gebhart/patrepeval huggingface dataset:
Ronald L. Phillips: pioneer, scholar, mentor, and gentleman. (2009)

Dr. Phillips’ early interest in agriculture was sparked by his parents’ work with a seed corn company in Indiana. He began his scientific career at Purdue University, completing a Bachelor of Science degree in 1961, and a Master of Science in 1963 under the supervision of Wayne F. Keim. He earned a Doctorate of Philosophy in 1966 from the University of Minnesota working on cytogenetics under the mentorship of Charles Burnham, one of the founding fathers of modern maize genetics and cytogenetics. He then studied Neurospora genetics in the laboratory of Adrian Srb at Cornell University as an NIH postdoctoral trainee. He returned to the University of Minnesota as a research associate in 1967, and joined the Faculty of the Department of Agronomy and Plant Genetics as an Assistant Professor in 1968. He was promoted to Associate Professor in 1972, Full Professor in 1976, was named Regents Professor in 1993 following his election to the National Academy of Science in 1991, and was chosen as the McKnight Presidential Chair in Genomics in 1999. He received many awards during his career including selection as a Fellow in the American Society of Agronomy, the Crop Science Society of America, and the American Association for the Advancement of Science. In addition, he was awarded the DeKalb Genetics Crop Science Society of America distinguished career award, an honorary Doctorate degree from Purdue University, the 2007 Wolf Prize in Agriculture, and the IAS Medal of Honour in Science from the University of Bologna in 2010. He served in various capacities for numerous national and international organizations, including service on the International Rice Research Institute Board of Trustees. Dr. Phillips is known for his scientific insight, honesty, integrity, and compassion. The respect that he has engendered is exemplified by the fact that many of the students, post-doctoral associates, and Maydica 54 (2009): 365-373
Context-modulated discrimination of similar vowels using second-order connectionist networks (1989)

Discrimination of medial adjacent vowels in the context of voiced and unvoiced stop consonants using connectionist networks is investigated. Separate discrimination networks were generated for one speaker from samples of the vowel centers of [e,æ] for the six contexts [b,d,g,p,t,k]. A single context-independent network was similarly generated. The context-specific error rate was 1%, whereas the context-independent error was 9%. A method for merging isomorphic networks into a single network is described. The method uses singular value decomposition to find a minimal basis for the set of context-specific weight vectors. Context-dependent linear combinations of the basis vectors may then be computed using second-order network units. Compact networks can thus be obtained in which the vowel discrimination surfaces are modulated by the phonetic context. In a preliminary experiment, as the number of basis vectors was reduced from 6 to 3, the error rate increased from 1% to 3%. Experiments with nonlinear optimization of context-modulated, second-order networks for this task are underway and will be reported.
Enhanced Oil Recovery in Carbonate Reservoirs Using Single Component Synthesized Surfactants under Harsh Reservoir Conditions (2023)

Surfactants are commonly used for enhanced oil recovery (EOR) applications in carbonate hydrocarbon reservoirs due to their ability to reduce oil/water interfacial tension (IFT) and/or alter rock wettability toward more water-wet conditions. They are usually used as formulations consisting of more than two surfactants to achieve optimum performance. Although this approach may result in extra recovery in coreflooding experiments, there is a risk of chromatographic separation and potential phase separation when these surfactants are injected into the reservoir. The current study, however, focuses on injecting a single component ethoxylated quaternary ammonium cationic Gemini surfactant (GS) or a betaine-type zwitterionic surfactant (ZIS), both synthesized in-house, to mitigate these potential issues. Several coreflooding experiments were conducted using Indiana limestone samples at 100 °C, pressures greater than 3000 psi, and seawater and formation water salinities of 57,745 ppm and 213,768, respectively. Continuous injection of either surfactant solution (at 2500 ppm in seawater) after seawater flooding recovered almost 11–12% of the initial oil in the core (OOIP). The results demonstrate that the GS or the ZIS alone can achieve this relatively high oil recovery without the need for additional cosolvent(s) or cosurfactant(s), unlike most of the previously developed surfactant formulations. Injecting a one-pore-volume slug of a standard acrylamide copolymer at 2000 ppm between the seawater and the surfactant floods increased the oil recovery by either surfactant to around 16–17% OOIP. This improvement in oil recovery was mainly due to wettability alteration from oil-wet to intermediate-wet conditions, as revealed by the contact angle and oil/water IFT measurements. Effluent analysis of the produced aqueous phase showed surfactant dynamic retention values of 0.44 and 0.61 mg/g-rock of both the GS and the ZIS, respectively. Such high oil recovery and low dynamic retention reflect the high efficiency of the GS and the ZIS for EOR applications in carbonate reservoirs.
Alterations in Bulk Modulus of Tracheae during Development (1980)

