gebhart/patrepeval huggingface dataset:
Syntheses and structural studies of [2-(6-methyl)pyridyl]- and (8-quinolyl)trimethylsilylamido-lithium complexes (1988)

Reactions of 6-methyl-2-trimethylsilyaminopyridine (Hmtmsap) with LiBun in hexane–diethyl ether, [LiBun(tmen)](tmen =N,N,N′,N′-tetramethylethylenediamine), or LiBun in hexane, yield, respectively, [{Li(OEt2)(mtmsap)}2](1), [Li(tmen)(mtmsap)](2), and [{Li(mtmsap)}2](3). Mixtures (5:2) of Hmtmsap and 2-amino-6-methylpyridine (Hamp) yield the complex molecule [Li7(mtmsap)5(amp)2](4). Corresponding compounds, prepared via metallation of 8-trimethylsilyl-aminoquinoline (Htmsaq), are [{Li(OEt2)(tmsaq)}2](5), [Li(tmen)(tmsaq)](6), and [{Li(tmsaq)}2](7). Compounds (1), (2), and (4)–(7) are crystalline and have been characterized by X-ray structure determination. Compounds (1) and (5) are dimeric with four-co-ordinate lithium centres, the amido-N bridging; (7) is based on the structure of (5), but with a gap in the metal co-ordination spheres where the ether ligands reside in (5). Compounds (2) and (6) are monomeric with four-co-ordinate metal centres, and (4) has seven different metal environments, each either three- or four-co-ordinate and with both bridging amido-N and pyridine-N centres.
Characterization of Cryptosporidium meleagridis of Human Origin Passaged through Different Host Species (2003)

Cryptosporidium meleagridis, a protozoon first observed in turkeys, has been linked by several investigators to cryptosporidiosis in humans. C. meleagridis is the only known Cryptosporidium species that infects both avian and mammalian species. We describe the successful propagation of C. meleagridis (isolate TU1867), originally purified from a patient with diarrhea, in laboratory animals including chickens, mice, piglets, and calves. TU1867 was readily transmitted from one animal host to another, maintaining genetic homogeneity and stability. The rate of infectivity and virulence of TU1867 for the mammalian species were similar to those of Cryptosporidium parvum. Laboratory propagation of genetically and phenotypically stable and well-characterized reference isolates, representing various Cryptosporidium species, particularly those infectious to humans, will improve considerably the spectrum and quality of laboratory and field investigations on this medically important protozoa.
Abstract 904: Stimulation and expansion of oncogene-reactive tumor infiltrating T cells through combined Ad-HER2Δ16 vaccination and anti-PD1 enable anti-tumor responses against established HER2 BC (2020)

Abstract Despite promising advances, overcoming immune suppression and driving productive immune responses in the tumor microenvironment remains a significant challenge. Using a spontaneous breast cancer model, we found that vaccination targeting HER2d16, a highly expressed driver of oncogenicity and HER2-therapeutic resistance, elicited significant anti-tumor responses. In contrast, vaccines targeting a non-driver tumor-specific antigen (GFP) or unique non-driver tumor neoepitopes had no impact on tumor occurrence or progression. While vaccine-induced HER2-specific CD8+ T cells were essential for responses, tumors treated therapeutically with a vaccine alone ultimately progressed. However, long-term tumor control and complete tumor regression was only achieved when vaccine was combined with immune-checkpoint blockade (anti-PD1). Single cell RNAsequencing of tumor-infiltrating T cells (TILs) revealed that while vaccination expanded CD8 T cells within the tumor, only the combination of vaccine with anti-PD1 therapy induced a tumor rejection activation signature that was identified in the expanded T cell clones. We go on to use the single cell data to clone and reexpress the TCRs from expanded TILs from vaccinated mice and show that they are HER2-reactive. This data conclusively demonstrates the efficacy of this vaccination strategy in expanding tumor rejection T cells and supports its further evaluation in an ongoing Phase II trial (NCT03632941). The workflow used to identify and clone expanded, tumor specific T cells has broad potential applications across tumor types and treatment platforms. Citation Format: Erika J. Crosby, Chaitanya Acharya, Christopher Rabiola, William J. Muller, Lewis A. Chodosh, Gloria Broadwater, Jonathan Shepherd, Daniel Hollern, Xiaping He, Charles M. Perou, Benjamin K. Ashby, Benjamin G. Vincent, Michael A. Morse, Herbert K. Lyerly, Zachary C. Hartman. Stimulation and expansion of oncogene-reactive tumor infiltrating T cells through combined Ad-HER2Δ16 vaccination and anti-PD1 enable anti-tumor responses against established HER2 BC [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 904.
Weak Fragment Crystallizable (Fc) Domain Interactions Drive the Dynamic Assembly of IgG Oligomers upon Antigen Recognition (2019)

