gebhart/patrepeval huggingface dataset:
Bioinformatics Screening of Genes Specific for Well-Regenerating Vertebrates Reveals c-answer, a Regulator of Brain Development and Regeneration (2019)

The molecular basis of higher regenerative capacity of cold-blooded animals comparing to warm-blooded ones is poorly understood. Although this difference in regenerative capacities is commonly thought to be a result of restructuring of the same regulatory gene network, we hypothesized that it may be due to loss of some genes essential for regeneration. We describe here a bioinformatic method that allowed us to identify such genes. For investigation in depth we selected one of them encoding transmembrane protein, named "c-Answer." Using the Xenopus laevis frog as a model cold-blooded animal, we established that c-Answer regulates regeneration of body appendages and telencephalic development through binding to fibroblast growth factor receptors (FGFRs) and P2ry1 receptors and promoting MAPK/ERK and purinergic signaling. This suggests that elimination of c-answer in warm-blooded animals could lead to decreased activity of at least two signaling pathways, which in turn might contribute to changes in mechanisms regulating regeneration and telencephalic development.
Relationship between Feeder Pig Frame Size and Market Hog Characteristics (1987)

Two experiments were conducted to evaluate the relationship between feeder pig frame size and market hog characteristics. For Exp. 1, 96 feeder pigs were selected for a 3 × 2 × 4 factorial with three frame sizes (large, medium and small), two sexes (barrows and gilts) and four weight endpoints (93, 100, 106.5 and 113.4 kg). Experiment II was conducted with 95 barrows in a 3 × 2 × 3 factorial using three frame sizes (large, medium and small), two capacity scores (low and high) and three slaughter endpoints (100, 106.5 and 113.4 kg). Feeder pigs were measured for skeletal dimensions. Pigs were slaughtered within 2.3 kg of their predetermined weight endpoint. One side was processed into wholesale cuts, and the four lean cuts were separated into lean, fat and bone. The separable lean from the four lean cuts and the skinless belly were separately ground and chemically analyzed for protein, moisture and fat. Feeder pig frame size affected (P<.05) feeder pig leg length, body length, body depth, last rib backfat, carcass length, radius length, carcass heart girth and percent bone. However, these differences were not consistent across experiments and in some instances interactions of sex and slaughter weight with frame score were involved. Gilts were leaner, had larger longissimus muscles and longer carcasses than barrows (P<.05). Low-capacity feeder pigs were longer bodied and taller than high-capacity feeder pigs; however, they were similar in body width, body depth and heart girth. High-capacity pigs had shorter carcasses and larger longissimus muscles than low-capacity pigs (P<.05). No differences were observed in growth between high- and low-capacity pigs or among frame sizes. Results from this study indicate that evaluators can predict skeletal traits from feeder pig characteristics, but were less able to predict slaughter hog growth or carcass composition.
Long-Living Budding Yeast Cell Subpopulation Induced by Ethanol/Acetate and Respiration (2019)

Budding yeast generate heterogeneous cells that can be separated into two distinctive cell types: short-living low-density and long-living high-density (HD) cells by density gradient centrifugation. We found that ethanol and acetate induce formation of HD cells, and mitochondrial respiration is required. From their transcriptomes and metabolomes, we found upregulated differentially expressed genes in HD cells involved in the RGT2/RGT1 glucose sensing pathway and its downstream genes encoding hexose transporters. For HD cells, we determined an abundance of various carbon sources including glucose, lactate, pyruvate, trehalose, mannitol, mannose, and galactose. Other upregulated differentially expressed genes in HD cells were involved in the TORC1-SCH9 signaling pathway and its downstream genes involved in cytoplasmic translation. We also measured an abundance of free amino acids in HD cells including valine, proline, isoleucine, and glutamine. These characteristics of the HD cell transcriptome and metabolome may be important conditions for maintaining a long-living phenotype.
Outer membrane protein a of Salmonella enterica serovar Typhimurium activates dendritic cells and enhances Th1 polarization (2010)