Tracheal dimensions, pressure-volume relationships, and bulk moduli, K, were determined in excised tracheae at different developmental ages: 21-, 27-1, and 31-day rabbit fetuses; 7-day pups; and adult rabbits 18 +/- 6 months of age. Alterations in tracheal dimensions paralleled the growth of the animal. At low segmental pressures such as 10 cm H2O, the tracheal segments became stiffer with age (K = 20.4 cm H2O for the 21-day fetus to K = 58.0 cm H2O for the adult). However, at segmental pressures greater than 15 cm H2O, the overdistended immature trachea became stiffer than even those of the adults. Developmental alterations in bulk modulus suggest significant changes in the material and mechanical properties of the wirways as a function of both pressure and developmental age.
Tailoring Regioisomeric Structures of π-Conjugated Polymers Containing Monofluorinated π-Bridges for Highly Efficient Polymer Solar Cells (2020)

Fluorine substitution has been vital to the molecular design of π-conjugated polymers toward highly efficient polymer solar cells because it results in improved intermolecular contacts. However, the understanding of how regioselectivity impacts relevant optoelectronic properties in nonsymmetric fluorinated systems remains poorly developed. In response, we herein incorporated a single fluorine atom onto the π-bridge of [1,2,3]triazolo[4,5-f]isoindole-5,7(2H,6H)-dione (TzBI)-polymers to construct two regioisomeric donors, denoted as PTzBI-dF and PTzBI-pF, and investigated how these subtle structural details impact the bulk properties of solar cells. We found that the fluorine substituent position has a profound effect on molecular conformations and thus the aggregated morphology, leading to notably different optical absorption and charge transport. The resulting polymer PTzBI-dF, with fluorine atom distal to the TzBI core, exhibited a power conversion efficiency of up to 17.3% that obviously outperforms the regioisomeric counterpart. These findings highlighted the strategic superiority of materials design toward high-performance solar cells.
Tomato Flavor and Aroma Quality as Affected by Storage Temperature (2000)

ABSTRACT: Studies were conducted to describe flavor and aroma in ripe tomatoes stored at 5, 10, 12.5 and 20 °C. Fruit stored for 2 d below 20 °C were rated by trained sensory panelists as significantly lower (P &lt; 0.05) in ripe aroma, tomato flavor, compared to those stored at 20 °C. Fruit stored at 5 °C for 4 d were rated significantly lower in ripe aroma, sweetness, tomato flavor, and significantly higher in sourness, compared to those stored at 20 °C. Following 8 and 12 d storage, fruit at 5 °C were rated lowest in ripe aroma and sweetness. Significant reductions in important GC aroma volatiles and chemical composition and electronic nose analyses concurred with sensory descriptor ratings.
Enhanced magnetoresistance due to charging effects in a molecular nanocomposite spin device (2009)

We have investigated a Coulomb-blockade effect and a higher order cotunneling effect in rubrene-Co nanocomposite spin devices, where the Co nanoparticles were uniformly embedded into the rubrene matrix and a large magnetoresistance (MR) effect appeared. A clear Coulomb gap was observed between $\ifmmode\pm\else\textpm\fi{}1.1\text{ }\text{V}$ at low temperature. Within the gap, the enhancement of the MR ratio was observed up to $\ensuremath{\sim}50%$, which has not been explained by previous theoretical studies. The enhancement is induced by higher-order cotunneling. Power-law dependence of an electric current for a bias voltage ($I\ensuremath{\sim}{V}^{2N\ensuremath{-}1}$; $N$ is an order of cotunneling) was observed in the Coulomb gap, which corroborates that at maximum fifth-order cotunneling is attributed to the enhancement of the MR ratio.
The Preparation of Poly(dihydroxyphenylene) through the Electro-Oxidative Polymerization of Hydroquinone (1990)

