gebhart/patrepeval huggingface dataset:
The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational State (2021)

The COVID-19 pandemic underwent a rapid transition with the emergence of a dominant viral variant (from the “D-form” to the “G-form”) that carried an amino acid substitution D614G in its “Spike” protein. The G-form is more infectious in vitro and associated with increased viral loads. To gain insight into the molecular-level underpinnings of these characteristics, we employed microsecond all-atom simulations. Here we show that changes in the protein energetics favor a higher population of infection-capable (open) states through release of hydrogen bonds of an asymmetry present in the D-form but not the G-form. Thus, the increased infectivity of the G-form is likely due to a higher rate of profitable binding encounters with the host receptor. It is also predicted to be more neutralization sensitive due to enhanced exposure of the receptor binding domain, a key target region for neutralizing antibodies. These results are significant for vaccine design. The Molecular Dynamics Simulations datasets generated in this study, namely that of the soluble form SARS-CoV-2 Spike protein are made available here. Details of the trajectory and supporting files are given in the README.txt file.
Rheological and molecular properties of chicken head gelatin as affected by combined temperature and time using warm water rendering (2021)

Physicochemical properties of gelatin extracted from chicken head at 60, 75, and 90 °C for 3 and 6 h, respectively were determined. Increased in extraction temperature (ETE) from 60 to 75 °C and extraction time (ETI) contributed to higher yield and bloom. ETE was highly correlated with yield (r = 0.954). Despite a higher yield, the gelatin bloom and viscoelastic properties began to drop at 90 °C. Gelatin extracted at 75 °C exhibited superior properties with high bloom strength of > 309 g, high in G’, G”, gelling (27–28 °C), and melting temperatures (33–34 °C) with great viscoelastic properties. All gelatins were of type A with α-chains as major protein. FTIR amide bands indicated different degrees of structural changed. Glycine was the main amino acid in G75/6 (20.69%) with total imino acid of 23.19%. Regression models were significant (p < .05), and highly fitted for yield and a* (R2 > 0.9090%). Present findings suggest the feasibility to extract high quality gelatin from chicken head by manipulating ETE and ETI.
Deep Learning and Its Application to Function Approximation for MR in Medicine: An Overview (2021)

This article presents an overview of deep learning (DL) and its applications to function approximation for MR in medicine. The aim of this article is to help readers develop various applications of DL. DL has made a large impact on the literature of many medical sciences, including MR. However, its technical details are not easily understandable for non-experts of machine learning (ML).The first part of this article presents an overview of DL and its related technologies, such as artificial intelligence (AI) and ML. AI is explained as a function that can receive many inputs and produce many outputs. ML is a process of fitting the function to training data. DL is a kind of ML, which uses a composite of many functions to approximate the function of interest. This composite function is called a deep neural network (DNN), and the functions composited into a DNN are called layers. This first part also covers the underlying technologies required for DL, such as loss functions, optimization, initialization, linear layers, non-linearities, normalization, recurrent neural networks, regularization, data augmentation, residual connections, autoencoders, generative adversarial networks, model and data sizes, and complex-valued neural networks.The second part of this article presents an overview of the applications of DL in MR and explains how functions represented as DNNs are applied to various applications, such as RF pulse, pulse sequence, reconstruction, motion correction, spectroscopy, parameter mapping, image synthesis, and segmentation.
SELECTIVE AND UPHILL TRANSPORT OF URANYL ION IN THE PRESENCE OF SOME BASE METALS AND THORIUM ACROSS BULK LIQUID MEMBRANE BY DI (2-ETHYLHEXYL) PHOSPHORIC ACID (2002)

Di (2-ethylhexyl) phosphoric acid has been successfully used as a selective carrier for the transport of uranyl ion across a bulk liquid membrane of chloroform. More than 98% uranium is selectively transported from a binary or a multi component mixture of cations in less than 3 hr. The pH of the feed solution was kept between 4.0 and 5.0 while 0.1 M hydrochloric acid served as a stripping agent in the receiving compartment. The co-transport of Zn2+ and Fe3+ was significantly small (<4%) but that of thorium was very high. However, the interference from Th(IV) and transition metal ions could be eliminated by the addition of EDTA (E. Merck (India) Ltd., Mumbai) to the feed solution. Different experimental parameters affecting the transport process were optimized and the membrane separation method was applied to the recovery and pre-concentration of uranium from synthetic seawater sample. It was concluded that approximately 98% of uranium could be recovered and a hundred fold pre-concentration of the metal could be accomplished in less than 3 hr.
Potential target sites for antiviral inhibitors of human immunodeficiency virus (HIV) (1989)

