gebhart/patrepeval huggingface dataset:
Isolation and Characterization of Putative Ethylene Receptor Genes from Zonal Geranium (1997)

In this study, the temporal and spatial regulation of putative ethylene receptor genes was examined during ethylene and pollination-induced flower petal abscission of zonal geranium ( Pelargonium × hortorum L.H. Bailey). We used the Arabidopsis thaliana ETR1 gene as a heterologous probe to isolate two full-length cDNA clones, GER1 and GER2, from an ethylene-treated geranium pistil cDNA library. Both cDNAs share a high degree of DNA sequence similarity to ETR1, and examinations of deduced amino acid sequences indicate that the proteins encoded by each gene have the conserved ethylene binding and response regulator domains found in ETR1. Experiments focused on determining the temporal regulation of these genes revealed that both genes are expressed in geranium florets much earlier than when the florets become responsive to ethylene treatment, which is sufficient to cause petal abscission in 1 hr. Both genes are expressed in pistils throughout floret development. Experiments focused on determining the spatial regulation of these genes revealed that both genes are expressed at moderate levels in leaves, pistils, anthers, and petals, and are expressed at very low levels in roots. Preliminary evidence suggests that GER2 is transcriptionally regulated by ethylene in pistils after exogenous ethylene treatment. Currently, the transcriptional regulation of these genes in pistils after pollination is unknown.
Role of Basic Fibroblast Growth Factor in Cancer: Biological Activity, Targeted Therapies, and Prognostic Value (2023)

Cancer is the leading cause of death worldwide; thus, it is necessary to find successful strategies. Several growth factors, such as vascular endothelial growth factor (VEGF), basic fibroblast growth factor (bFGF, FGF2), and transforming growth factor beta (TGF-β), are involved in the main processes that fuel tumor growth, i.e., cell proliferation, angiogenesis, and metastasis, by activating important signaling pathways, including PLC-γ/PI3/Ca<sup>2+</sup> signaling, leading to PKC activation. Here, we focused on bFGF, which, when secreted by tumor cells, mediates several signal transductions and plays an influential role in tumor cells and in the development of chemoresistance. The biological mechanism of bFGF is shown by its interaction with its four receptor subtypes: fibroblast growth factor receptor (FGFR) 1, FGFR2, FGFR3, and FGFR4. The bFGF-FGFR interaction stimulates tumor cell proliferation and invasion, resulting in an upregulation of pro-inflammatory and anti-apoptotic tumor cell proteins. Considering the involvement of the bFGF/FGFR axis in oncogenesis, preclinical and clinical studies have been conducted to develop new therapeutic strategies, alone and/or in combination, aimed at intervening on the bFGF/FGFR axis. Therefore, this review aimed to comprehensively examine the biological mechanisms underlying bFGF in the tumor microenvironment, the different anticancer therapies currently available that target the FGFRs, and the prognostic value of bFGF.
New advances in MR-compatible bioartificial liver (2020)

MR-compatible bioartificial liver (BAL) studies have been performed for 30 years and are reviewed. There are two types of study: (i) metabolism and drug studies using multinuclear MRS; primarily short-term (< 8 h) studies; (ii) the use of multinuclear MRS and MRI to noninvasively define the features and functions of BAL systems for long-term liver tissue engineering. In the latter, these systems often undergo not only modification of the perfusion system, but also the construction of MR radiofrequency probes around the bioreactor. We present novel MR-compatible BALs and the use of multinuclear MRS (13C, 19F, 31P) for the noninvasive monitoring of their growth, metabolism and viability, as well as 1H MRI methods for the determination of flow profiles, diffusion, cell distribution, quality assurance and bioreactor integrity. Finally, a simple flexible coil design and circuit, and life support system, are described that can make almost any BAL MR-compatible.
The Effect of Flow Distribution on the Concentration of NO Produced by Pulsed Arc Discharge (2007)

As a new method to cure acute respiratory distress syndrome (ARDS), high blood pressure and some illnesses related to the lung, NO has recently received more attention. Thermal plasmas produced by arc discharge can create medical NO, but the concentration of NO2 produced by arc discharge must be controlled simultaneously. This paper investigates the characteristics and regulations of NO production at different flow distribution by pulsed arc discharge in dry air with a special pulsed power. The experimental results show that the flow distribution has a considerable effect on the NO concentration, the stabilization of NO. The production of NO2 could be controlled and the ratio of NO2/NO was decreased to about 10% in the arc discharge. Therefore, the arc discharge could produce stable inhaled NO for medical treatment by changing the flow distribution.
Is precoding for massive MIMO systems well-analyzed? (2014)

