jimnoneill/paper-to-field-training huggingface dataset:
THE PROTEIN NON-FOLDING PROBLEM: AMINO ACID DETERMINANTS OF INTRINSIC ORDER AND DISORDER

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

To investigate the determinants of protein order and disorder, three primary and one derivative database of intrinsically disordered proteins were compiled. The segments in each primary database were characterized by one of the following: X-ray crystallography, nuclear magnetic resonance (NMR), or circular dichroism (CD). The derivative database was based on homology. The three primary disordered databases have a combined total of 157 proteins or segments of length.30 with 18,010 residues, while the derivative database contains 572 proteins from 32 families with 52,688 putatively disordered residues. For the four disordered databases, the amino acid compositions were compared with those from a database of ordered structure. Relative to the ordered protein, the intrinsically disordered segments in all four databases were significantly depleted in W, C, F, I, Y, V, L and N, significantly enriched in A, R, G, Q, S, P, E and K, and inconsistently different in H, M, T, and D, suggesting that the first set be called order-promoting and the second set disorder-promoting. Also, 265 amino acid properties were ranked by their ability to discriminate order and disorder and then pruned to remove the most highly correlated pairs. The 10 highest-ranking properties after pruning consisted of 2 residue contact scales, 4 hydrophobicity scales, 3 scales associated with.-sheets and one polarity scale. Using these 10 properties for comparisons of the 3 primary databases suggests that disorder in all 3 databases is very similar, but with those characterized by NMR and CD being the most similar, those by CD and X-ray being next, and those by NMR and X-ray being the least similar.
Fast centroid molecular dynamics: A force-matching approach for the predetermination of the effective centroid forces

Field: Chemistry (Physical Sciences)

A fast centroid molecular dynamics (CMD) methodology is proposed in which the effective centroid forces are predetermined through a force-matching algorithm applied to a standard path integral molecular dynamics simulation. The resulting method greatly reduces the computational cost of generating centroid trajectories, thus extending the applicability of CMD. The method is applied to the study of liquid para-hydrogen at two state points and liquid ortho-deuterium at one state point. The static and dynamical results are compared to those obtained from full adiabatic CMD simulations and found to be in excellent agreement for all three systems; the transport properties are also compared to experiment and found to have a similar level of agreement.
720-780 nm AlGaAs/GaAs DFB lasers with InGaAsP waveguiding layers

Field: Engineering (Physical Sciences)

Distributed-feedback AlGaAs lasers of 720-780 nm emmision wavelength with GaAs lattice matched InGaAsP waveguide layers are fabricated. The LOC structure is grown on GaAs substrate by liquid phase epitaxy, and the laser diode fabrication is the same as the V-channeled substrate inner stripe lasers. They operate in a single-longitudinal -mode during temperature range of 40 °C. The threshold current as low as 145 mA for 720 nm and 120 mA for 780 nm are obtained under cw operation at room temperature.
Comparative Effects of Household and Manufactured Feeds on Heavy Metal Accumulation and Proximate Composition in Labeo rohita and Oreochromis niloticus under Tank Conditions

Field: Agricultural and Biological Sciences (Life Sciences)

This research evaluated the effects of household versus manufactured feeds on heavy metal accumulation and proximate composition in Labeo rohita and Oreochromis niloticus in controlled tank environments. Fish were raised under three feeding regimes: household feed, manufactured feed, and a control group. Analysis of heavy metals revealed that L. rohita receiving manufactured feed had the highest levels of chromium (8.464 mg/kg in muscle), cadmium (0.949 mg/kg in viscera), and lead (0.411 mg/kg in viscera), compared to the household-fed and control groups. In O. niloticus, elevated cadmium (Cd) and lead (Pb) levels were observed in fish-fed manufactured diets, whereas chromium levels were relatively lower. The findings indicate that manufactured feeds may increase the risk of heavy metal accumulation. Proximate composition analysis showed that L. rohita fed manufactured feed exhibited the highest crude protein (15.92%) and ash (5.23%) content, whereas household feed produced moderate protein levels (15.73%) and slightly elevated lipid content. In O. niloticus, household feed increased lipid content (3.11%) while slightly decreasing protein levels (14.33%) in comparison to manufactured feed (14.99%). The control group exhibited a higher moisture content for both species. These results highlight the significance of choosing safe and balanced feed formulations for sustainable aquaculture techniques by pointing to a trade-off between nutritional advantages and possible contamination hazards.
Probabilistic Forecast Paths in Economics and Finance

