gebhart/patrepeval huggingface dataset:
Chance‐constrained operation of the water‐energy nexus with conflicting objectives (2021)

Abstract This paper focuses on the short‐term operation of the water‐energy nexus, where the energy sectors include electricity, natural gas, and heating power. The uncertainties of the renewable generation outputs and the heterogeneous load demands are considered, and their impacts on the operation of the water‐energy nexus are characterised through chance‐constrained modelling. Meanwhile, to achieve a reasonable trade‐off among different conflicting operation goals, such as the out‐of‐the‐pocket energy production costs and the water consumption amount, a bi‐objective decision‐making framework is established. The intractable chance constraints are converted into tractable ones under practical assumptions on the distributions of the uncertainties, where the Gaussian Mixture Model is used to fit the probability density distribution of wind power generation. The nonlinearities and nonconvexities in the proposed model are replaced by their convex approximations. An iterative penalty method is devised to recover the solution feasibility with respect to the original model. A fair compromise between the two conflicting objectives is obtained by the means of Nash bargaining. Simulation results verify the necessity and effectiveness of the proposed model and methods.
Supplementary Fig. S1 from Quantitative live imaging of cancer and normal cells treated with Kinesin-5 inhibitors indicates significant differences in phenotypic responses and cell fate (2023)

Supplementary Fig. S1 from Quantitative live imaging of cancer and normal cells treated with Kinesin-5 inhibitors indicates significant differences in phenotypic responses and cell fate
Reconstitution of a telomeric replicon organized by CST (2021)

Abstract Telomeres, the natural ends of linear chromosomes, are comprised of repeat-sequence DNA and associated proteins1. Replication of telomeres allows continued proliferation of human stem cells and immortality of cancer cells2. Replication begins with telomerase3 extending the single-stranded DNA (ssDNA) of the telomeric G-strand [(TTAGGG)n]; the synthesis of the complementary C-strand [(CCCTAA)n] is much less well characterized. The CST (CTC1-STN1-TEN1) protein complex, a DNA Polymerase α-primase accessory factor4,5, is known to be required for telomere replication in vivo6,7,8,9, and the molecular analysis presented here reveals key features of its mechanism. We find that CST uses its ssDNA-binding activity to specify the origins for telomeric C-strand synthesis by bound Polα-primase. CST-organized DNA polymerization can copy a telomeric DNA template that folds into G-quadruplex structures, but the suboptimality of this template likely contributes to telomere replication problems observed in vivo. Combining telomerase, a short telomeric ssDNA primer, and CST-Polα-primase gives complete telomeric DNA replication, resulting in the same sort of ssDNA 3’-overhang found naturally on human telomeres. We conclude that the CST complex not only terminates telomerase extension10,11 and recruits Polα-primase to telomeric ssDNA4,12,13, but it also orchestrates C-strand synthesis. Because replication of the telomere has features distinct from replication of the rest of the genome, targeting telomere-replication components including CST holds promise for cancer therapeutics.
BASIC PROPERTIES AND HYDRATION MECHANISMS OF THE MORTARS USING CALCIUM ALUMINATES AS A FINE AGGREGATE (2016)

本研究では、カルシウムアルミネートを細骨材として利用した場合のモルタル物性に及ぼす影響について調査した。その結果、圧縮・曲げ強さは珪砂、川砂、石灰砂と同程度であった。一方、モルタルのフロー値は他の細骨材と比較して小さくなる傾向が確認された。その原因として骨材の実績率による影響に加えて、骨材表面にてカルシウムアルミネート系水和物が生成したことに起因すると推測した。また、水中養生下では膨張性を示した。一方で乾燥収縮は他の骨材と比べて大きくなり、物性をコントロールする上では、初期養生条件に配慮する必要があることも明らかとなった。
Fusion of the antiferritin antibody VL domain to barnase results in enhanced solubility and altered pH stability (2004)

