gebhart/patrepeval huggingface dataset:
Small Animal Models for Human Immunodeficiency Virus (HIV), Hepatitis B, and Tuberculosis: Proceedings of an NIAID Workshop (2019)

The main advantage of animal models of infectious diseases over in vitro studies is the gain in the understanding of the complex dynamics between the immune system and the pathogen. While small animal models have practical advantages over large animal models, it is crucial to be aware of their limitations. Although the small animal model at least needs to be susceptible to the pathogen under study to obtain meaningful data, key elements of pathogenesis should also be reflected when compared to humans. Well-designed small animal models for HIV, hepatitis viruses and tuberculosis require, additionally, a thorough understanding of the similarities and differences in the immune responses between humans and small animals and should incorporate that knowledge into the goals of the study. To discuss these considerations, the NIAID hosted a workshop on 'Small Animal Models for HIV, Hepatitis B, and Tuberculosis' on May 30, 2019. Highlights of the workshop are outlined below.
Identification of Retinoic Acid Receptor Agonists in Sewage Treatment Plants (2009)

Retinoic acid receptor (RAR) agonists are speculated to be one possible cause for the widely observed frog deformities in North America, although little is known about the specific RAR agonists in aquatic environments. We identified the specific RAR egonists in sewage treatment plants (STPs) and receiving rivers using an RAR yeast two-hybrid bioassay. Water samples were extracted by solid-phase extract cartridges, which were successively eluted by hexane, ethyl acetate, and methanol for bioassay. Among the three fractions, the ethyl acetate fraction showed the highest RAR agonistic activities. The bioassay-derived activity, expressed as all-trans-retinoic acid (all-transRA) equivalents (ATRA-EQ) were 10.9 +/- 2.2 and 1.7 +/- 1.0 ng/L in the STP influents and effluents, respectively, while the ATRA-EQs were as high as 7.1 and 8.3 ng/L in the two rivers receiving STP effluents. Following a two-step fractionation using high-performance liquid chromatography and ultra-performance liquid chromatography (UPLC) directed by the bioassay, two bioactive fractions were obtained from Gaobeidian STP influent and all-trans-4-oxo-RA (4.7-10.4 ng/L in influents, < 0.2-0.9 ng/L in effluents) and 13-cis-4-oxo-RA (2.3-7.1 ng/L in influents, < 0.4-1.1 ng/L in effluents) were identified in these fractions with UPLC-MS/MS. The EC50 for all-trans-4-oxo-RA or 13-cis-4-oxo-RA relative to that of all-trans-RA in exhibiting RARalpha agonistic activity was calculated to be 3.87 and 0.46, respectively.
ChemInform Abstract: High Activity Ethylene Trimerization Catalysts Based on Diphosphine Ligands. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Seasonal changes in serum leptin, food intake, and body weight in photoentrained woodchucks (2001)

Male woodchucks (Marmota monax) were maintained in northern vs. southern hemisphere photoperiods, provided feed and water ad libitum, and evaluated every 2 wk for 23 mo for body weight, absolute and relative food intake, body temperature, serum testosterone, and serum concentrations of leptin measured using an anti-mouse leptin enzyme-linked immunoassay. During late spring and summer, body weight increased 56 +/- 4% above winter nadirs, and during the autumn and early winter weights decreased 27 to 43% below midsummer maxima. Serum leptin initially increased during increases in body weight, in the late spring, reached peak values (490 +/- 32 pg/ml) in summer during the initial decline in body weight, and later decreased along with body weight to reach basal values (20 +/- 5 pg/ml) in late winter. Spontaneous declines in food intakes in summer began 2-6 wk before resulting declines in body weight and occurred during increases in leptin >100 pg/ml. The rate of decline in food intakes was greatest when serum leptin was at or near peak values. Food intake increased in late winter when leptin was low and 7-10 wk before resulting increases in body weight. Testis recrudescence occurred when leptin was declining to near basal levels. The results suggest that leptin is involved in the hormonal regulation of the circannual cycle in the drive for voluntary food intake in this species.
Temperature dependence of the Oregonator model for the Belousov-Zhabotinsky reaction (2009)