Field: Economics, Econometrics and Finance (Social Sciences)

Communicating interest rate strategies constitutes a primary task of monetary policy-makers. The US Federal Reserve and other central banks frequently give guidance to financial markets about the likely path of the short interest rate over time. In this paper, we review briefly the existing approaches adopted by policymakers and contrast them with the probabilistic methods adopted by the Australian shadow board at the Centre for
Cavernous angioma within an olfactory groove meningioma

Field: Medicine (Health Sciences)

✓The authors present the case of a 60-year-old woman who was admitted to their institution after suffering a subarachnoid hemorrhage (SAH). Neuroimaging data demonstrated an olfactory groove meningioma surrounded by a slight edema, but there was no evidence of SAH, although results of the lumbar puncture demonstrated xanthochromic cerebrospinal fluid. Angiography confirmed the diagnosis of meningioma, but results of magnetic resonance imaging led the authors to suspect a cavernoma within the meningioma. This diagnosis was established by pathological examination of the resected lesion. The patient did well and was discharged soon after surgery. This very rare association and the propensity of each of these lesions to be revealed by hemorrhage are discussed.
Continuum studies of magnetic polarons and bipolarons in antiferromagnets

Field: Physics and Astronomy (Physical Sciences)

We present a simple scaling model of magnetic-polaron and magnetic-bipolaron formation in antiferromagnetic systems. Within this picture, we determine the criteria for an excess electron forming a magnetic polaron and for a pair of excess electrons forming a (triplet) magnetic bipolaron. The dependence of the formation criteria on the dimensionality of the electronic system is specifically addressed. In addition, we consider the effect of the electron-lattice interaction on the size and energetic stability of magnetic polarons and bipolarons as a function of the system's dimensionality. Beyond the formation of isolated magnetic polarons and/or magnetic bipolarons, we consider how a system composed of magnetic polarons within an antiferromagnetic system is driven ferromagnetic as the density of magnetic polarons is increased. Finally, we discuss the large paramagnetic susceptibility associated with the formation of magnetic polarons. The magnetic susceptibility is composed of a Curie-like temperature-dependent component as well as a temperature-independent component. The temperature-dependent term arises from the reorienting of the magnetic polarons under the influence of a magnetic field. The temperature-independent contribution arises from the expansion and contraction of magnetic polarons which are, respectively, aligned parallel or antiparallel with the applied magnetic field.
Electron-Transfer Dynamics in DTDCI/MoS2 and DTDCI/WS2 Nanoclusters

Field: Chemistry (Physical Sciences)

The kinetics of forward and reverse electron transfer (ET) between an organic cyanine dye and semiconductor nanoclusters have been studied. The systems studied are MoS2/DTDCI and WS2/DTDCI (DTDCI ≡ diethylthiodicarbocyanine iodide). The static spectroscopy of these systems indicates that the dye adsorbs on the nanoclusters as monomers. The vast majority of excited-state dye molecules are quenched by rapid (<10 ps) electron injection in the nanocluster. The reverse ET kinetics are elucidated by time-resolved absorption (bleach recovery) measurements. The results indicate that there are two components of reverse ET that take place on the tens to hundreds of picoseconds and >10 ns time scales. These components are assigned to reverse ET from shallow (tens to hundreds of picoseconds) and deep (>10 ns) trap states. The shorter time scale component is nonexponential and is fit with distributed kinetics model, in which the Bohr radius of the trapped electron is about 2.2 nm. This value of the Bohr radius is comparable to that obtained from electron/hole recombination studies.
Adherence to Antiretroviral Therapy and Outcomes in HIV-Infected Patients Enrolled in An Induction/Maintenance Randomized Trial