Activation of membrane receptors through clustering is a common mechanism found in various biological systems. Spatial proximity of receptors may be transduced across the membrane to initiate signaling pathways or alternatively be recognized by peripheral proteins or immune cells to trigger external effector functions. Here we show how specific immunoglobulin G (IgG) binding induces clustering of monomeric target molecules in lipid membranes through Fc-Fc interactions. We visualize and characterize the dynamic IgG oligomerization process and the molecular interactions involved using high-speed atomic force microscopy, single-molecule force spectroscopy, and quartz crystal microbalance experiments. We found that the Fc-Fc interaction strength is precisely tuned to be weak enough to prevent IgG oligomerization in solution at physiological titers, but enabling IgG oligomerization when Fabs additionally bind to their cognate surface epitopes, a mechanism that ultimately targets IgG-mediated effector functions such as classical complement activation to antigenic membranes.
Atrial Tachycardia Transition During Ablation of Persistent Atrial Fibrillation: What is the Mechanism? (2007)

Case Reports
Not Just Streaks: Towards Ground Truth for Single Image Deraining (2022)

We propose a large-scale dataset of real-world rainy and clean image pairs and a method to remove degradations, induced by rain streaks and rain accumulation, from the image. As there exists no real-world dataset for deraining, current state-of-the-art methods rely on synthetic data and thus are limited by the sim2real domain gap; moreover, rigorous evaluation remains a challenge due to the absence of a real paired dataset. We fill this gap by collecting a real paired deraining dataset through meticulous control of non-rain variations. Our dataset enables paired training and quantitative evaluation for diverse real-world rain phenomena (e.g. rain streaks and rain accumulation). To learn a representation robust to rain phenomena, we propose a deep neural network that reconstructs the underlying scene by minimizing a rain-robust loss between rainy and clean images. Extensive experiments demonstrate that our model outperforms the state-of-the-art deraining methods on real rainy images under various conditions. Project website: https://visual.ee.ucla.edu/gt_rain.htm/.
An international Delphi consensus statement on metabolic dysfunction-associated fatty liver disease and risk of chronic kidney disease (2023)

This Delphi-based consensus statement provided guidance on the epidemiology, mechanisms, management and treatment of MAFLD and CKD, as well as the relationship between the severity of MAFLD and risk of CKD, which establish a framework for the early prevention and management of these two common and interconnected diseases.
Pectin Methylesterase and Pectin Remodelling Differ in the Fibre Walls of Two Gossypium Species with Very Different Fibre Properties (2013)

Pectin, a major component of the primary cell walls of dicot plants, is synthesized in Golgi, secreted into the wall as methylesters and subsequently de-esterified by pectin methylesterase (PME). Pectin remodelling by PMEs is known to be important in regulating cell expansion in plants, but has been poorly studied in cotton. In this study, genome-wide analysis showed that PMEs are a large multi-gene family (81 genes) in diploid cotton (Gossypium raimondii), an expansion over the 66 in Arabidopsis and suggests the evolution of new functions in cotton. Relatively few PME genes are expressed highly in fibres based on EST abundance and the five most abundant in fibres were cloned and sequenced from two cotton species. Their significant sequence differences and their stage-specific expression in fibres within a species suggest sub-specialisation during fibre development. We determined the transcript abundance of the five fibre PMEs, total PME enzyme activity, pectin content and extent of de-methylesterification of the pectin in fibre walls of the two cotton species over the first 25-30 days of fibre growth. There was a higher transcript abundance of fibre-PMEs and a higher total PME enzyme activity in G. barbadense (Gb) than in G. hirsutum (Gh) fibres, particularly during late fibre elongation. Total pectin was high, but de-esterified pectin was low during fibre elongation (5-12 dpa) in both Gh and Gb. De-esterified pectin levels rose thereafter when total PME activity increased and this occurred earlier in Gb fibres resulting in a lower degree of esterification in Gb fibres between 17 and 22 dpa. Gb fibres are finer and longer than those of Gh, so differences in pectin remodelling during the transition to wall thickening may be an important factor in influencing final fibre diameter and length, two key quality attributes of cotton fibres.
Single-Chain Folding of Polymers for Catalytic Systems in Water (2011)