It is well known that temperature plays an important role in the chemical dynamics of Belousov-Zhabotinsky (BZ) reactions. The five-step Oregonator model of the BZ reaction has been elaborated here to investigate the temperature effect. The bifurcation dynamics has been calculated in the phase space spanned by initial reagents concentration ratio, stoichiometric factor and temperature. The combination of activation energies of the individual reaction steps governs the dependence of oscillation period and amplitude with temperature. The analysis reveals the existence of temperature limits beyond which no oscillations occur.
New Challenges and Design for High Mach High Flow Coefficient Impeller for Large Size LNG Plant (2018)

The large scale of Liquefied Natural Gas plant, has always meant large size of compression train for refrigeration duty, most of the time driven by high power driver in the range of 40-60 MW.The new generation of LNG plant are moving toward a larger size, that mean larger compression stations, driven by higher power gas turbine that can arrive and exceed 100 MW.This increase of specific power means also increase in compression gas flow and so the need to have compressors that are able to handle it in efficient way.This is true in particular for impeller stages equipping the Propane Compressors that will be selected at higher specific flow coefficient and Mach number.The higher the flow coefficient and the peripheral Mach number the higher are the losses and so it is difficult to continue to keep a good level of stage efficiency and operating range, that are the main key performance parameter for the refrigerant compressor for LNG.The present paper illustrates an improved impeller stage designed in particular to fit this duty, the need of a multidisciplinary optimization, from aerodynamic, structural mechanic, aeromechanic and rotordynamic.The paper illustrates the main design challenges for this type of impeller design, the validation done by the OEM and the benefits of their usage by mean of dedicated Case studied.
Characterization of OFDM Radio Link Under PLL-Based Oscillator Phase Noise and Multipath Fading Channel (2012)

We propose a discrete-time model for phase noise processes occurring in phase locked loop (PLL) based oscillators. By using linear time-invariant analysis in the phase domain, we arrive at a parallel auto-regressive moving-average phase noise model that captures the major noise sources and corresponding loop transfer functions of the PLL circuitry. The acquired model allows us to derive analytically the distribution of the inter-carrier interference (ICI) power in the receiver, shown to be a sum of correlated gamma random variables with a model-specific covariance matrix. Finally, we utilize the derived ICI distribution and proceed to analyze the effects of phase noise and multipath fading on the performance of OFDM radio links. For example, we evaluate the rate loss without ICI compensation or knowledge at the receiver, and illustrate the trade-off introduced by phase noise between the OFDM symbol length and the overhead caused by the cyclic prefix. Throughout the paper, simulations confirm the accuracy of the analytical expressions.
Enumeration and identity of Campylobacter spp. in Italian broilers (2006)

Transmission of Campylobacter to humans has been prominently associated with mishandling or improperly preparing contaminated poultry carcasses. The number of organisms per carcass represents an important measure of human exposure to the agent. Therefore, we wished to estimate this public exposure over 1 yr among Italian broiler carcasses. We sampled 213 broiler carcasses from rinse water samples collected from a single slaughterhouse. Groups of carcasses had mean processed weights ranging from 1.2 to 2.7 kg. These were produced from 22 commercial broiler chicken flocks collected from 12 different farms, 3 of which were seasonally tested. Carcasses were rinsed with sterile water, and the rinse suspension was then serially diluted and spread-plated directly onto Campy-Cefex agar plates. One to 5 typical Campylobacter colonies per plate were identified by polymerase chain reaction as Campylobacter thermo-tolerant species. The overall estimated mean count per carcass in our study was 5.16 +/- 0.80 log10 cfu. This value increased in summer and autumn, as well as on carcasses collected from farms located > 100 km far from the slaughterhouse. A total of 678 Campylobacter colonies were identified by polymerase chain reaction. The majority of isolates were classified as Campylobacter jejuni (49.2%) or Campylobacter coli (47.5%). The overall number of C. jejuni was significantly higher on 1) carcasses weighing > 2 kg, 2) carcasses belonging to flocks with > 10,000 birds, and 3) carcasses collected from farms located > 100 km from the slaughterhouse. Moreover, among farms tested seasonally, C. jejuni was significantly greater than C. coli in winter. These data provide the first results of a continuing survey on Campylobacter loads and species identification from Italian broiler carcasses and represents an important baseline to estimate the human exposure to Campylobacter in Italy.
Analyse der Spontanmotorik im 1. Lebensjahr: Markerlose 3-D-Bewegungserfassung zur Früherkennung von Entwicklungsstörungen (2020)