Chimeric immunotoxins that combine antigen recognition domains of antibodies and cytotoxic RNases have attracted much attention in recent years as potential targeted agents for cancer immunotherapy. In an attempt to obtain a structurally minimized immunofusion for folding/stability studies, we constructed the chimeric protein VL-barnase. The chimera comprises a small cytotoxic enzyme barnase, ribonuclease from Bacillus amyloliquefaciens, fused to the C-terminus of the light chain variable domain (VL) of the anti-human ferritin monoclonal antibody F11. While the individual VL domain was expressed in Escherichia coli as insoluble protein packed into inclusion bodies, its fusion to barnase resulted in a significant ( approximately 70%) fraction of soluble protein, with only a minor insoluble fraction ( approximately 30%) packed into inclusion bodies. The in vivo solubilizing effect of barnase was also observed in vitro and suggests a chaperone-like role that barnase exerted with regard to the N-terminal VL domain. Cytoplasmic VL-barnase was analyzed for structural and functional properties. The dimeric state of the chimeric protein was demonstrated by size-exclusion chromatography, thus indicating that fusion to barnase did not abrogate the intrinsic dimerization propensity of the VL domain. Ferritin-binding affinity and specificity in terms of constants of association with isoferritins were identical for the isolated VL domain and its barnase fusion, and RNase activity remained unchanged after the fusion. Intrinsic fluorescence spectra showed a fully compact tertiary structure of the fusion protein. However, significantly altered pH stability of the fusion protein versus individual VL and barnase was shown by the pH-induced changes in both intrinsic fluorescence and binding of ANS. Together, the results indicate that VL-barnase retained the antigen-binding affinity, specificity and RNase activity pertinent to the two individual constituents, and that their fusion into a single-chain chimeric protein resulted in an altered tertiary fold and pH stability.
WE‐EF‐204‐02: Murine Model Systems for Co‐Clinical Trials (2015)

As molecular biology breakthroughs in understanding cancers and other diseases, hundreds of new drugs wait testing. In the last decade, mouse models have been evolved to better mimic human diseases genetically and biologically. These reliable mouse models allow us to determine which genetic elements, pathways and mutations impact on therapy. The co‐clinical trial strategy is to conduct a human clinical trial for a therapeutic drug and test it in mouse models at the same time. This strategy has the potential to accelerate the drug testing process and identify the patient population that will respond to the drug. Imaging plays an important role in co‐clinical trials. In this symposium, four speakers will discuss advancements and issues in pre‐clinical imaging, murine models, imaging hardware and software, and funding opportunities in co‐clinical trials. Learning Objectives: Multi‐modality pre‐clinical imaging hardware and software, and new technologies (e.g., hyperpolarized MRI) Selection of animal models from physiological and genetic perspectives with examples in colon, pancreatic and lung cancers NCI funding opportunities
A sub-1V, 120 nW, PVT-variation Tolerant, Tunable and Scalable Voltage Reference with 60 d (2017)

This paper presents a novel low-power process, voltage and temperature (PVT)-variation tolerant voltage reference generator that can be easily redesigned across various CMOS technologies. The proposed circuit architecture can be used in standalone analog integrated circuits that may not require nano-scale technologies as well as system-on-a-chip applications that need analog circuits in a much lower technology node due to their dominant digital counterparts. The reference generator implements weighted averaging of a PTAT (proportional to absolute temperature) and a CTAT (complementary to absolute temperature) voltage at zero temperature coefficient (ZTC) point. PVT-variation tolerant behavior is achieved by using an on-chip shift register based switching circuit that adjusts the bias current of a key transistor in the circuit. The proposed reference generator is fabricated in 180 nm mixed-mode CMOS technology and also designed in 65 and 28 nm technologies using foundry provided models. For a temperature range from 0 to 75 °C at 1.8 V supply, the measured tuned output voltage varies by only ±0.33% across 17 chips, which is significantly lower than all previously reported works.
Polar effects in the homolytic methylation of pyrimidine: orientation and polysubstitution (1984)

The homolytic methylation of pyrimidine in aqueous solution has been investigated with three different radical sources: ButOOH–Fe2+, MeCO2H–S2O82––Ag+, and MeSOMe–H2O2–Fe2+. This last reagent, used for the first time in homolytic aromatic substitution, turned out to be the most efficient. The orientation of mono-and poly-methylated derivatives is discussed on the basis of polar effects.
Modeling flow-based electrophoretic deposition for functionally graded materials (2021)

Electrophoretic deposition is an industrially proven technique to create materials from colloidal suspensions using an electric field, including functionally graded materials. While typically the composition of the colloidal suspension is held constant during deposition, leading to deposits of uniform composition or distinct layers, several researchers have reported forming functionally graded materials via electrophoretic deposition by changing the composition during the deposition. This article explores electrophoretic deposition in a flow cell that allows arbitrary gradients in the deposited material to be formed by actively mixing two colloidal suspensions during deposition. Under certain combinations of flow rate and applied electric field, the morphology of the deposit strongly deviates from the desired uniform thickness to a distinct wedge shape. To understand this phenomenon and leverage it for improved designs, a multiphysics model is developed that describes the spatial-temporal colloidal transport of particles in the suspension and reveals that suspension flow rate is the key factor influencing deposit morphologies observed in the experiment. Crucially, a distinct transition is found in deposit morphology from wedge shaped to flat at a dimensionless electric Froude number of approximately 10.
Characterization of the Cleavage of β-Glucosidic Linkage by Trichoderma viride Cellulase Using Regioselectively Substituted Methylcelluloses (1994)