The rapid identification of anti-HIV compounds in the laboratory following the isolation of the causative virus in 1983 and their subsequent use in the clinic was not unexpected. Three decades of previous work had established a scientific basis for the evaluation of antiviral compounds. However, no antiviral yet discovered can cause total blockade of a virus replicating in a cell. The combination of properties of HIV including latency, antigenic and biochemical variation is unusual and the virus represents a daunting challenge for chemotherapy. But at least 90 antiviral compounds have been discovered, many inhibiting the virus reverse transcriptase. Other targets for inhibition are possible including viral regulatory gene products, viral protease and endonuclease enzymes but compounds for initial study will have to be found by random searching. X-ray crystallography of HIV proteins will shortly be possible, enabling the commencement of a more molecular specific search for inhibitors. Meanwhile, advantage can be taken of comparative nucleotide sequences of the HIV-1 and -2 genomes to test short oligonucleotides as potential inhibitors of mRNA transcription. The pol gene also has a zinc finger amino acid sequence suggesting that chelation chemotherapy may have a potential role. In the absence of HIV vaccines, and associated theoretical problems in their development, antiviral chemotherapy is expected to occupy a central role in combating the AIDS epidemic.
Spatial Distribution Patterns of Chlorophyll-a and Suspended Matter in the Yangtze Estuary and the Hangzhou Bay as Observed with the Hyperspectral Imager for the Coastal Ocean (HICO) (2013)

Data from the Hyperspectral Imager for the Coastal Ocean (HICO) were used to identify gradients and patchiness due to chl-a and suspended matter in the Yangtze Estuary and the Hangzhou Bay in China. HICO images were classified using the spectral analysis to identify frontal systems and areas of plankton patchiness in these water bodies. The results obtained from the analysis were compared with results obtained from previous studies conducted in these water bodies. The chl-a concentrations estimated from atmospherically corrected HICO images were comparable to chl-a concentrations measured in situ previously in this region. The spatial patterns of chl-a distribution derived from the HICO data matched well with the spatial patterns derived from a MODIS image acquired on the same day.
Wettability of Molten Carbonate Fuel Cell Materials (2016)

The wettability of molten carbonate fuel cell materials by molten carbonate mixtures under MCFC operating conditions was studied by means of the sessile drop method using an optical instrumental system. Observations were made of the melting and spreading of a solid carbonate pellet upon controlled temperature increase, under either a reducing atmosphere (80%H2/20%CO2 humidified at 45oC) or pure CO2. The mass of the carbonate pellet was found to have an effect on the development of the contact angle on dense and smooth Ni foil (purity 99.5%) under a reducing atmosphere. The contact angle showed a significant decrease (suggesting increased wettability) when the mass of the carbonate decreased below a certain weight. This appeared to be correlated with the generation of gas bubbles at the interface which decreased the effective contact of solid Ni surface with the liquid carbonate. It was observed that large bubbles were generated under reducing atmosphere, which disappeared quickly when the gas atmosphere was changed to the pure CO2 atmosphere. On the contrary, small bubbles were generated but disappeared quickly and spontaneously during the melting and wetting of the carbonate on a solid smooth Ni surface under pure CO2 atmosphere, while large bubbles reappeared at the interface of the solid Ni surface and liquid carbonate after switching to the reducing gas. We infer from this that the water gas shift equilibrium CO2+H2=CO+H2O (1) 
is established very rapidly at the scale of individual droplets or films of molten carbonate on nickel, and leads to gas bubble formation due to the very different levels of solubility of H2, CO, and CO2 in molten carbonate. To determine the effect of porosity of the anode on the wetting by molten carbonate, spreading and absorption of carbonate by potential Ni-Al alloy anode substrate with porosity of 25-35% was tested using carbonate pellets of various mass.
New electron optical column with large field for nanometer e-beam lithography system (1995)

An electron beam lithography system for nanometer devices has been developed. The target specifications of the system are a Gaussian beam diameter of 10 nm and a beam current of 1 nA, an acceleration voltage of 50 kV, a 500 micrometers X 500 micrometers deflection field and an overlay accuracy of 10 nm (3(sigma) ). To realize such high performance, the following two technologies have been developed for the design of the electron optical column: (1) a low aberration objective lens system with a one stage electrostatic deflector and (2) a thermal field emission (TFE) gun system with a low energy spread and a high brightness Zr/O/W cathode. The exposed results shown are a 30 nm isolated line and a 40 nm lines and spaces. An overlay accuracy of 10 nm are also obtained. This system is capable of being put into practical use in the fabrication of nanometer devices.
Thermal conductivity, electron transport, and magnetic properties of single-crystalCa3Co2O6 (2009)