Field: Medicine (Health Sciences)

Objective To examine the effect of adherence to therapy on early virological response, later virological failure, and occurrence of adverse events in HIV-infected patients. Design A randomized trial of 3-month induction period of zidovudine/lamivudine/indinavir followed by a maintenance phase of zidovudine/lamivudine/indinavir, zidovudine/lamivudine or zidovudine/indinavir. Main outcomes Adherence was assessed by pill count. In the induction phase, early virological response was defined as plasma HIV-RNA<500 copies/ml at month 2 and in the maintenance phase, virological failure was defined as plasma HIV-RNA >500 copies/ml in two consecutive specimens. Results The median adherence rate was 97% in both induction ( n=366) and maintenance phase ( n=237). In the maintenance phase, pairwise comparisons showed a lower adherence rate in zidovudine/lamivudine/indinavir versus zidovudine/lamivudine ( P=0.03), or versus zidovudine/indinavir ( P=0.05). Only 13% of patients had an adherence over the maintenance phase of 80% or lower, while 40% of patients occasionally had an adherence rate of 80% or lower during this phase. Among the 362 patients with documented HIV-RNA at month 2, 86% had an early virological response. Adherence of 80% or greater was the only variable statistically predictive to early virological response ( P<0.001), while baseline CD4, baseline HIV-RNA, and adherence of 95% or greater were not associated to virological response. In the maintenance phase, adherence, baseline HIV-RNA, HIV-RNA at month 3 and treatment groups were independently predictive to time to virological failure. Analysis by randomized groups indicated that difficulty in adherence (<80%) was predictive to time to failure ( P<0.001) only in both indinavir-containing regimens. Occurrence of two or more severe adverse events (grade 3 and 4) was higher in patients with poor adherence although not statistically associated ( P=0.12), while no association was found with minor adverse events. Conclusion Adherence rate was globally lower in patients maintaining the original triple-drug therapy compared with those receiving less intensive regimens. Adherence rate was a time-dependent variable. Adherence to antiviral regimen of 80% or greater was predictive to early virological response, and adherence rate lower than 80% or 95% was predictive to virological failure, especially in indinavir-containing regimens. Occurrence of adverse events was not clearly associated to adherence.
Effects of Essential Oils from Plants on Growth of Food Spoilage Yeasts

Field: Agricultural and Biological Sciences (Life Sciences)

ABSTRACT Thirty‐two essential oils from plants were screened for inhibitory effects on 13 food‐spoilage and industrial yeasts. Of these, essential oils of allspice, cinnamon, clove, garlic, onion, oregano, savory, and thyme were most inhibitory. Oils were subsequently tested for their effects on biomass production and pseudomycelium formation of eight genera of yeasts. Garlic oil was a potent inhibitor of yeast growth at concentrations as low as 25 ppm. The oils of onion, oregano and thyme were also strongly inhibitory. Essential oils (100 ppm) had no effect on pseudomycelium production by Candida lipolytica . However, all eight essential oils delayed pseudomycelium formation by Hansenula anomala , whereas six oils stimulated pseudomycelium production by Lodderomyces elongisporus . Cinnamon and clove oils were clearly stimulatory to pseudomycelium production by Saccharomyces cerevisiae .
Immunomodulatory properties of T. muris antigens

Field: Immunology and Microbiology (Life Sciences)

Helminth parasites are complex multicellular organisms capable of maintaining long lasting, chronic infections in human hosts. To ensure their survival and successful reproduction, helminth parasites have developed immunomodulatory mechanisms to modulate their host�¢����s immune system to minimise the physical and immunological pathology to the host and prevent parasite expulsion. Many cells of the immune system are targets for parasite mediated immune modulation including T cells, macrophages and dendritic cells. Further, many inflammatory diseases feature an imbalance between the main subsets of macrophages, M1 and M2, in favour of the M1 pro-inflammatory phenotype. Also, many helminth products have been shown to be able to skew immune responses away from M1 macrophages, thus potentially attenuating disease progression. Therefore, the excretory/secretory products (ES) of the adult stage of the gastrointestinal nematode parasite Trichuris muris have been studied to explore their potential to modulate macrophage biology. Bone marrow derived macrophages (BMDM) were selected to (a) evaluate the ability of T. muris ES to down regulate pro-inflammatory macrophage responses; (b) explore the intracellular mechanisms underlying any immunomodulatory activity and (c) assess the potential of ES molecules to confer protection from inflammatory and autoimmune disorders.

