and "CP/PV-Aft" films. The stability of the CP/PV hybrid films against the sterilization processes (ethanol, UV/ozone, and autoclave treatments) and subsequent immersion process in a phosphate buffer saline (PBS) was also demonstrated. As a result, the CP/PV hybrid films were successfully coated on TCPS through the mediation by PV with preserving the vesicle structure. The morphologies and physicochemical properties of the films depended on the film formation process as well as the mineralizing time. It is presumed that two functional groups of cationic choline and negative phosphate in the phosphatidylcholine molecule can act as the CP nucleation sites in SBF and the subsequent CP crystal growth would occur along the PV surfaces. Furthermore, it was confirmed that amorphous calcium phosphate and calcium pyrophosphate dihydrate were mainly formed in the initial mineralization stage and were eventually converted to the hydroxyapatite phase. The conversion was accelerated by the autoclave treatment. Therefore, these CP/PV films have transparency, unique structures, and good stability against sterilization treatments, suggesting the application for cell culture plates.
Fuzzy agents bargaining at a farmer's market

Field: Computer Science (Physical Sciences)

Computational models of the bargaining process at a farmers' market require modeling subjective preferences of the buyers and sellers and their subjective assessments of the produce. The proposed fuzzy agents based model employs a number of fuzzy inference systems modeled as Standard Additive Models that perform the subjective decision making for the agents. Survey results of different vendors and customers at different farmers' markets provide the rule base coded in these fuzzy expert systems. The results show a steady convergence to a bargain weighted towards the greedier of the two players. Repeated simulations with the proposed model of varying buyers, sellers and the produce indicate that fuzzy agents can model bargaining at a farmers' market.
Multiple Foreign Gene Delivery Can Induce Antibody Production in Mice

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Exogenous gene delivery may activate the immune system to generate the corresponding antibody; however, it is unknown whether all of the exogenous genes can induce such immune responses at the same level, and the result of simultaneous delivery of two or more genes is also unknown. To address the question, ELISA was used to determine antibody titers in serum against the most frequent gene doping such as growth hormone (GH), insulin-like growth factor α (IGF-α), and mechano growth factor (MGF), which were delivered into mice by naked vectors. There was no antibody against GH when saline, pCI-neo, or the pCI-GH plasmid alone was injected, but significant antibody was induced when the pCI-GH plasmid was injected in combination with either pCI-MGF or pCI-IGF-I plasmid (p < 0.05). Therefore, not all of exogenous genes can induce such immune response or the induced intensity is different, and multi-gene delivery was more likely than single gene to stimulate the immune system, which may be a potential method to detect gene doping.
On vertical resolution for seismic acquisition geometries in complex 3D media

Field: Earth and Planetary Sciences (Physical Sciences)

Summary Exploration frequency and spatial sampling have significant effects on both the horizontal and vertical resolutions of seismic imaging, but how to quantify their influence still remains controversial for complex media. The conventional criteria for vertical resolution are based on the theory of geometric seismology with the assumption of infinite bandwidth and simple media. The bandlimited and spatial-sampling effects on vertical resolution are important for seismic imaging in complex media. In this article, based on focal beam analysis, we define two parameters to quantify the vertical resolution of acquisition geometry: the main-lobe width (MLW) in a focal beam along the vertical direction and the ratio of its main-lobe amplitude to the total amplitude (RMT). MLW defines the vertical resolution to image the target, whereas RMT describes the clarity of the imaging. Comparisons of focal beams with increasing bandwidth and spatial sampling to classic criteria for the vertical resolution show that the MLW and RMT of focal beams can be more accurate to describe the vertical resolution of exploration seismology. Case studies of seismic migration with 3D seismic data from an oilfield in China, demonstrate how acquisition geometries with different MLW and RMT values influence performance of seismic imaging. Prior MLW and RMT analyses of acquisition geometry to predict the quality of acquired datasets can optimize the design of acquisition geometries before the implementation of seismic acquisition.
Growth of Mouse Oocytes to Maturity from Premeiotic Germ CellsÂ In Vitro

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

In the present study, we established an in vitro culture system suitable for generating fertilizable oocytes from premeiotic mouse female germ cells. These results were achieved after first establishing an in vitro culture system allowing immature oocytes from 12–14 day- old mice to reach meiotic maturation through culture onto preantral granulosa cell (PAGC) monolayers in the presence of Activin A (ActA). To generate mature oocytes from premeiotic germ cells, pieces of ovaries from 12.5 days post coitum (dpc) embryos were cultured in medium supplemented with ActA for 28 days and the oocytes formed within the explants were isolated and cocultured onto PAGC monolayers in the presence of ActA for 6–7 days. The oocytes were then subjected to a final meiotic maturation assay to evaluate their capability to undergo germinal vesicle break down (GVBD) and reach the metaphase II (MII) stage. We found that during the first 28 days of culture, a significant number of oocytes within the ovarian explants reached nearly full growth and formed preantral follicle-like structures with the surrounding somatic cells.
Biliary Lipid Excretion After Hepatic Portoenterostomy