Our findings suggest that OmpA-sal modulates the adaptive immune responses to S. enterica serovar Typhimurium by activating dendritic cells and driving Th1 polarization, which are important properties to consider in the development of effective S. enterica serovar Typhimurium vaccines and immunotherapy adjuvant.
Recovery of microbial community structure and functioning after wildfire in semi-arid environments: optimising methods for monitoring and assessment (2015)

Soil samples were collected from 10 similar ecosystems in the Pilbara with analogous native vegetation, but differing levels of post-fire disturbance (i.e. 3 months, 1 year, 5, 7 and 14 years after wildfire). Soil microbial activity was measured with the Solvita test which determines soil microbial respiration rate based on the measurement of the CO2 burst of a dry soil after it is moistened. Soils were dried and re-wetted and a CO2 probe was inserted before incubation at constant conditions of 25 C during 24 h. Measurements were taken with a digital mini spectrometer. Microbial (bacteria and fungi) biomass and community composition were measured by phospholipid fatty acid analysis (PLFA). Results Immediately after the fire (i.e. 3 months), soil microbial activity and microbial biomass are similar to 14 years ‘undisturbed’ levels (53.18 3.68 ppm CO2-CO and 14.07 0.65 mg kg-1, respectively). However, after the first year post-fire, with larger plant productivity, microbial biomass and microbial activity increase rapidly, peaking after 5-7 years post fire (70.70 8.94 ppm CO2-CO and 21.67 2.62 mg kg-1, respectively). Microbial activity measured with the Solvita test was significantly correlated (R Pearson > 0.7; P < 0.001) with microbial parameters analysed with PLFA such as microbial biomass, bacteria biomass or mycorrhizhal fungi. This method has proven to be reliable, fast and easy to interpret for assessment of soil microbial activity in the recovery of soil quality during the recovery after fire.
Structural analogues of isatin and their antimicrobial activity. (1980)

A series of 5-haloisatins were aminomethylated in position 1 and hydrazino groups were introduced in position 3. Synthesized N-Mannich bases and hydrazones were biologically tested against various kinds of bacteria and fungi. Results from these in vitro studies showed a considerable growth inhibition of some gram negative bacteria caused by chlorinated N-Mannich bases of isatin. Comparing the inhibition zones of the halogenated isatin N-Mannich bases with structural analogues of nonhalogenated ones as well as with isatin itself, an increase in antimicrobial activity was observed, thus, indicating the importance of both substituents, namely, halogen in position 5 and an amino moiety in position 1. The most biologically active compound was found to be diisopropylamino-N-Mannich base of 5-chloroisatin.
Cell Culture of Foam Cells Prepaired from Athreromatous Aorta (1982)

We posturated that lysosomes involved in the accumulation of cholesterol ester in atheromatous aorta. To elucidale the mechanism further, we have developed cell culture system of foam cells from atheromatous aorta. The cells were prepared by the digestion of enzymes such as elastase, hyaluronidase and collagenase. Cross image, which may correspond to cholesterol ester inclusion bodies, was observed in living foam cells.
Minimally Invasive Muscle Embedding Generates Donor-Cell-Derived Muscle Fibers that Express Desmin and Dystrophin (2020)

In MIME-treated muscles, 22% ± 7% and 78% ± 7% muscle fibers were RFP+ and GFP+, respectively (mean ± standard deviation); and all RFP+ fibers were positive for desmin and dystrophin. Conclusion. We conclude that MIME helps generate muscle fibers of donor origin, in host muscle.
Two Competing Mechanisms for the Copper-Free Sonogashira Cross-Coupling Reaction (2008)

The mechanism of the copper-free Sonogashira cross-coupling was investigated using a model reaction with differently para-substituted phenylacetylenes and 4-iodobenzotrifluoride as coupling partners and a Pd 2 (dba) 3 -CHCl 3 -AsPh 3 catalyst system in methanol. A carbopalladation mechanism was ruled out through a series of experiments in which the equivalent of a carbopalladation reaction intermediate was synthesized by an alternate route, and its conversion to product was monitored. A Hammett correlation study revealed a possible mechanistic changeover when going from electron-rich to electron-poor alkynes in the model reaction. It is advocated that the reaction mechanism changes from a pathway involving a fast proton transfer from a slowly forming cationic Pd complex to a pathway involving a slow proton transfer from a neutral Pd complex on going from electron-rich to electron-poor alkynes. The amine base is believed to act as a base in both pathways and as a nucleophile promoting the formation of the cationic complex in the reactions involving electron-rich alkynes. This was substantiated by the observation of a primary isotope effect (K Alkyne-H /K Aikyne-D ≈ 2) for the electron-poor alkyne and a pronounced base dependence for the electron-rich one. © 2008 American Chemical Society.
Effect of Surface Oxides and Intermetallics on Nanostructured Diamond Coating of Nitinol (2006)