A recent neutron-diffraction study on the magnetic insulator ${\text{Ca}}_{3}{\text{Co}}_{2}{\text{O}}_{6}$ shows that spins in the $c$-axis chains of alternating Co1 octahedral and Co2 trigonal-prismatic face-sharing ${\text{CoO}}_{6/2}$ sites are ordered below ${T}_{N}$ with a long-wavelength modulation instead of a simple ferromagnetic chain as thought previously. Frustrated antiferromagnetic interchain interactions compete with ferromagnetic intrachain coupling to invalidate an Ising model despite a strong spin-orbit coupling $\ensuremath{\lambda}\mathbf{L}\ensuremath{\cdot}\mathbf{S}$ on the Co2 ions. We have carried out thermal conductivity, electron transport, and magnetic measurements on single-crystal ${\text{Ca}}_{3}{\text{Co}}_{2}{\text{O}}_{6}$ in order to characterize this complicated magnetic system. An anisotropic thermal-conductivity component superimposed at high temperatures on an isotropic phonon component is consistent with an exchange-interaction-mediated heat transfer. This observation is incompatible with an Ising model. The ferromagnetic intrachain interactions are argued to reflect a one-dimensional itinerant-electron band that is split by the $c$-axis translational symmetry and the on-site intra-atomic Hund exchange interaction with a localized $S=3/2$ spin on the Co2 ions.
Write Protrusion Modulation for Sub-Nanometer Contact Interference (2005)

With the continual reduction in slider to disk clearance in hard disk drives, new methods to measure this clearance with high accuracy are needed. Understanding the contact dynamics when touching the disk at sub-nanometer interference levels is an important aspect of the problem. We have developed a new methodology to gradually bring the slider into contact with the disk, based on controlled and localized thermal expansion of the slider as it occurs during the regular write process (write induced protrusion). By applying short pulses to produce time controlled thermal protrusion, the duration of contact can be limited to a few milliseconds, by which short contacts and their contact hysteresis can be investigated.
CO oxidation over nobel metals supported on copper oxide: effect of Cu+/Cu2+ ratio (2020)

In this work, CuO supported with 0.5, 1 and 3 wt.% Au or Pd nanoparticles were synthesized. The activity of the synthesized catalysts was tested in the highly environmentally impacted carbon monoxide oxidation reaction. A variety of physicochemical characterization tools were applied to study the catalysts. The results confirmed the formation of a mixture of Cu+/Cu2+ species after Au or Pd nanoparticles deposition, with a higher ratio in the case of Pd rather than Au nanoparticles. The results also confirmed the enhancement of CuO reducibility and the formation of a higher ratio of surface lattice oxygen especially in Pd supported catalysts. The catalytic activity study showed a direct relation with Nobel metal and its size, Cu+/Cu2+ and surface lattice oxygen ratios, where 3PdCuO exhibited a total conversion of CO at 47 °C. The catalysts also showed high stability and durability for 24 h with 100% CO conversion under the reaction conditions.
Plasma vasopressin levels and urinary flow during cardiopulmonary bypass in patients with valvular heart disease: effect of pulsatile flow. (1979)

The effect of pulsatile flow on plasma vasopressin levels during cardiopulmonary bypass (CPB) was studied in 20 patients undergoing open valve replacement. Routine bypass was used in 10 patients and the AVCO pulsatile bypass pump was utilized in the other 10. In Group I (nonpulsatile) during CPB, the vasopressin level was markedly elevated (3.1 +/- 2 to 80 +/- 22 pg/ml) as was urine flow (0.6 +/- 0.2 to 5.9 +/- 2 ml/min) and urine Na+ concentration (69 +/- 19 to 116 +/- 7 mEq/L). In Group II (pulsatile) during CPB, the vasopressin level (3.8 +/- 3 to 54 +/- 14 pg/ml), urine flow (0.6 +/- 0.1 to 16.2 +/- 4.8 ml/min), and urine Na+ concentrations (61 +/- 13 to 97 +/- 10 mEq/L) were also elevated. The rise in vasopressin and urine Na+ was less in the pulsatile group (p less than 0.05) whereas the urine flow was higher (p less than 0.05). To maintain comparable blood pressure, the pulsatile flow group required significantly higher flows (4.5 +/- 0.2 compared to 3.8 +/- 0.2; p less than 0.05). These data suggest that CPB produces a marked vasopressin stress response which is beyond the physiological range for an antidiuretic effect on the kidney. At these levels vasopressin can exert a vasopressor effect to maintain resistance and affect renal blood flow, as well as producing an Na+ diuresis. The addition of pulsatile flow creates a more physiological situation attenuating the vasopressin response and producing a decrease in systemic resistance and a less pronounced Na+ diuresis.
Cellular Adenosine Triphosphate Production and Consumption in the Descending Thin Limb of Henle’s Loop in the Rat (1990)