Enzymes are a source of inspiration for chemists attempting to create versatile synthetic catalysts. In order to arrive at a polymeric chain carrying catalytic units separated spatially, it is a prerequisite to fold these polymers in water into well-defined compartmentalized architectures thus creating a catalytic core. Herein, we report the synthesis, physical properties, and catalytic activity of a water-soluble segmented terpolymer in which a helical structure in the apolar core is created around a ruthenium-based catalyst. The supramolecular chirality of this catalytic system is the result of the self-assembly of benzene-1,3,5-tricarboxamide side chains, while the catalyst arises from the sequential ruthenium-catalyzed living radical polymerization of the different monomers followed by ligand exchange. The polymers exhibit a two-state folding process and show transfer hydrogenation in water.
Investigation of separation of A1050 aluminum and SS400 steel joined body by foaming (2022)

Porous aluminum is fabricated by heating and foaming a precursor, which is fabricated by adding a foaming agent and a thickening agent to solid aluminum. In recent years, joining technologies have been developed owing to multi-materialization, but from the viewpoint of recycling, it is necessary to separate the joined materials when they are to be disposed. It is well known that the strength of porous material decreases compared with that of the base material. Taking advantage of this fact, we attempted to reduce the strength of the joining area by adding a foaming agent to the joining area when joining dissimilar metals, and then heating and foaming the joining area at the time of disposal for the purpose of easy separation. As a result, it was found that the fracture load and absorbed energy required to fracture the specimen can be reduced just by heat treatment, but they can be further reduced by heating and foaming the joining area compared with those in the case of a nonporous specimen.
Fifteen compelling open questions in plant cell biology (2021)

As scientists, we are at least as excited about the open questions-the things we do not know-as the discoveries. Here, we asked 15 experts to describe the most compelling open questions in plant cell biology. These are their questions: How are organelle identity, domains, and boundaries maintained under the continuous flux of vesicle trafficking and membrane remodeling? Is the plant cortical microtubule cytoskeleton a mechanosensory apparatus? How are the cellular pathways of cell wall synthesis, assembly, modification, and integrity sensing linked in plants? Why do plasmodesmata open and close? Is there retrograde signaling from vacuoles to the nucleus? How do root cells accommodate fungal endosymbionts? What is the role of cell edges in plant morphogenesis? How is the cell division site determined? What are the emergent effects of polyploidy on the biology of the cell, and how are any such "rules" conditioned by cell type? Can mechanical forces trigger new cell fates in plants? How does a single differentiated somatic cell reprogram and gain pluripotency? How does polarity develop de-novo in isolated plant cells? What is the spectrum of cellular functions for membraneless organelles and intrinsically disordered proteins? How do plants deal with internal noise? How does order emerge in cells and propagate to organs and organisms from complex dynamical processes? We hope you find the discussions of these questions thought provoking and inspiring.
Thermodynamic Analysis of Isomerization Equilibria of Chlorotoluenes and Dichlorobenzenes in a Biphasic Reaction Systems Containing Highly Acidic Chloroaluminate Melts (2016)