Microwave plasma chemical vapor deposition (CVD) was used to grow nanostructured diamond onto mechanically polished superelastic Nitinol (NiTi) alloy. As determined by glancing-angle x-ray diffraction, mechanical polishing of the heavily oxidized as-received samples resulted in removal of nickel, Ni3Ti, and TiO2 surface phases, leaving the NiTi austenite (B2 type, CsCl structure) to be detected. Diamond nucleation and growth was impractically slow on the mechanically polished samples and could only yield continuous films at practical growth rates when they were first exposed to plasma annealing to allow formation of oxide and intermetallic phases (Ni3Ti, NiTi2). The ability of a surface layer (composed of oxides and/or the intermetallic phases) to act as a barrier to carbon diffusion may be responsible for an observed increase in interfacial TiC formation leading to practical diamond growth rates of about 1 m/hour.
The need for an animal model of chronic pain (1976)

Pain Treatment Center, Scripps Clinic Medical Group, La Jolla, Calif. 92037 U.S.A. Accepted November 14, 1975.
Statistical timing based on incomplete probabilistic descriptions of parameter uncertainty (2006)

Existing approaches to timing analysis under uncertainty are based on restrictive assumptions. Statistical STA techniques assume that the full probabilistic distribution of parameter uncertainty is available; in reality, the complete probabilistic description often cannot be obtained. In this paper, a new paradigm for parameter uncertainty description is proposed as a way to consistently and rigorously handle partially available descriptions of parameter uncertainty. The paradigm is based on a theory of interval probabilistic models that permit handling uncertainty that is described in a distribution-free mode - just via the range, the mean, and the variance. This permits effectively handling multiple real-life challenges, including imprecise and limited information about the distributions of process parameters, parameters coming from different populations, and the sources of uncertainty that are too difficult to handle via full probabilistic measures (e.g. on-chip supply voltage variation). Specifically, analytical techniques for bounding the distributions of probabilistic interval variables are proposed. Besides, a provably correct strategy for fast Monte Carlo simulation based on probabilistic interval variables is introduced. A path-based timing algorithm implementing the novel modeling paradigm, as well as handling the traditional variability descriptions, has been developed. The results indicate the proposed algorithm can improve the upper bound of the 90/sup th/-percentile circuit delay, on average, by 5.3% across the ISCAS'85 benchmark circuits, compared to the worst-case timing estimates that use only the interval information of the partially specified parameters.
Computed tomography-based radiomics for the differential diagnosis of pneumonitis in stage IV non-small cell lung cancer patients treated with immune checkpoint inhibitors (2023)

Radiomic biomarkers applied to computed tomography imaging may support clinicians making the differential diagnosis of pneumonitis in patients with NSCLC receiving immunotherapy, especially when the radiologic assessment is non-conclusive.
Talking Drawings as a University Classroom Assessment Technique (2008)

Increased focus on assessment of student learning, within college classrooms, has lead many professors to routinely employ classroom assessment techniques as a means to make adjustments in teaching during the instructional process. This article describes a technique, Talking Drawings, which was developed by a high school teacher as a teaching strategy. The authors describe the reconceptualization of Talking Drawings, into a classroom assessment technique, which is appropriate for a variety of uses at the college/university level. The primary purpose of this technique is to provide the instructor with feedback as to the effectiveness of teaching and to find out what students are or are not learning. Illustrated, in this article, is the Talking Drawings classroom assessment technique, examples for application, and procedures for utilization within the classroom.
Zika virus infection in asymptomatic persons in Myanmar, 2018 (2019)