Pre-treatment of murine BMDMs with T. muris ES and its fractions significantly suppressed the expression of the pro-inflammatory mediators TNF, IL-27, CCL2, IL-6, IL-I���², and Nos2 upon LPS stimulation. T. muris ES also reduced the phosphorylation of p65 at serine 536, downregulated the expression of the histone acetyl transferase (HAT) p300 family, and upregulated the expression of histone deacetylases (HDACs). Moreover, bone marrow cells differentiated to BMDM in the presence of T. muris ES reduced the inflammatory responses of the mature BMDM through modifying the expression of the epigenetic enzymes (HATs and HDACs), with these effects of ES being reversed by epigenetic inhibitors. ES also increased the expression of macrophage cell surface markers on differentiated BMDMs. T. muris ES suppressed multiple LPS-driven genes in the TLR signalling pathway of both murine BMDM pre-incubated with ES, and BMDM derived from ES-exposed bone marrow cells. Ingenuity pathway analyses suggested the involvement of intracellular pathway regulators that orchestrate the expression of the inflammatory genes. Thus, T. muris ES has the potential to limit the pathology associated with inflammatory and autoimmune diseases.
Comparison of three treatment methods for simple bone cyst in children

Field: Medicine (Health Sciences)

Abstract Background Unicameral bone cyst (UBC) is a benign tumor whose clinical treatments and efficacy are controversial. The purpose of this study was to evaluate the efficacy of the elastic stable intramedullary nail (ESIN), the injection of autologous bone marrow (ABM) and the combination of ESIN and ABM in the treatment of simple bone cyst of children. Methods 83 children with simple bone cyst were analyzed retrospectively. 28 cases were treated with ABM. 28 cases were treated with ESIN. 27 cases were treated with ABM and ESIN. All cases were diagnosed through X-ray, CT or MRI scans. For the suspicious ones, pathological biopsy was performed for an accurate diagnosis. X-ray examinations were carried out for the postoperative follow-up. Capanna criteria for bone cyst was used for the postoperative evaluation of the three methods. Results All the cases accomplished the follow-up. The effective rate of ABM+ESIN group was significantly higher than that of the ABM group ( P <0.05), and the cure rates of ESIN group and ABM+ESIN group were higher than that of ABM group ( P <0.05, respectively). The cure time in ESIN group was lower than that of the other two groups ( P <0.05, respectively). The times for admission were 2.0±0.0 in ESIN group, 5.7±1.9 in ABM group and 4.7±2.4 in ABM+ESIN group ( P <0.05 when compared with each other). Conclusions The method of ABM combined with ESIN for children bone cyst has the highest effective and curative rates. For individual method, ESIN has a higher effective rate and curative rate than that of ABM. Meanwhile, it has the fewest hospitalizations.
Preliminary tests with some N-substituted p-ethoxybenzamides for synergistic action in allethrin fly sprays /

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Several groups of compounds have been examined at the Beltsville, Md., laboratory in an effort to find new synergists for pyrethrins and aetna!In this study a group of p-ethoxybenzamides were tested for possible synergism with allethrin.All the compounds were prepared by reacting p-ethoxybenzoyl chloride with various amines under suitable conditions.They may be represented by the general formula O
Simulation and Experimental Investigations on the Strain Measurement of the Uniform Strength Beam Using a FBG sensor

Field: Engineering (Physical Sciences)