Abstract Hydroquinone is electro-oxidatively polymerized to poly(dihydroxyphenylene) on the Pt electrode, whose structure was confirmed by spectroscopic measurements. The polymerization proceeds via an oxidative and cationic mechanism. The poly(dihydroxyphenylene) thus formed is a Nernstian-type electro-active polymer (E°=0.7 V vs. Ag/AgCl in an acidic medium) and shows a redox reaction through two-electron transfer, accompanied by proton dissociation on the Pt electrode.
Reconsidering the Affordable Care Act’s Restrictions on Physician-Owned Hospitals (2017)

Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
Automatic Registration of Scanned Satellite Imagery with a Digital Map Data Base. (1980)

Analysis of digital remote sensing images can, and should employ all the information that is available about the area of interest. Maps often do exist, so that the question arises how map information can be automatically used to direct image analysis. With an appropriate organization of digital map data banks it becomes possible to merge image and map. Attention is concentrated on areal features. The algorithms and data structures used for the task are described and experiences using specific examples of Landsat images in Southern Germany and Austria to automatically recognize features for subsequent rectification are reported. (Author)
Benefits of Pd Doped Zeolites for Cold Start HC/NOx Emission Reductions for Gasoline and E85 Fueled Vehicles (2018)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;In the development of HC traps (HCT) for reducing vehicle cold start hydrocarbon (HC)/nitrogen oxide (NOx) emissions, zeolite-based adsorbent materials were studied as key components for the capture and release of the main gasoline-type HC/NOx species in the vehicle exhaust gas. Typical zeolite materials capture and release certain HC and NOx species at low temperatures (&amp;lt;200°C), which is lower than the light-off temperature of a typical three-way catalyst (TWC) (≥250°C). Therefore, a zeolite alone is not effective in enhancing cold start HC/NOx emission control. We have found that a small amount of Pd (&amp;lt;0.5 wt%) dispersed in the zeolite (i.e., BEA) can significantly increase the conversion efficiency of certain HC/NOx species by increasing their release temperature. Pd was also found to modify the adsorption process from pure physisorption to chemisorption and may have played a role in the transformation of the adsorbed HCs to higher molecular weight species. Both these processes led to desorption at higher temperatures and more efficient conversion. Laboratory studies on BEA zeolite, with and without Pd, are described. These studies show the benefits of Pd-zeolite on the capture and release of HC/NOx species such as ethanol, ethylene, propylene, and toluene. It was also observed that the benefit of Pd in the zeolite was not stable under high-temperature rich conditions. This indicates a possible limitation for the application of Pd-beta in stoichiometric engine exhaust. A base metal was also added to the Pd-zeolite that stabilized emissions trapping after high-temperature rich aging conditions. Parallel vehicle emission test results also confirmed the benefits of the base metal-stabilized Pd-BEA zeolite in reducing cold start HC emissions.&lt;/div&gt;&lt;/div&gt;
Granzyme B degradation by autophagy decreases tumor cell susceptibility to natural killer-mediated lysis under hypoxia (2013)

Recent studies demonstrated that autophagy is an important regulator of innate immune response. However, the mechanism by which autophagy regulates natural killer (NK) cell-mediated antitumor immune responses remains elusive. Here, we demonstrate that hypoxia impairs breast cancer cell susceptibility to NK-mediated lysis in vitro via the activation of autophagy. This impairment was not related to a defect in target cell recognition by NK cells but to the degradation of NK-derived granzyme B in autophagosomes of hypoxic cells. Inhibition of autophagy by targeting beclin1 (BECN1) restored granzyme B levels in hypoxic cells in vitro and induced tumor regression in vivo by facilitating NK-mediated tumor cell killing. Together, our data highlight autophagy as a mechanism underlying the resistance of hypoxic tumor cells to NK-mediated lysis. The work presented here provides a cutting-edge advance in our understanding of the mechanism by which hypoxia-induced autophagy impairs NK-mediated lysis in vitro and paves the way for the formulation of more effective NK cell-based antitumor therapies.
ChemInform Abstract: Formation of Porous Metal Oxides via Sol‐Gel Type Hydrolysis of Metal Alkoxide Complexes Modified with Organic Templates. (1993)

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.
Supplementary Figure S5 from AZD4573 Is a Highly Selective CDK9 Inhibitor That Suppresses MCL-1 and Induces Apoptosis in Hematologic Cancer Cells (2023)

&lt;p&gt;In vitro sensitivity to AZD4573 accurately predicts in vivo efficacy in hematological tumor xenograft models, and combinations with venetoclax are efficacious and tolerated.&lt;/p&gt;
In silico strategies on prion pathogenic conversion and inhibition from PrPC–PrPSc (2017)