Abstract Regioselectively substituted methylcelluloses having a uniform structure, 6-O-methylcellulose, was degraded by the cellulase of Trichoderma viride while 2,3-di-O-methylcellulose(2) was not. In contrast, a substrate having a trace amount of unsubstituted units in compound 2 was depolymerized by the cellulase, suggesting that glucosidic bonds between non-substituted and 2,3-di-O-substituted units were selectively cleaved.
Data from Genetically Defined Subsets of Human Pancreatic Cancer Show Unique <i>In Vitro</i> Chemosensitivity (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Pancreatic cancer is the fourth cause of death from cancer in the western world. Majority of patients present with advanced unresectable disease responding poorly to most chemotherapeutic agents. Chemotherapy for pancreatic cancer might be improved by adjusting it to individual genetic profiles. We attempt to identify genetic predictors of chemosensitivity to broad classes of anticancer drugs.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Using a panel of genetically defined human pancreatic cancer cell lines, we tested gemcitabine (antimetabolite), docetaxel (antimicrotubule), mitomycin C (MMC; alkylating), irinotecan (topoisomerase I inhibitor), cisplatin (crosslinking), KU0058948 (Parp1 inhibitor), triptolide (terpenoid drug), and artemisinin (control).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; All pancreatic cancer cell lines were sensitive to triptolide and docetaxel. Most pancreatic cancer cells were also sensitive to gemcitabine and MMC. The vast majority of pancreatic cancer cell lines were insensitive to cisplatin, irinotecan, and a Parp1 inhibitor. However, individual cell lines were often sensitive to these compounds in unique ways. We found that &lt;i&gt;DPC4/SMAD4&lt;/i&gt; inactivation sensitized pancreatic cancer cells to cisplatin and irinotecan by 2- to 4-fold, but they were modestly less sensitive to gemcitabine. Pancreatic cancer cells were all sensitive to triptolide and 18% were sensitive to the Parp1 inhibitor. &lt;i&gt;P16/CDKN2A&lt;/i&gt;-inactivated pancreatic cancer cells were 3- to 4-fold less sensitive to gemcitabine and MMC.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Chemosensitivity of pancreatic cancer cells correlated with some specific genetic profiles. These results support the hypothesis that genetic subsets of pancreatic cancer exist, and these genetic backgrounds may permit one to personalize the chemotherapy of pancreatic cancer in the future. Further work will need to confirm these responses and determine their magnitude &lt;i&gt;in vivo&lt;/i&gt;. &lt;i&gt;Clin Cancer Res; 18(23); 6519–30. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Identification of a Novel Organic Anion Transporter Mediating Carnitine Transport in Mouse Liver and Kidney (2010)

This study identifies a novel organic anion transporter Oat9 expressed in mouse liver and kidney. Two variants were detected by screening a mouse liver cDNA library; these varients consist of 1815 (designated Oat9S) and 2165 (Oat9L) base pairs which encode 443 and 551 amino acid proteins, respectively. Oat9S has a predicted structure containing eight transmembrane domains (TMD); whereas, Oat9L possesses twelve TMD. Oat9 mRNA expression was detected in kidney and liver. This transporter was located at the apical side of the late portion of proximal tubules and at the sinusoidal side of hepatocytes. When expressed in Xenopus oocytes, Oat9S mediated the transport of L-carnitine (Km = 2.9 µM), a representative zwitterion, as well as cimetidine (Km = 16.1 µM) and salicylic acid (Km = 175.5 µM), while Oat9L did not show any transport activity. Oat9S-mediated L-carnitine uptake was inhibited by D-carnitine, acetylcarnitine, octanoylcarnitine, betaine, and other organic compounds, suggesting that quaternary ammonium cation bulkiness and relative hydrophobicity are important factors for Oat9S-substrate interactions. Among OATs, Oat9S appears to be the first member to mediate the transport of carnitine and possesses eight TMD. Overall, these new results provide added insight into the structure-activity relationship comprising the organic ion-permeation pathway.
Convolutional Embedding of Attributed Molecular Graphs for Physical Property Prediction (2017)

The task of learning an expressive molecular representation is central to developing quantitative structure-activity and property relationships. Traditional approaches rely on group additivity rules, empirical measurements or parameters, or generation of thousands of descriptors. In this paper, we employ a convolutional neural network for this embedding task by treating molecules as undirected graphs with attributed nodes and edges. Simple atom and bond attributes are used to construct atom-specific feature vectors that take into account the local chemical environment using different neighborhood radii. By working directly with the full molecular graph, there is a greater opportunity for models to identify important features relevant to a prediction task. Unlike other graph-based approaches, our atom featurization preserves molecule-level spatial information that significantly enhances model performance. Our models learn to identify important features of atom clusters for the prediction of aqueous solubility, octanol solubility, melting point, and toxicity. Extensions and limitations of this strategy are discussed.
Discovering the unknown: Detection of emerging pathogens using a label‐free light‐scattering system (2010)