The model of force analysis on a uniform strength beam is built by the general finite element program (ANSYS software). The flexivity profile produced by uniform strength beam with different forces is simulated by ANSYS software. In experiment, a fiber Bragg grating sensor is fixed on the uniform strength beam with modified acrylate. The flexivity and strain are varied by changing the load on the end of the beam. The strain of the uniform strength beam is measured with FBG when applied force is varied from 2.45N to14.7N with a step of 2.45N. Both the simulated and experimental results show that, the strain induced by the uniform strength beam is linear with the load force. The sensitivity is 18.32μ/N for experimental measurement, and 19.72μ/N for simulation. The experimental results are consistent with the simulation results, with the maximum measurement error of strain being 7.4%. It indicates that, the FBG sensor fixed with modified acrylate is proved to be effectively and reliably in the applications of civil engineering.
Enhanced Luminescence of NaY0.6–xCe0.1Gd0.3EuxF4 Nanorods by Energy Transfers between Ce3+, Gd3+, and Eu3+

Field: Materials Science (Physical Sciences)

In this study, hexagonal-phase NaY0.6–xCe0.1Gd0.3EuxF4 nanorods were synthesized via a mild solvothermal method. By modifying the Eu3+ dopant concentration, the crystal phase, morphology, and luminescent properties were well controlled. A broad excitation band centered at around 260 nm corresponding to the 2F5/2 → 4f-5d transition of Ce3+ was detected in the hosts containing Gd3+ ions by monitoring the Eu3+ emissions, indicating that an efficient Ce3+ → Eu3+ energy transfer occurred via the Gd3+ sublattice. Luminescence decay behaviors of the NaY0.6–xCe0.1Gd0.3EuxF4 nanorods were studied, and the energy transfer mechanism was discussed. An obvious rising edge on the luminescence decay curve of Eu3+ ions in the NaY0.6–xCe0.1Gd0.3EuxF4 nanorods was observed. The rising time is proposed to describe the energy migration time from Ce3+ to Eu3+ via the Gd3+ sublattice.
Dynamic Media Assemblage

Field: Computer Science (Physical Sciences)

This paper presents dynamic media assemblage, which is a new presentation and summarization method for images and videos on a 2-D canvas. Instead of using the keyframes of the videos to generate a still image summarization, our method allows the videos to play simultaneously on the canvas while utilizing the limited space efficiently. This technique uses an efficient iterative packing algorithm, and as a result is well suited for interactive manipulations of media files within the assemblages in real time, such as insertion, deletion, and rearrangement. Our method starts by detecting shot boundaries and dividing longer input videos into individual shots. Within each shot, its temporal-spatial salient regions are extracted and used to recover camera motions. These saliency information further defines important regions within individual videos or images, which allows us to preserve visually important regions while packing the media files more efficiently into media assemblages. Our algorithm is iterative and can therefore quickly adjust to new canvas sizes or other user intentions. We demonstrate the effectiveness of our techniques by applying our methods to several applications, including media collection presentation, single video dynamic summary, personal media file browser, and interactive video wall.
LEFT VENTRICULAR ROTATION, TWIST AND UNTWIST: PHYSIOLOGICAL ROLE AND CLINICAL RELEVANCE

Field: Medicine (Health Sciences)

The helical ventricular myocardial band of Torrent-Guasp is a new concept, which provides strong grounds for reconciliation of some important aspects in cardiovascular medicine. Oblique fiber orientation provides left ventricular rotation, which in addition to radial thickening and longitudinal shortening, is predicted as an essential component of the effective left ventricular pumping. Left ventricular rotation can be measured in clinical practice noninvasively using echocardiography and this provides new opportunities for the assessment of different aspects of left ventricular mechanical function.
The Flora of Emmet County, lowa

Field: Agricultural and Biological Sciences (Life Sciences)

The original paper with this title, prepared in the late 1920's, was submitted for publication in 1932, and appeared in Volume 39 of the Proceedings of the Iowa Academy of Science. In the introduction to that list there was a brief description of the topography and of the natural areas of the county. It has not been considered necessary to repeat such description in this paper except to indicate some of the changes that have taken place since that time and which have affected the flora. The greatest changes, consisting of bringing the prairie under cultivation, draining most of the marshes and prairie ponds, and clearing and pasturing many woodlands, had most of them come by the close of the previous century, or shortly thereafter.