Thermodynamics and kinetics of the isomerization of chlorotoluenes and dichlorobenzene to the technically desired meta-isomers have been studied in the presence of highly acidic chloroaluminate melts with alkali metal and organic imidazolium cations. Enthalpies of four isomerization processes in reacting systems of chlorotoluenes and dichlorobenzene were obtained from temperature dependencies of the corresponding equilibrium constants in the liquid phase. Experimental reaction enthalpies, enthalpies of vaporization, and absolute vapor pressures of chlorotoluenes and dichlorobenzene have been used for the validation of quantum-chemical methods to predict thermodynamic functions of the four reactions under study successfully. Values of the standard Gibbs energies of formation, standard enthalpies and entropies of formation of chlorotoluenes and dichlorobenzenes in the liquid and in the gas phase have been derived. These values allow optimization of liquid-liquid biphasic manufacturing technologies for halogen-substituted benzenes.
Using best-worst scaling choice experiments to elicit the most important domains of health for health-related quality of life in Singapore (2018)

Health-related quality of life (HRQOL) instruments are sometimes used without explicit understanding of which HRQOL domains are important to a given population. In this study, we sought to elicit an importance hierarchy among 27 HRQOL domains (derived from the general population) via a best-worst scaling survey of the population in Singapore, and to determine whether these domains were consistently valued across gender, age, ethnicity, and presence of chronic illnesses. We conducted a community-based study that sampled participants with quotas for gender, ethnicity, age, presence of chronic illness, and interview language. For the best-worst scaling exercise, we constructed comparison sets according to a balanced incomplete block design resulting in 13 sets of questions, each with nine choice tasks. Each task involved three HRQOL domains from which participants identified the most and least important domain. We performed a standard analysis of best-worst object scaling design (Case 1) using simple summary statistics; 603 residents participated in the survey. The three most important domains of health were: "the ability to take care of self without help from others" (best-worst score (BWS): 636), "healing and resistance to illness" (BWS: 461), and "having good relationships with family, friends, and others" (BWS: 373). The 10 top-ranked domains included physical, mental, and social health. The three least important domains were: "having a satisfying sex life" (BWS: -803), "having normal physical appearance" (BWS: -461), and "interacting with others (talking, shared activities, etc.)" (BWS: -444). Generally, top-ranked domains were consistently valued across gender, age, ethnicity, and presence of chronic illness. We conclude that the 10 top-ranked domains reflect physical, mental, and social dimensions of well-being suggesting that the sampled population's views on health are consistent with the World Health Organization's definition of health, "a state of complete physical, mental and social well-being and not merely the absence of disease or infirmity".
Aspects of Osmotic Regulation in Crabs Showing the Terrestrial Habit (1955)

1. Terrestrial and semi-terrestrial crabs generally demonstrate the ability to regulate osmotically in dilute and concentrated sea water. 2. Osmotic regulation in terrestrial and semi-terrestrial crabs is not adaptive for aquatic life since osmotic stresses such as dilute and concentrated sea water are rarely experienced by these animals. Besides many such animals drown when completely immersed. 3. The branchial chamber of Pachygrapsus contains a volume of fluid equal to a maximum of about 3 per cent of the body volume. Thus, regulation against branchial fluid made concentrated by evaporation would not be adaptive as proposed by Jones because the total salt therein could not elevate the blood concentration above concentrations normally experienced in nature. 4. The respiratory rate of Pachygrapsus decreases when the crab is desiccated. This explains why the terrestrial behavior of Pachygrapsus is limited to brief periods. 5. Pachygrapsus can absorb water against a gradient when it has been desiccated. 6. The ability to regulate in concentrated sea water (hypo-osmotic regulation) is believed to be a manifestation of a mechanism for the conservation of water, namely, elimination of salts. 7. The mechanism involved in hyper-osmotic regulation seems to be necessary to the mechanism of hypo-osmotic regulation but apparently has no adaptive consequence such as salt elimination. 8. The coconut crab, Birgus latro, shows special adaptations to terrestrial life. a. It can drink water from small puddles. b. It can keep its respiratory membranes moist by placing water into the gill chamber without becoming immersed. c. It can control the concentration of its body fluids by selecting water of the appropriate salinity.
Shoe-Surface Friction Influences Movement Strategies during a Sidestep Cutting Task (2010)