We conclude that ZIKV infection was increasing among asymptomatic persons in the same area in Myanmar during 2018 compared with 2017. It is highly recommended to strengthen the surveillance system for ZIKV to prevent possible outbreaks.
Extracting legal knowledge by means of a multilayer neural network application to municipal jurisprudence (1991)

This paper describes an experiment dealing with extraction of legal deeision rules from a multilayer neuml network. The rules that are extracted can be used for designing the knowledge base of an expert system. The experiment is based on a corpus of Councif of State dceisions (administrative law). This method can be efficiently applied to the legal domain. An interpretation of the extractal rules is attempted in terms of statutes and judges' impficit knowledge.
Validation of Nasal Potential Difference Measurements in Gut-Corrected CF Knockout Mice (2008)

Attempts at correcting the nasal potential difference (PD) in cystic fibrosis (CF) mice have long been used in preclinical gene and small molecule therapy development. However, in general, CF mice suffer from intestinal disease, are runted, and have high mortality rates; they are therefore difficult to work with, especially if large numbers are required. Because of this, large-scale PD studies in CF mice have not been performed. Working with CF mice has become substantially easier after the generation of the gut-corrected CF-knockout mouse. Fatty acid-binding promoter (FABp)-mediated expression of CFTR in the gut, but not the airways, prevents the intestinal disease of the CF knockout mouse. This model has given us the unique opportunity to systematically study PDs in large numbers of CF mice. The nose, but not the lungs, of these animals mimic the bioelectric defect seen in humans. We have therefore assessed the bioelectrics of the respiratory epithelium comparing FABp-CF and wild-type mice. The large body of data gathered in CF and wild-type mice allowed us, for the first time, to establish power calculations that should inform sample sizes required in gene and small molecule therapy development. In addition, we address the important issues of intra-animal variability as well as intra- and inter-operator variability for scoring the traces, and the effect of age and sex on nasal PD in CF mice. These data should allow a more informed use of CF animals in future studies.
Stargazer—A Mouse to Seize! (2005)

The goals of this short review are to familiarize readers with the stargazer mouse and to outline the major functional defects associated with this mutant. The roles of the stargazin protein in calcium channel function and alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-receptor trafficking are discussed; focus is placed on studies regarding the thalamus, whence absence seizures potentially originate, and the cerebellum, which is associated with the ataxic phenotype. Finally, two additional alleles of stargazer, waggler and stargazer 3Jackson (3J), illustrate the value of an allelic series for understanding stargazin function.
Methane Leaks from North American Natural Gas Systems (2014)

Methane emissions from U.S. and Canadian natural gas systems appear larger than official estimates.
Resolution of dimly fluorescent particles: A practical measure of fluorescence sensitivity (1998)

Flow cytometry is usually used to analyze subpopulations of cells, not simply to measure the mean fluorescence level of a mixture. Thus, resolution or coefficient of variation (CV) of dimly stained populations is the most appropriate measure of fluorescence “sensitivity.” Methods used to measure sensitivity that are in routine use do not unambiguously and completely determine the ability of a flow cytometer to resolve dimly fluorescent populations from each other. Since fluorescence sensitivity depends on two factors, background light (B) and detection efficiency (Q, the detected photoelectrons per fluorochrome molecule on an analyzed particle), one cannot uniquely define the operating condition of a flow cytometer with just one of these factors. In general, it is not possible to define the ability of a flow cytometer to resolve dim subpopulations by using a single number such as “noise level” or “detection threshold”—the description requires a “two-parameter” measure. A carefully characterized flow cytometer was used to determine the inherent fluorescent CV of dimly fluorescing beads. The fluorescence from the beads is also calibrated in terms of molecules of equivalent soluble fluorophore (MESF). The beads with known inherent CV and MESF provide a standard against which the instrument contribution to the CV of dim fluorescence can be measured. By measuring the standard deviation (SD) of the fluorescence histogram from unstained beads (noise) we obtain a second measure of instrument performance. The bead CV and noise SD are a sufficient pair of factors to determine the optical capability of a flow cytometer to resolve dim subpopulations of particles. It is also possible to use the measurements to calculate B and Q and use this information to predict the shapes of fluorescence histogram distributions of dim particles. Cytometry 33:267–279, 1998. © 1998 Wiley-Liss, Inc.
Physically Based Modeling of Cold Load Pickup (1981)