Literatures on precoding for massive MIMO, one disruptive technology for enabling 5G, have been mainly about metrics such as capacity and peak-to-average reduction. But for practical systems, block error rate (BLER) is one essential parameter that decides whether the system can work properly. In this work, we consider BLER of different precoding methods, and find that when applied to OFDM based massive MIMO, existing precoding methods would hardly work if applied to multiple resource blocks (RBs). Then, we propose a precoding method that intends to minimize the inter-user interference over the subcarriers. Through numerical results, we show that with this method, precoding can now be performed on multiple RBs. Overall, we have shown that precoding analysis for massive MIMO still needs further careful investigations.
Sexual Dimorphism and Aging Differentially Regulate Adaptive Homeostasis (2017)

External and internal stimuli cause modifications to gene and biochemical pathways. In turn, demonstrating that biological systems continuously make short-term adaptations both to set-points, and to the range of "normal" capacity, due to mild conditional changes, or to subtoxic, nondamaging levels of chemical agents. This is termed as "Adaptive Homeostasis," defined with the following: "The transient expansion or contraction of the homeostatic range in response to exposure to sub-toxic, nondamaging, signaling molecules or events, or the removal or cessation of such molecules or events." Research from several laboratories, including our own, found that adaptive homeostasis declines with age in organisms as diverse as worms, flies, and mammals, and decreases with senescence in mammalian cell cultures. We suggest that diminishing adaptive homeostasis may play a causal role as a factor responsible for the aging phenotype. Furthermore, although studies of humans, animals, and model organisms are often limited to a single sex, and cell culture studies may even be conducted with lines whose donor's sex was unknown, studies reveal distinct sexual dimorphism in adaptive homeostasis. Interestingly, although young males and females may exhibit dramatic differences in adaptive capacities and/or preferences, these distinctions are lost with age as adaptive homeostasis patterns converge.
Learning Cross-Modal Embeddings for Cooking Recipes and Food Images (2017)

In this paper, we introduce Recipe1M, a new large-scale, structured corpus of over 1m cooking recipes and 800k food images. As the largest publicly available collection of recipe data, Recipe1M affords the ability to train high-capacity models on aligned, multi-modal data. Using these data, we train a neural network to find a joint embedding of recipes and images that yields impressive results on an image-recipe retrieval task. Additionally, we demonstrate that regularization via the addition of a high-level classification objective both improves retrieval performance to rival that of humans and enables semantic vector arithmetic. We postulate that these embeddings will provide a basis for further exploration of the Recipe1M dataset and food and cooking in general. Code, data and models are publicly available.
A 240W dual-band 870 and 2140 MHz Envelope Tracking GaN PA designed by a probability distribution conscious approach (2011)

In this paper, we present the design of a dual-band power amplifier (PA) for envelope tracking (ET) operation. The design was based on a multi-section transmission line matching technique and has taken into account the actual probability distribution function of the WCDMA 3GPP DL signal. The technique was applied to a concurrent 870 and 2140 MHz ET PA designed around a GaN HEMT. The ET friendly design method has proven capable to meet the performance equal to those of each single band pulsed load pull with minor loss, over a bandwidth of 100 MHz, reporting an average drain efficiency of 69.5% and 51.0%, and peak power levels of 54.86 dBm and 53.96 dBm at the design frequencies. A detailed discussion of the design method and validating experimental results data are reported.
Polyethylene liner dissociation from humeral tray: impediment to closed reduction of dislocated reverse total shoulder replacement (2022)

Dissociation of polyethylene liner from the humeral tray can be associated with an RTSA dislocation and is a contraindication for CR. A radiographic finding of the metallic humeral tray articulating directly with the glenosphere is an indication that the polyethylene liner is dissociated from the humeral tray.
PHOSPHO1 puts the breaks on thermogenesis in brown adipocytes (2020)