To characterize the properties of cellular adenosine triphosphate (ATP) production and consumption in the descending thin limb of Henle's loop (DTL) in rats, we measured the cellular ATP content by applying the microchemiluminescence method. For ATP production, isolated DTL from the short- and long-loop nephron (SDL and LDL, respectively) was incubated with several substrates such as alanine, glucose, glutamine, beta-hydroxybutyrate (beta-HBA), lactate, and pyruvate; for ATP production from each substrate indicated that glucose and pyruvate were the preferred substrates to maintain cellular ATP in both SDL and LDL. ATP production from glutamine, beta-HBA, and lactate was substantial in LDL. In SDL, glutamine was the preferred substrate, and beta-HBA and lactate were minimal. The utilization of alanine was minimal in both LDL and SDL. The cellular ATP was significantly restored by ouabain at concentrations of 1.5 x 10(-5) and 1.5 x 10(-3) M in LDL, but in SDL only at 1.5 x 10(-3) M. In both segments, the cellular ATP level was significantly decreased by monensin above the concentrations of 1 micrograms/ml in LDL and 5 micrograms/ml in SDL. From these observations, we conclude that there exist clear differences between LDL and SDL in ATP-supplying substrate specificities and ATP-consuming properties.
Effective treatment with the selective cytokine inhibitor BNZ-1 reveals the cytokine dependency of T-LGL leukemia (2023)

T-cell large granular lymphocytic leukemia (T-LGLL) is a clonal proliferation of cytotoxic T lymphocytes that can result in severe neutropenia, anemia, and bone marrow failure. Strong evidence from patients and mouse models demonstrate the critical role of interleukin-15 (IL-15) in T-LGLL pathogenesis. BNZ-1 is a pegylated peptide that selectively inhibits the binding of IL-15 and other γc cytokines to their cellular receptor complex, which has demonstrated efficacy in ex vivo T-LGLL cells and transgenic mice in preclinical studies. We conducted a phase 1/2 trial of BNZ-1 in patients with T-LGLL who had hematocytopenias (anemia or neutropenia) and required therapy. Clinical responses were assessed using hematologic parameters (improvement in hematocytopenias) based on response criteria from the Eastern Cooperative Oncology Group 5998 T-LGLL trial. BNZ-1 demonstrated clinical partial responses in 20% of patients with T-LGLL with minimal toxicity and the maximum tolerated dose was not reached. Furthermore, T-LGL leukemic cells showed significantly increased apoptosis in response to BNZ-1 treatment as early as day 2, including in clinical nonresponders, with changes that remained statistically different from baseline throughout treatment (P < .005). We report first-in-human proof that T-LGL leukemic cells are dependent on IL-15 and that intervention with IL-15 inhibition with BNZ-1 in patients with T-LGLL shows therapeutic effects, which carries important implications for the understanding of the pathogenesis of this disease. This trial was registered at www.clinicaltrials.gov as #NCT03239392.
Data from Limited Environmental Serine and Glycine Confer Brain Metastasis Sensitivity to PHGDH Inhibition (2023)

&lt;div&gt;Abstract&lt;p&gt;A hallmark of metastasis is the adaptation of tumor cells to new environments. Metabolic constraints imposed by the serine and glycine–limited brain environment restrict metastatic tumor growth. How brain metastases overcome these growth-prohibitive conditions is poorly understood. Here, we demonstrate that 3-phosphoglycerate dehydrogenase (PHGDH), which catalyzes the rate-limiting step of glucose-derived serine synthesis, is a major determinant of brain metastasis in multiple human cancer types and preclinical models. Enhanced serine synthesis proved important for nucleotide production and cell proliferation in highly aggressive brain metastatic cells. &lt;i&gt;In vivo&lt;/i&gt;, genetic suppression and pharmacologic inhibition of PHGDH attenuated brain metastasis, but not extracranial tumor growth, and improved overall survival in mice. These results reveal that extracellular amino acid availability determines serine synthesis pathway dependence, and suggest that PHGDH inhibitors may be useful in the treatment of brain metastasis.&lt;/p&gt;Significance:&lt;p&gt;Using proteomics, metabolomics, and multiple brain metastasis models, we demonstrate that the nutrient-limited environment of the brain potentiates brain metastasis susceptibility to serine synthesis inhibition. These findings underscore the importance of studying cancer metabolism in physiologically relevant contexts, and provide a rationale for using PHGDH inhibitors to treat brain metastasis.&lt;/p&gt;&lt;p&gt;&lt;i&gt;This article is highlighted in the In This Issue feature, p. 1241&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Interleukin-6 Overcomes p21WAF1 Upregulation and G1 Growth Arrest Induced by Dexamethasone and Interferon-γ in Multiple Myeloma Cells (1997)