Field: Medicine (Health Sciences)

Since 1974, 16 consecutive infants with biliary atresia have been treated by hepatic portoenterostomy employing an exteriorized Roux-en-Y intestinal segment (Miluliez). Simultaneous, sequential analyses of bile pigments and lipids in serum and biliary drainage were performed. In the 11 patients with sustained bile drainage, progressive increases in bile volume, bilirubin and biliary lipid concentrations correlated well with their subsequent return toward normal in the serum. Despite relief of biliary obstruction, four patients have had progressive liver cirrhosis. The other 7 have residual liver damage which has been stable, or in two instances, improved, at late biopsy. The clinical and biochemical results suggest that both obstructive and parenchymal factors are operative in infants with biliary atresia.
Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): infection with Brucella abortus, B. melitensis and B. suis

Field: Veterinary (Health Sciences)

The infection with Brucella abortus, Brucella melitensis and Brucella suis has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on the eligibility of the infection with B. abortus, B. melitensis and B. suis to be listed, Article 9 for the categorisation of the infection with B. abortus, B. melitensis and B. suis according to disease prevention and control rules as in Annex IV and Article 8 on the list of animal species related to the infection with B. abortus, B. melitensis and B. suis. The assessment has been performed following a methodology composed of information collection and compilation, expert judgement on each criterion at individual and, if no consensus was reached before, also at collective level. The output is composed of the categorical answer, and for the questions where no consensus was reached, the different supporting views are reported. Details on the methodology used for this assessment are explained in a separate opinion. According to the assessment performed, the infection with B. abortus, B. melitensis and B. suis can be considered eligible to be listed for Union intervention as laid down in Article 5(3) of the AHL. The disease complies with the criteria as in Sections 2, 3, 4 and 5 of Annex IV of the AHL, for the application of the disease prevention and control rules referred to in points (b), (c), (d) and (e) of Article 9(1). The animal species to be listed for the infection with B. abortus, B. melitensis and B. suis according to Article 8(3) criteria are several mammal species, as indicated in the present opinion.
A novel needle-based miniature x-ray generating system

Field: Medicine (Health Sciences)

The basic concept, design and performance of a novel needle-based x-ray system for medical applications are reported. The main principle of the system is based on a two-stage production of x-rays. The system comprises a conventional x-ray tube with an Ag anode, any known type of conditioning optics and a 2.2 mm diameter hollow needle with an interchangeable Mo target. The target can be moved along the needle axis and rotated around the needle axis. The needle x-ray device allows for adjustment in energy and flux intensity of the x-rays emitted by the target. The depth dependence of the intensity, dose rate as well as spatial and energy distribution of the radiation emitted by the target have been experimentally measured. The depth dose rate results have been compared with theoretical calculations using a Monte Carlo simulation of the x-ray production process. These studies have experimentally confirmed that the concept of this x-ray system is correct. Further improvement of the device can increase the dose rate up to the levels required for clinical applications.
Oxidative scission of plant cell wall polysaccharides by ascorbate-induced hydroxyl radicals

Field: Agricultural and Biological Sciences (Life Sciences)

Scission of plant cell wall polysaccharides in vivo has generally been assumed to be enzymic. However, in the presence of l-ascorbate, such polysaccharides are shown to undergo non-enzymic scission under physiologically relevant conditions. Scission of xyloglucan by 1 mM ascorbate had a pH optimum of 4.5, and the maximum scission rate was reached after a 10–25-min delay. Catalase prevented the scission, whereas added H2O2 (0.1–10 mM) increased the scission rate and shortened the delay. Ascorbate caused detectable xyloglucan scission above approx. 5 µM. Dehydroascorbate was much less effective. Added Cu2+ (&gt; 0.3 µM) also increased the rate of ascorbate-induced scission; EDTA was inhibitory. The rate of scission in the absence of added metals appeared to be attributable to the traces of Cu (2.8 mg·kg-1) present in the xyloglucan. Ascorbate-induced scission of xyloglucan was inhibited by radical scavengers; their effectiveness was proportional to their rate constants for reaction with hydroxyl radicals (•OH). It is proposed that ascorbate non-enzymically reduces O2 to H2O2, and Cu2+ to Cu+, and that H2O2 and Cu+ react to form •OH, which causes oxidative scission of polysaccharide chains. Evidence is reviewed to suggest that, in the wall of a living plant cell, Cu+ and H2O2 are formed by reactions involving ascorbate and its products, dehydroascorbate and oxalate. Systems may thus be in place to produce apoplastic •OH radicals in vivo. Although •OH radicals are often regarded as detrimental, they are so short-lived that they could act as site-specific oxidants targeted to play a useful role in loosening the cell wall, e.g. during cell expansion, fruit ripening and organ abscission.