Children with motor development disorders benefit greatly from early interventions. An early diagnosis in pediatric preventive care (U2-U5) can be improved by automated screening. Current approaches to automated motion analysis, however, are expensive, require lots of technical support, and cannot be used in broad clinical application. Here we present an inexpensive, marker-free video analysis tool (KineMAT) for infants, which digitizes 3‑D movements of the entire body over time allowing automated analysis in the future.Three-minute video sequences of spontaneously moving infants were recorded with a commercially available depth-imaging camera and aligned with a virtual infant body model (SMIL model). The virtual image generated allows any measurements to be carried out in 3‑D with high precision. We demonstrate seven infants with different diagnoses. A selection of possible movement parameters was quantified and aligned with diagnosis-specific movement characteristics.KineMAT and the SMIL model allow reliable, three-dimensional measurements of spontaneous activity in infants with a very low error rate. Based on machine-learning algorithms, KineMAT can be trained to automatically recognize pathological spontaneous motor skills. It is inexpensive and easy to use and can be developed into a screening tool for preventive care for children.
Large-scale screening identifies a novel microRNA, miR-15a-3p, which induces apoptosis in human cancer cell lines (2013)

MicroRNAs (miRNAs) have been found to be involved in cancer initiation, progression and metastasis and, as such, have been suggested as tools for cancer detection and therapy. In this work, a large-scale screening of the complete miRNA mimics library demonstrated that hsa-miR-15a-3p had a pro-apoptotic role in the following human cancer cells: HeLa, AsPc-1, MDA-MB-231, KB3, ME180, HCT-116 and A549. MiR-15a-3p is a novel member of the pro-apoptotic miRNA cluster, miR-15a/16, which was found to activate Caspase-3/7 and to cause viability loss in B/CMBA.Ov cells during preliminary screening. Subsequent microarrays and bioinformatics analyses identified the following four anti-apoptotic genes: bcl2l1, naip5, fgfr2 and mybl2 as possible targets for the mmu-miR-15a-3p in B/CMBA.Ov cells. Follow-up studies confirmed the pro-apoptotic role of hsa-miR-15a-3p in human cells by its ability to activate Caspase-3/7, to reduce cell viability and to inhibit the expression of bcl2l1 (bcl-xL) in HeLa and AsPc-1 cells. MiR-15-3p was also found to reduce viability in HEK293, MDA-MB-231, KB3, ME180, HCT-116 and A549 cell lines and, therefore, may be considered for apoptosis modulating therapies in cancers associated with high Bcl-xL expression (cervical, pancreatic, breast, lung and colorectal carcinomas). The capability of hsa-miR-15a-3p to induce apoptosis in these carcinomas may be dependent on the levels of Bcl-xL expression. The use of endogenous inhibitors of bcl-xL and other anti-apoptotic genes such as hsa-miR-15a-3p may provide improved options for apoptosis-modulating therapies in cancer treatment compared with the use of artificial antisense oligonucleotides.
A Compact High-Efficiency Boost Converter With Time-Based Control, RHP Zero-Elimination, and Tracking Error Compensation (2022)