The nonshivering heat production in mitochondria-rich brown or beige adipocytes allows rodents and humans to adapt to cold stress (1). The best-characterized thermogenic effector is uncoupling protein 1 (UCP1), which dissipates energy as heat by proton transport across the mitochondrial inner membrane. Of note, there are also important UCP1-independent pathways mediating brown adipose tissue (BAT) thermogenesis (2). The discovery of significant brown and beige adipose depots in humans initiated efforts to leverage the thermogenic process as a means to increase the metabolic rate to prevent metabolic disease, such as obesity and diabetes (3). Currently, there are limited browning regimens for increased energy expenditure in humans short of cold exposure (4). In PNAS, Jiang et al. (5) investigated how the enzyme phosphoethanolamine and phosphocholine phosphatase 1 (PHOSPHO1) regulates thermogenesis in BAT, triggering changes in systemic insulin sensitivity and energy balance. PHOSPHO1 catalyzes the hydrolysis of phosphocholine (PC) to choline as well as of phosphoethanolamine (PEA) to ethanolamine and in the process, releases an inorganic phosphate group.

PHOSPHO1 is not widely expressed, although it has been well characterized as the PC and PEA phosphatase in bone, where free inorganic phosphate is essential for bone mineralization (6). Additionally, PHOSPHO1 is a key regulator that coordinates the change in PC and phospholipid composition during terminal erythropoiesis (7). It is remarkable that bone and red blood cell progenitors rely on different aspects of PHOSPHO1 enzymatic activity. The authors discovered that PHOSPHO1 is highly enriched in murine BAT and accumulates during in vitro differentiation of primary brown adipocytes. PHOSPHO1 expression also increased during cold exposure in mice. Furthermore, they determined that metabolically active BAT from humans at the fetal stage has high levels of PHOSPHO1 vs. adult fat tissues.

There is little known about the role of PHOSPHO1 in adipose tissue. Based on the literature, the … 

[↵][1]1To whom correspondence may be addressed. Email: philipp.scherer{at}utsouthwestern.edu.

 [1]: #xref-corresp-1-1
SU‐C‐202‐07: Protocol and Hardware for Improved Flood Field Calibration of TrueBeam FFF Cine Imaging (2016)

Purpose: Flattening filter free photon energies are commonly used for high dose treatments such as SBRT, where localization accuracy is essential. Often, MV cine imaging may be employed to verify correct localization. TrueBeam Electronic Portal Imaging Devices (EPIDs) equipped with the 40×30cm 2 Image Detection Unit (IDU) are prone to image saturation at the image center especially for higher dose rates. While saturation often does not occur for cine imaging during treatment because the beam is attenuated by the patient, the flood field calibration is affected when the standard calibration procedure is followed. Here we describe the hardware and protocol to achieve improved image quality for this model of TrueBeam EPID. Methods: A stainless steel filter of uniform thickness was designed to have sufficient attenuation to avoid panel saturation for both 6XFFF and 10XFFF at the maximum dose rates (1400 MU/min &amp; 2400 MU/min, respectively). The cine imaging flood field calibration was then acquired with the filter in place for the FFF energies under the standard calibration geometry (SDD=150cm). Image quality during MV cine was assessed with &amp; without the modified flood field calibration using a low contrast resolution phantom and an anthropomorphic phantom. Results: When the flood field is acquired using the standard procedure (no filter in place), a pixel gain artifact is clearly present in the image center (r=3cm for 10XFFF at 2400 MU/min) which appears similar to and may be mis‐attributed to panel saturation in the subject image. The artifact obscured all low contrast inserts at the image center and was also visible on the anthropomorphic phantom. Using the filter for flood field calibration eliminated the artifact. Conclusion: Use of a modified flood field calibration procedure improves image quality for cine MV imaging with TrueBeams equipped with the 40×30cm 2 IDU.
The Effects of Asymmetry on Business Process Redesign (1996)

The effective design of business processes is a subject of considerable importance to corporations today. Our research focuses on developing a theoretical framework for process design in order to provide some guidelines for managers. The abundance of context specific case studies which exist today share many success stories but provide little in terms of a general methodological approach. In this paper, we describe a typical business process and critically evaluate typical pre and post reengineering process designs.
Extracellular manganese-stimulated deoxyribonuclease as a marker event in sporulation of Bacillus subtilis (1978)