A general, physically based, probabilistic model of power system load has been developed [1]. The model is suitable for short-term prediction of system demand by composition, and accounts for lifestyle dependency and weather dependency as well as effects of other exogenous processes. The conceptual framework and notation applicable to a wide range of load modeling problems have been the key issues in developing a general model.
High Speed HPD for Photon Counting (2008)

We have succeeded in the development of a high-speed Hybrid Photodetector (HPD), by using a reduced electron lens and a newly developed avalanche diode (AD) with very low capacitance. The HPD shows fast time response of less than 500 ps in both rise and fall times, and good timing resolution of 26 ps (one sigma) for single photons at full illumination on a photocathode 8 mm in diameter. Limiting factors of the timing resolution were further investigated, and were found to be the transit time difference of electrons in vacuum along the photocathode and the jitter of the electronics. The timing resolution is 15 ps for illumination of less than 5 mm on the central part of the photocathode, which includes the jitter of 13 ps from the electronics. This resolution is the world's highest for HPDs, and matches the resolution of MCP-PMTs. Both a GaAsP photocathode having close to 50% quantum efficiency in the visible and a bialkali photocathode having 34% QE in the UV were fabricated in view of making this device available for various applications. In this paper, we report the results of our evaluation, including discussion about the limiting factors of the timing resolution for the new HPD.
Control of swimming in crucian carp: Stimulation of the brain using an implantable wire electrode (2013)

Control of locomotion in different kinds of animals, or so-called bio-robot, has been reported. Bio-robot is a technology based on the information communication between the nerve tissue and the computer. In this work, to study the locomotion control in carp's brain, a Parylene-based wire microelectrode is fabricated for stimulation in midbrain. Compared with traditional microelectrodes, wire electrodes provide better bio-compatibility and good mechanical stability. The whole electrode was covered by Parylene C film, except the stimulation sites which are exposed by lift-off process, thus the interface impedance is significantly reduced. After the fabrication, crucian carps was anesthetized in MS-222 water solution and the cranium was partially removed to expose the midbrain. After all these steps, electrodes are tested to see if they are properly insulated. Then one electrode is implanted into the crucian carp's midbrain by surgical procedure and the movement of the fish is observed by a video camera. The caudal fin movement of crucain carp is successfully induced by applying a single polar pulse train. This result proved the former theory that control region of carp is located in midbrain. On the other hand, the experiment shows great potential and promising future in the bio-robotic fish.
NLRP3-Inflammasome Inhibition during Respiratory Virus Infection Abrogates Lung Immunopathology and Long-Term Airway Disease Development (2021)

Respiratory syncytial virus (RSV) infects most infants by two years of age. It can cause severe disease leading to an increased risk of developing asthma later in life. Previously, our group has shown that RSV infection in mice and infants promotes IL-1β production. Here, we characterized the role of NLRP3-Inflammasome activation during RSV infection in adult mice and neonates. We observed that the inhibition of NLRP3 activation using the small molecule inhibitor, MCC950, or in genetically modified NLRP3 knockout (<i>Nlrp3-/-</i>) mice during in vivo RSV infection led to decreased lung immunopathology along with a reduced expression of the mucus-associated genes and reduced production of innate cytokines (IL-1β, IL-33 and CCL2) linked to severe RSV disease while leading to significant increases in IFN-β. NLRP3-inflammasome inhibition or deletion diminished Th2 cytokines and inflammatory cell infiltration into the lungs. Furthermore, NLRP3 inhibition or deletion during early-life RSV infection led to reducing viral-exacerbated allergic response in a mouse model of RSV-induced allergy exacerbation. Here, we demonstrated the critical role of NLRP3-inflammasome activation in RSV immunopathology and the related long-term airway alteration. Moreover, these findings suggest the NLRP3-inflammasome as a potential therapeutic target to attenuate severe RSV disease and limit childhood asthma development.