Time-based signal processing has been recently demonstrated to be more area- and power-efficient compared with traditional analog based, making it an interesting approach for the design of compact high-efficiency dc–dc converters for portable applications. This work presents a novel boost converter, with a time-based control, a scheme for right-half plane (RHP) zero mitigation requiring no extra power switch nor external capacitor, and a pulse frequency modulation (PFM) operating mode with steady-state error correction and seamless PFM-to-continuous conduction mode (CCM) transition. The prototype implemented in a 0.18- <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\mu$</tex-math></inline-formula> m bipolar-CMOS-DMOS (BCD) process generates an output voltage of 5 V from an input voltage ranging between 2.5 and 4.5 V, and has an 800-mA load current capability. The controller area occupation is 0.27 mm <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$^{2}$</tex-math></inline-formula> and the quiescent current in CCM is 300 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\mu$</tex-math></inline-formula> A for the controller and 40 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\mu$</tex-math></inline-formula> A for the tracking error compensation. The peak efficiency is 96 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\%$</tex-math></inline-formula> at 4.5-V input and above 90 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\%$</tex-math></inline-formula> at light loads down to 50 mA current. Compared with a peak-current mode control, both the controller area and the current consumption of the proposed time-based architecture are lower by about 40%. The achieved closed-loop bandwidth of 130 kHz is six times larger than in a conventional boost converter with RHP zero.
Charge Invariant Protein–Water Relaxation in GB1 via Ultrafast Tryptophan Fluorescence (2014)

The protein-water interface is a critical determinant of protein structure and function, yet the precise nature of dynamics in this complex system remains elusive. Tryptophan fluorescence has become the probe of choice for such dynamics on the picosecond time scale (especially via fluorescence "upconversion"). In the absence of ultrafast ("quasi-static") quenching from nearby groups, the TDFSS (time-dependent fluorescence Stokes shift) for exposed Trp directly reports on dipolar relaxation near the interface (both water and polypeptide). The small protein GB1 contains a single Trp (W43) of this type, and its structure is refractory to pH above 3. Thus, it can be used to examine the dependence of dipolar relaxation upon charge reconfiguration with titration. Somewhat surprisingly, the dipolar dynamics in the 100 fs to 100 ps range were unchanged with pH, although nanosecond yield, rates, and access all changed. These results were rationalized with the help of molecular dynamics (including QM-MM) simulations that reveal a balancing, sometimes even countervailing influence of protein and water dipoles. Interestingly, these simulations also showed the dominant influence of water molecules which are associated with the protein interface for up to 30 ps yet free to rotate at approximately "bulk" water rates.
Simulation of Indentation Fracture in Crystalline Materials Using Mesoscale Self-Assembly (2002)

A new physical model based on mesoscale self-assembly is developed to simulate indentation fracture in crystalline materials. Millimeter-scale hexagonal objects exhibiting atom-like potential functions were designed and allowed to self-assemble into two-dimensional (2D) aggregates at the interface between water and perfluorodecalin. Indentation experiments were performed on these aggregates, and the stresses and strains involved in these processes were evaluated. The stress field in the aggregates was analyzed theoretically using the 2D elastic Hertz solution. Comparison of the experimental results with theoretical analysis revealed that fracture develops in regions subjected to high shear stress and some, albeit low, tensile stress. The potential for the broader application of the model is illustrated using indentation of assemblies with point defects and adatoms introduced at predetermined locations, and using a two-phase aggregate simulating a compliant film on a stiff substrate.
Standoff detection of ozone in an open environment using photoacoustic spectroscopy technique (2012)

The current work reports a practical photoacoustic spectroscopy (PAS) technique that can be applied for the standoff detection of ozone in an open environment. The developed PAS detection system consists of a laser, a parabolic acoustic reflector, and an acoustic resonator that acts as a lock-in amplifier to extract only the signals resonating with the laser chopping frequency. The design of the acoustic resonator is described, and a detection capability of 700 ppb ozone at 2 m distance in the ambient air is demonstrated. The system would have broad applications for open-air detection of chemicals in various forms.
PACAP Induces Light Aversion in Mice by an Inheritable Mechanism Independent of CGRP (2021)