A considerable amount of Mn2+-stimulated DNAase (deoxyribonuclease) activity is released by Bacillus subtilis 168 during sporulation in a glucose-deficient medium; much smaller amounts are released during starvation for phosphate or nitrogen. Protein synthesis is required. Two forms of evidence are presented that production of the DNAase is associated with events late in stage II of sporulation. 19 Thymidine starvation, which inhibits the biochemical events associated with sporulation, also inhibits release of the DNAase. 2. Several asporogenous mutants blocked at stage II or earlier and unable to produce alkaline phosphatase (a stage-II event) do not produce the enzyme. Mutants blocked towards the end of stage II or later produce both enzymes. During sporulation of the wild-type strain, the DNAase appears about 1 h after alkaline phosphatase. The results suggest that production of the DNAase is controlled by a still-undiscovered stage-II genetic locus.
Cytosolic delivery of large proteins using nanoparticle-stabilized nanocapsules (2016)

We report an effective intracellular delivery strategy for proteins of high molecular weight using AuNP stabilized capsules. This strategy provides direct delivery to the cytosol, avoiding endosomal entrapment.
Exercise capacity and cardiac function of rats with drug-induced cardiac enlargement (1982)

A study was undertaken to determine if sustained administration of isoproterenol (ISO) alters biochemical and functional properties of hearts and the submaximal and maximal exercise capacity of rodents. Compared with sham-treated controls of the same age, sex, and body weight, 4 wk of ISO (0.2--0.4 mg/kg sc) produced an approximate 30% increase in combined ventricle wet weight (P less than 0.001). Respiratory capacity of homogenates, total muscle protein concentration, and actomyosin and myofibril ATPase of heart muscle of the ISO-treated group were the same as in the control group. Various cardiac function parameters in situ, obtained under control conditions and in response to tyramine-induced norepinephrine release, were similar for the two groups. ISO-treated rats had slightly greater endurance for running submaximally on a treadmill than the control rats (P less than 0.10), but their maximal capacity to utilize oxygen (VO2max) was not different from controls. These findings suggest that rodent hearts moderately enlarged by relatively low doses of isoproterenol possess normal metabolic and functional capacity. However, this cardiac enlargement had no apparent effect on maximal exercise performance of the whole animal.
Origins of the “Nucleation” Free Energy in the Hybridization Thermodynamics of Short Duplex DNA (2009)

Thermodynamic parameters deltaH(cal), deltaS(cal), and deltaG(cal) of the melting transitions for 19 short DNA/DNA duplexes ranging in length from 6 to 35 base pairs were systematically evaluated by differential scanning calorimetry melting experiments carried out at four salt concentrations from 85 mM to 1.0 M [Na+]. As expected, thermodynamic stabilities of the DNA duplexes increased with length and increasing [Na+]. From plots of deltaG25 versus duplex length, extrapolation to N = 0 provided estimates on values of deltaG(cal)25 (N = 0) as a function of [Na+], corresponding to the free-energy of the "hypothetical duplex" having zero base pairs, but occupying precisely the same molar volume as the fully base paired duplex. The values obtained for deltaG(cal)25 (N = 0) were 3.68, 5.59, 7.86, and 8.68 kcal/mol in 1.00, 0.60, 0.30, and 0.085 M Na+, respectively. These values are in reasonable agreement with published values of the nucleation or initiation free-energy, attributed to formation of the first base pair in a short duplex compared to formation of the remaining base pairs. A statistical thermodynamic formulation of the association of two strands accounting for displaced solvent was utilized to relate [Na+]-dependent deltaG(cal)25 (N = 0) values to configuration integrals for both single and duplex strands. Relative differences between two single strands in their standard states and the duplex (in its standard state), and solvent displaced during the annealing process was taken into account. This analysis provides a new vantage point to view what has historically been referred to as the helix initiation or nucleation parameter and provides an alternate interpretation and mechanism for the nucleation complex in duplex formation.
Water-Soluble Chiral Cyclic Peptoids and Their Sodium and Gadolinium Complexes: Study of Conformational and Relaxometric Properties (2023)

Cyclic peptoids are macrocyclic oligomers of N-substituted glycines with specific folding abilities and excellent metal binding properties. In this work, we show how strategic positioning of chiral (S)- and (R)-(1-carboxyethyl)glycine units influences the conformational stability of water-soluble macrocyclic peptoids as sodium complexes. The reported results are based on nuclear magnetic resonance spectroscopy, extensive computational studies, and X-ray diffraction analysis using single crystals grown from aqueous solutions. The studies include 1H relaxometric investigations of hexameric cyclic peptoids in the presence of the Gd3+ ion to assess their thermodynamic stabilities and relaxivities.
Supercritical CO2 Extraction and Purification of Compounds with Antioxidant Activity (2006)