The risk analysis of ACL injury should consider the biomechanical movement changes that occur for a shoe-surface condition with high friction.
Front-electrode design for efficient near-field thermophotovoltaics (2019)

In near-field TPV cells, the effects of the necessary front electrode are considered and shown to be of great importance. The electrode tradeoff between required high dc conductivity but low photonic absorption becomes detrimental for the efficiency in the very near field, as the thermal-emitter evanescent waves decay fast and are absorbed inside the electrode without penetrating sufficiently into the semiconductor. Therefore, near-field cells fail to deliver ultra-high power efficiently, as hoped. Still, efficient mid-power conversion is possible, and we compare the performance of several tunable-by-doping conducting-electrode materials. Moreover, novel phenomena arise in the near field, such as the inability to use thick transparent electrodes, while instead the feasibility of ultra-thin ‘opaque’ ones. The metallic-grid fingers exhibit an ‘anomalous’ shading loss, significantly smaller than predicted by geometry, by suppressing the thermal emission in the emitter regions across them.
Fast Inactivation of Voltage-dependent Calcium Channels (2000)

We recently described domains II and III as important determinants of fast, voltage-dependent inactivation of R-type calcium channels (Spaetgens, R. L., and Zamponi, G. W. (1999) J. Biol. Chem. 274, 22428-22438). Here we examine in greater detail the structural determinants of inactivation using a series of chimeras comprising various regions of wild type alpha(1C) and alpha(1E) calcium channels. Substitution of the II S6 and/or III S6 segments of alpha(1E) into the alpha(1C) backbone resulted in rapid inactivation rates that closely approximated those of wild type alpha(1E) channels. However, neither individual or combined substitution of the II S6 and III S6 segments could account for the 60 mV more negative half-inactivation potential seen with wild type alpha(1E) channels, indicating that the S6 regions contribute only partially to the voltage dependence of inactivation. Interestingly, the converse replacement of alpha(1E) S6 segments of domains II, III, or II+III with those of alpha(1C) was insufficient to significantly slow inactivation rates. Only when the I-II linker region and the domain II and III S6 regions of alpha(1E) were concomitantly replaced with alpha(1C) sequence could inactivation be abolished. Conversely, introduction of the alpha(1E) domain I-II linker sequence into alpha(1C) conferred alpha(1E)-like inactivation rates, indicating that the domain I-II linker is a key contributor to calcium channel inactivation. Overall, our data are consistent with a mechanism in which inactivation of voltage-dependent calcium channels may occur via docking of the I-II linker region to a site comprising, at least in part, the domain II and III S6 segments.
Surgical Management of Brainstem Gliomas (2005)

Dr. Teo is Director, Center for Minimally Invasive Neurosurgery, Sydney, Australia; Dr. Siu is Registrar; Department of Neurosurgery, Prince of Wales Hospital, Randwick, Australia; and Dr. Nakaji is Staff Neurosurgeon and Director of the Neurosurgical Intensive Care Unit, Division of Neurological Surgery, Barrow Neurological Institute, 350 W. Thomas Road; Phoenix, AZ 85013; E-mail: [email protected]. The authors have disclosed that they have no significant relationships with or financial interests in any commercial organizations pertaining to this educational activity. Wolters Kluwer Health has identified and resolved all faculty conflicts of interest regarding this educational activity. Category: Tumor
Light Duty Truck Aftertreatment - Experience and Challenges (2000)

Detroit Diesel's test experience on light duty truck PM aftertreatment technology development will be presented. The Tier-II extremely low emissions standards combined with the light-duty test cycle impose a significant challenge for the development of production-viable emissions technologies. A robust general path to achieve these emissions targets will be outlined.
Acceleration of a Phosphate Diester Transesterification Reaction by Bis(alkylguanidinium) Receptors Containing an Appended General Base (1995)

Rate enhancements up to 290-fold are possible for the transesterification of 2-hydroxypropyl-p-nitrophenylphosphate when bis(guanidinium) catalysts bearing basic groups are added. The combination of the appended base and the electrostatic complementarity of substrate and receptor (see complex 1) make the guanidinium compounds efficient enzyme mimics. These types of compounds may have therapeutic applications as artificial nucleases.