To date, various therapeutic strategies identified numerous anti-prion compounds and antibodies that stabilize PrP<sup>C</sup>, block the conversion of PrP<sup>C</sup>-PrP<sup>Sc</sup> and increased effect on PrP<sup>Sc</sup> clearance. However, no suitable drug has been identified clinically so far due to the poor oral absorption, low blood-brain-barrier [BBB] penetration, and high toxicity. Although some of the drugs were proven to be effective in prion-infected cell culture and whole animal models, none of them increased the rate of survival compared to placebo. Areas covered: In this review, the authors highlight the importance of in silico approaches like molecular docking, virtual screening, pharmacophore analysis, molecular dynamics, QSAR, CoMFA and CoMSIA applied to detect molecular mechanisms of prion inhibition and conversion from PrP<sup>C</sup>-PrP<sup>Sc</sup>. Expert opinion: Several in silico approaches combined with experimental studies have provided many structural and functional clues on the stability and physiological activity of prion mutants. Further, various studies of in silico and in vivo approaches were also shown to identify several new small organic anti-scrapie compounds to decrease the accumulation of PrP<sup>res</sup> in cell culture, inhibit the aggregation of a PrP<sup>C</sup> peptide, and possess pharmacokinetic characteristics that confirm the drug-likeness of these compounds.
Aberrant anti-viral response of natural killer cells in severe asthma (2020)

Rhinovirus infections are the main cause of asthma exacerbations. As natural killer (NK) cells are important actors of the antiviral innate response, we aimed at evaluating the functions of NK cells from severe asthma patients in response to rhinovirus-like molecules or rhinoviruses.Peripheral blood mononuclear cells from patients with severe asthma and healthy donors were stimulated with pathogen-like molecules or with the rhinoviruses (RV)-A9 and RV-2. NK cell activation, degranulation and interferon (IFN)-γ expression were analysed.NK cells from severe asthma patients were less cytotoxic than those from healthy donors in response to toll-like receptor (TLR)3, TLR7/8 or RV-A9 but not in response to RV-2 stimulation. Furthermore, when cultured with interleukin (IL)-12+IL-15, cytokines which are produced during viral infections, NK cells from patients with severe asthma were less cytotoxic and expressed less IFN-γ than NK cells from healthy donors. NK cells from severe asthmatics exhibited an exhausted phenotype, with an increased expression of the checkpoint molecule Tim-3.Together, our findings indicate that the activation of NK cells from patients with severe asthma may be insufficient during some but not all respiratory infections. The exhausted phenotype may participate in NK cell impairment and aggravation of viral-induced asthma exacerbation in these patients.
Stimulation of T Cells by Lenalidomide Involves Putative Lenalidomide Binding Proteins CD3-Epsilon-Associated Protein and GDP-Mannose Pyrophosphorylase a (2008)