The neuropeptides CGRP (calcitonin gene-related peptide) and PACAP (pituitary adenylate cyclase-activating polypeptide) have emerged as mediators of migraine, yet the potential overlap of their mechanisms remains unknown. Infusion of PACAP, like CGRP, can cause migraine in people, and both peptides share similar vasodilatory and nociceptive functions. In this study, we have used light aversion in mice as a surrogate for migraine-like photophobia to compare CGRP and PACAP and ask whether CGRP or PACAP actions were dependent on each other. Similar to CGRP, PACAP induced light aversion in outbred CD-1 mice. The light aversion was accompanied by increased resting in the dark, but not anxiety in a light-independent open field assay. Unexpectedly, about one-third of the CD-1 mice did not respond to PACAP, which was not seen with CGRP. The responder and nonresponder phenotypes were stable, inheritable, and not sex linked, although there was a trend for greater responses among male mice. RNA-sequencing analysis of trigeminal ganglia yielded hierarchical clustering of responder and nonresponder mice and revealed a number of candidate genes, including greater expression of the <i>Trpc5</i> and <i>Kcnk12</i> ion channels and glycoprotein hormones and receptors in a subset of male responder mice. Importantly, an anti-PACAP monoclonal antibody could block PACAP-induced light aversion but not CGRP-induced light aversion. Conversely, an anti-CGRP antibody could not block PACAP-induced light aversion. Thus, we propose that CGRP and PACAP act by independent convergent pathways that cause a migraine-like symptom in mice.<b>SIGNIFICANCE STATEMENT</b> The relationship between the neuropeptides CGRP (calcitonin gene-related peptide) and PACAP (pituitary adenylate cyclase-activating polypeptide) in migraine is relevant given that both peptides can induce migraine in people, yet to date only drugs that target CGRP are available. Using an outbred strain of mice, we were able to show that most, but not all, mice respond to PACAP in a preclinical photophobia assay. Our finding that CGRP and PACAP monoclonal antibodies do not cross-inhibit the other peptide indicates that CGRP and PACAP actions are independent and suggests that PACAP-targeted drugs may be effective in patients who do not respond to CGRP-based therapeutics.
Genetic Encoding of Arylazopyrazole Phenylalanine for Optical Control of Translation (2023)

An arylazopyrazole was explored for its use as an enhanced photoswitchable amino acid in genetic code expansion. This new unnatural amino acid was successfully incorporated into proteins in both bacterial and mammalian cells. While photocontrol of translation required pulsed irradiations, complete selectivity for the <i>trans</i>-configuration by the pyrrolysyl tRNA synthetase was observed, demonstrating expression of a gene of interest selectively controlled via light exposure.
Remodelin Is a Cryptic Assay Interference Chemotype That Does Not Inhibit NAT10-Dependent Cytidine Acetylation (2020)

Remodelin is a putative small molecule inhibitor of the RNA acetyltransferase NAT10 which has shown preclinical efficacy in models of the premature aging disease Hutchinson-Gilford Progeria Syndrome (HGPS). Here we evaluate remodelin's assay interference characteristics and effects on NAT10-catalyzed RNA cytidine acetylation. We find the remodelin chemotype constitutes a cryptic assay interference compound, which does not react with small molecule thiols but demonstrates protein reactivity in ALARM NMR and proteome-wide affinity profiling assays. Biophysical analyses find no direct evidence for interaction of remodelin with the NAT10 acetyltransferase active site. Cellular studies verify that N4-acetylcytidine (ac4C) is a nonredundant target of NAT10 activity in human cell lines and find that this RNA modification is not affected by remodelin treatment in several orthogonal assays. These studies display the potential for remodelin's chemotype to interact with multiple protein targets in cells and indicate remodelin should not be applied as a specific chemical inhibitor of NAT10-catalyzed RNA acetylation.
Task-Based Visual Interactive Modeling: Decision Trees and Rule-Based Classifiers (2021)

Visual analytics enables the coupling of machine learning models and humans in a tightly integrated workflow, addressing various analysis tasks. Each task poses distinct demands to analysts and decision-makers. In this survey, we focus on one canonical technique for rule-based classification, namely decision tree classifiers. We provide an overview of available visualizations for decision trees with a focus on how visualizations differ with respect to 16 tasks. Further, we investigate the types of visual designs employed, and the quality measures presented. We find that (i) interactive visual analytics systems for classifier development offer a variety of visual designs, (ii) utilization tasks are sparsely covered, (iii) beyond classifier development, node-link diagrams are omnipresent, (iv) even systems designed for machine learning experts rarely feature visual representations of quality measures other than accuracy. In conclusion, we see a potential for integrating algorithmic techniques, mathematical quality measures, and tailored interactive visualizations to enable human experts to utilize their knowledge more effectively.