Supercritical fluid extraction (SCFE), based on the utilization of a fluid under supercritical conditions, is a technology suitable for extraction and purification of a variety of compounds, particularly those that have low volatility and/or are susceptible to thermal degradation. The interest in SCFE is promoted by legal limitations of conventional solvents for food and pharmaceutical uses. The physicochemical properties of supercritical CO2 (higher diffusivity, lower viscosity, and lower surface tension than conventional solvents) facilitate mass transfer and allow an environmentally friendly operation. This article presents a comprehensive compilation of data on the supercritical CO2 extraction of antioxidant compounds from vegetal materials, with particular attention to those of a phenolic nature. Aspects concerning the supercritical operation for extraction and fractionation of antioxidants compounds are considered, including equilibrium solubility of pure compounds and effects of the operational conditions on the antioxidant activity of isolated fractions. The data are compared to those reported for synthetic antioxidants and natural extracts obtained by conventional solvent extraction from vegetal matrices.
Morphology of poly(oxyethylene) methyl-n-alkyl ethers as determined by small-angle X-ray and Raman scattering (1987)

Poly(oxyethylene) methyl-n-alkyl ethers with oxyethylene block lengths of 13, 27, 40 or 53 oxyethylene units and n-alkyl end-block lengths in the range 12 to 21 methylene units have been studied in their solid state by low-frequency Raman scattering and small-angle X-ray diffraction. The low-frequency Raman transitions observed are assigned to longitudinal acoustical modes of unfolded chains in either monolayer or bilayer lamellae or of folded chains probably in bilayer lamellae, the morphology being dependent on the molecular structure and the crystallisation conditions.
Isoprenylated Flavonoids from Roots of Artocarpus styracifolius (2016)

Seven isoprenylated flavonoids were isolated from Artocarpus styracifolius, including one new triisoprenylated flavone, styracifolin D (1,) and six known ones, artocarpone B (2), kuwanon C (3), 6-C-prenyl luteolin (4), albanin A (5), 2,4,2',4'-tetrahydroxy-3'-(3-methyl-2-butenyl)-chalcone (6), and 3'-[γ-hydroxymethyl-(E)- γ-methylallyl]-2,4,2',4'-tetrahydroxychalcone 11'-0-coumarate (7). The structures of these compounds were determined by analysis of their spectroscopic and mass spectrometric data. Of them, 3 and 5 exhibited inhibitory effects on cathepsin K with IC(50) values of 114.6 and 7.4 μM, respectively.
Iron Differentially Stimulates Translation of Mitochondrial Aconitase and Ferritin mRNAs in Mammalian Cells (1998)

Utilization of mRNAs containing iron-responsive elements (IREs) is modulated by iron-regulated RNA-binding proteins (iron regulatory proteins). We examine herein whether iron differentially affects translation of ferritin and mitochondrial aconitase (m-Acon) mRNAs because they contain a similar but not identical IRE in their 5'-untranslated regions. First, we demonstrate that m-Acon synthesis is iron-regulated in mammalian cells. In HL-60 cells, hemin (an iron source) stimulated m-Acon synthesis 3-fold after 4 h compared with cells treated with an iron chelator (Desferal). Furthermore, hemin stimulated m-Acon synthesis 2-4-fold in several cell lines. Second, we show that iron modulates the polysomal association of m-Acon mRNA. We observed m-Acon mRNA in both ribonucleoprotein and polyribosomal fractions of HL-60 cells. Hemin significantly increased the polyribosomal association and decreased the ribonucleoprotein abundance of m-Acon mRNA in HL-60 cells. Third, our results indicate that iron differentially regulates translation of m-Acon and ferritin mRNAs. A dose response to hemin in HL-60 cells elicited a 2-2.4-fold increase in m-Acon synthesis within 5 h compared with untreated cells, whereas ferritin synthesis was stimulated 20-100-fold. We conclude that iron modulates m-Acon synthesis at the translational level and that iron regulatory proteins appear to differentially affect translation of IRE-containing mRNAs.