Abstract Introduction: Lenalidomide is approved in the US for the treatment of transfusion-dependent patients with anemia due to Low- or Intermediate-1-risk myelodysplastic syndromes associated with a del (5q) cytogenetic abnormality, with or without additional cytogenetic abnormalities. Lenalidomide is also approved for use in the US and Europe in combination with dexamethasone in previously treated multiple myeloma patients. In vitro and ex vivo studies have shown that lenalidomide has a direct antiproliferative effect against tumor cells and induces antiangiogenesis. It has also been shown to have immunomodulatory activity, including co-stimulatory effects on T and NK cells. Using the yeast 3-hybrid system, based on a leukemia cDNA library and biotinylated lenalidomide analog, we identified 16 putative lenalidomide-binding proteins from 700,000 clones screened. These included CD3-epsilon-associated protein (CAST) and GDP-mannose pyrophosphorylase A (GMPPA). CAST binds to the T cell receptor and is also part of the RNA polymerase 1 complex. GMPPA is a nucleotidyl transferase that converts mannose-1-phosphate and GTP to GDP-mannose, which is involved in the production of N-linked oligosaccharides. To determine whether these proteins are required for lenalidomide-induced immunomodulatory activity, we evaluated the lenalidomide-induced upregulation of interleukin-2 (IL-2) production in primary T cells transfected with siRNA against CAST and GMPPA. Methods: Primary human peripheral blood T cells were transfected with CAST or GMPPA siRNA, or mock siRNA as a control. Reduction of CAST and GMPPA expression was confirmed by qRT-PCR. After 24 hours, transfected cells were stimulated with anti-CD3 mAb in the presence or absence of 0.1 and 1 μM lenalidomide 48 hours. Cells were lysed after 48 hours, and IL-2 mRNA and mature protein levels were quantified using qPCR and ELISA, respectively. Results: CAST gene expression in T cells was reduced by 60% (p&amp;lt;0.05) in CAST siRNA-transfected cells. GMPPA gene expression was reduced by 66% (p&amp;lt;0.05) in GMPPA siRNA-transfected T cells. Lenalidomide-induced IL-2 mRNA production was reduced from 9-fold in controls to 6-fold in CAST siRNA transfectants (p&amp;lt;0.05) and from 15-fold in controls to 6-fold in GMPPA siRNA transfectants (p&amp;lt;0.05). Lenalidomide-induced IL-2 protein production was reduced from 22-fold in controls down to 8-fold in CAST siRNA transfectants (p&amp;lt;0.05) and from 5.6-fold in the controls down to 1.6-fold in GMPPA siRNA transfectants (p&amp;lt;0.05). Conclusion: These findings support the hypothesis that CAST and GMPPA play an important role in the lenalidomide IL-2 induction mechanism in primary T cells.
Evaluation of the New Photosensitizer Stakel (WST-11) for Photodynamic Choroidal Vessel Occlusion in Rabbit and Rat Eyes (2008)

Unlike verteporfin PDT, Stakel PDT does not cause direct damage to the RPE cell layer or retina. These observations indicate that Stakel PDT may have a high potential for beneficial therapeutic outcomes in treatment of AMD.
Pathogenesis of adenovirus type 5 pneumonia in cotton rats (Sigmodon hispidus) (1993)

Cotton rats (Sigmodon hispidus) were inoculated intranasally with 10(2.0) to 10(10.0) PFU of human adenovirus type 5. The virus replicated to a high titer in pulmonary tissues, with the peak titer being proportional to the input dose. The 50% lethal dose was 10(9.4) PFU. Histopathologic changes were proportional to the infecting inoculum and included the infiltration of interstitial and intra-alveolar areas, moderate damage to bronchiolar epithelium, and cellular infiltration of peribronchiolar and perivascular regions. These changes could be divided into two phases: an early phase (affecting alveoli, bronchiolar epithelium, and peribronchiolar regions) with an infiltrate consisting primarily of monocytes-macrophages and neutrophils, with occasional lymphocytes, and a later phase (affecting peribronchiolar and perivascular regions) with an infiltrate consisting almost exclusively of lymphocytes. In both phases, the predominant process was the response of the host to infection, rather than direct viral damage to infected cells. An infecting inoculum of 10(8.0) PFU or larger caused severe damage to type II alveolar cells, which were swollen, showed a loss of lamellar bodies, and were surrounded by polymorphonuclear leukocytes and macrophages. No evidence of complete viral replication was found in type II alveolar cells.
Deep learning nuclei detection: A simple approach can deliver state-of-the-art results (2018)

The basic PMap approach is greatly affected by certain parameters. Our evaluation provides guidance on their impact and best settings. When configured properly, this simple and efficient approach can yield equal detection quality as more complex and time-consuming state-of-the-art approaches.
Protection from diet-induced obesity and insulin resistance in mice lacking CCL19-CCR7 signaling (2015)

The CCL19-CCR7 pathway associates with the development of high-fat-induced obesity and insulin resistance.
Fast interior-point inference in high-dimensional sparse, penalized state-space models (2012)

We present an algorithm for fast posterior inference in penalized high-dimensional state-space models, suitable in the case where a few measurements are taken in each time step. We assume that the state prior and observation likelihoods are log-concave and have a special structure that allows fast matrix-vector operations. We derive a second-order algorithm for computing the maximum a posteriori state path estimate, where the cost per iteration scales linearly both in time and memory. This is done by computing an approximate Newton direction using an efficient forward-backward scheme based on a sequence of low rank updates. We formalize the conditions under which our algorithm is applicable and prove its stability and convergence. We show that the state vector can be drawn from a large class of prior distributions without affecting the linear complexity of our algorithm. This class includes both Gaussian and nonsmooth sparse and group sparse priors for which we employ an interior point modification of our algorithm. We discuss applications in text modeling and neuroscience.