Interleukin-6 (IL-6) is a growth factor for multiple myeloma (MM) cells and can inhibit MM cell apoptosis. Our recent studies show that IL-6 facilitates MM cell growth via phosphorylation of retinoblastoma protein (pRB); however, the effects of IL-6 on those cyclins, cyclin-dependent kinases (CDKs), and CDK inhibitors (CDIs) that are known to regulate phosphorylation of pRB have not been defined in MM cells. In the present report, we cultured MM cell lines and patient cells with IL-6 and/or dexamethasone (Dex) and characterized changes in cell cycle; expression and association of cyclins, CDKs, and CDIs; and phosphorylation of pRB. Dex induced G1 growth arrest in MM cells, whereas IL-6 facilitated G1 to S phase transition; moreover, the effect of Dex was blocked by IL-6. p21WAF1 (p21) protein was constitutively expressed in the majority of MM cells independent of the status of p53. Its expression was upregulated by Dex and downregulated by IL-6; again, IL-6 inhibited the increase in p21 triggered by Dex. These alterations in p21 expression in MM cells were associated with changes in p21 binding to CDK2, CDK4, and CDK6; CDK2, CDK4, and CDK6 kinase activities; and phosphorylation of pRB. In contrast, expression of G1 cell cycle regulatory proteins, including p27KIP1, cyclin D2, and cyclin E, was not altered in MM cells cultured with Dex and/or IL-6. Finally, interferon-gamma (IFN-gamma) also induced G1 growth arrest and upregulated p21 protein expression; as with Dex, affects of IFN-gamma were inhibited by IL-6. Our results therefore show that changes in cell cycle distribution in MM cells triggered by Dex, IL-6, and IFN-gamma correlate with changes in p21 protein expression and implicate p21 in the coupling of Dex-, IL-6-, and IFN-gamma-related signals to G1 cell cycle regulation in MM cells.
Influence of NG‐nitro‐L‐arginine on non‐adrenergic non‐cholinergic relaxation in the guinea‐pig gastric fundus (1992)

1. The influence of NG-nitro-L-Arginine (L-NNA) on non-adrenergic non-cholinergic (NANC) relaxations induced by electrical field stimulation was investigated in circular muscle strips of the guinea-pig gastric fundus. 2. In the presence of 10(-6) M atropine and 4 x 10(-6) M guanethidine, electrical field stimulation (40 V, 1 ms, 0.125-16 Hz) with 10 s trains at 5 min intervals induced short-lasting, frequency-dependent relaxations. Continuous stimulation, with cumulative increase of the stimulation frequency, induced sustained frequency-dependent relaxations. Both types of response were abolished by 3 x 10(-6) M tetrodotoxin. 3. L-NNA (10(-5) M and 10(-4) M) concentration-dependently reduced both types of NANC response. Pre-incubation with 2 x 10(-3) M L-arginine prevented the inhibitory action of 10(-5) M L-NNA and partially antagonized that of 10(-4) M L-NNA. D-arginine (2 x 10(-3) M) did not protect against the inhibitory effect of L-NNA. 4. L-NNA did not consistently influence the basal tone of the tissues. L-Arginine and D-arginine likewise did not influence basal tone; they also had no influence on the electrically-induced NANC relaxations. 5. NO (10(-6)-10(-4) M) induced short-lasting concentration-dependent relaxations, while vasoactive intestinal polypeptide (VIP, (10(-9)-10(-7) M) induced more sustained relaxations, that developed at a slower rate. The NO- and VIP-induced relaxations were not influenced by 10(-4) M L-NNA.6. These results suggest that NO is involved in NANC neurotransmission of the guinea-pig gastric fundus; its contribution to sustained NANC relaxation in the guinea-pig gastric fundus is much more important than in the rat.