A recently introduced technique for pathogen recognition called BARDOT (BActeria Rapid Detection using Optical scattering Technology) belongs to the broad class of optical sensors and relies on forward-scatter phenotyping (FSP). The specificity of FSP derives from the morphological information that bacterial material encodes on a coherent optical wavefront passing through the colony. The system collects elastically scattered light patterns that, given a constant environment, are unique to each bacterial species and serovar. The notable similarity between FSP technology and spectroscopies is their reliance on statistical machine learning to perform recognition. Currently used methods utilize traditional supervised techniques which assume completeness of training libraries. However, this restrictive assumption is known to be false for most experimental conditions, resulting in unsatisfactory levels of accuracy, poor specificity, and consequently limited overall performance for biodetection and classification tasks. The presented work demonstrates application of the BARDOT system to classify bacteria belonging to the Salmonella class in a nonexhaustive framework, that is, without full knowledge about all the possible classes that can be encountered. Our study uses a Bayesian approach to learning with a nonexhaustive training dataset to allow for the automated detection of unknown bacterial classes.
Effects of composition segregation in Cu-In precursor films on microstructures of CIS films (2004)

Cu-In precursor films with a Cu/In atomic ratio approaching 1 were prepared using middle frequency A.C. magnetron sputtering with a Cu-In alloy target to investigate local agglomeration in Cu-In alloy layers and its effects on the element distributions and microstructure of selenized CuInSe2 (CIS) films. CIS absorbers for solar cells were then formed by the selenization process in a selenium atmosphere. Scanning electron microscopy and energy dispersive X-ray analysis were used to observe the surface morphologies and to determine the compositions of both the Cu-In precursor films and the CIS films. Their microstructures were characterized by X-ray diffraction and Raman spectroscopy. The results show that the Cu-In alloy films are mainly composed of a Cu11In9 phase with an in-rich solid solution appearing as particles in the films. Stoichiometric CIS film can be synthesized with a homogeneous element distribution and a single chalcopyrite phase from the Cu-In precursor film with a Cu/In atomic ratio of 1. The CIS film exhibits p-type conduction and has a resistivity reaching 1.2 kΩ·cm.
Clinical manifestations of essential thrombocythemia in young adults (1990)

Essential thrombocythemia (ET) is a myeloproliferative disorder characterized by isolated overproduction of platelets, thrombohemorrhagic complications, and a median age of 50-60. When it occurs in younger patients, the incidence of complications has been reported to be quite low, with a good long-term prognosis. We report a retrospective review of 13 patients with ET between the ages of 22 and 35 in which 11 were symptomatic at diagnosis, with only one remaining asymptomatic during follow-up. Three patients presented with potentially life-threatening complications (two myocardial infarctions, one stroke), although no deaths were observed. The majority of the nonlife-threatening complications were vaso-occlusive in nature, including erythromelalgia and transient neurologic symptoms. We conclude that ET in young adults is not always a benign disease and that potentially life-threatening complications are not rare. The optimum approach to treatment in this or any other age group remains uncertain.
Effect of Intravaginal Prasterone on Sexual Dysfunction in Postmenopausal Women with Vulvovaginal Atrophy (2015)

The present data show that all the six domains of the FSFI are improved over placebo (from P = 0.047 to 0.0005), thus confirming the previously observed benefits of intravaginal DHEA on female sexual dysfunction by an action exerted exclusively at the level of the vagina, in the absence of biologically significant changes of serum steroids levels.
Non-wettable, Oxidation-Stable, Brightly Luminescent, Perfluorodecyl-Capped Silicon Nanocrystal Film (2014)

Here we describe for the first time the synthesis of colloidally stable, brightly luminescent perfluorodecyl-capped silicon nanocrystals and compare the properties of solutions and films made from them with those of their perhydrodecyl-capped relatives. The perfluorodecyl capping group compared to the perhydrodecyl capping group yields superior hydrophobicity and much greater resistance to air oxidation, the enhanced electron-withdrawing character induces blue shifts in the wavelength of photoluminescence, and the lower-frequency carbon-fluorine stretching modes disfavor non-radiative relaxation pathways and boost the absolute photoluminescence quantum yield. Together these attributes bode well for advanced materials and biomedical applications founded upon perfluorodecyl-protected silicon nanocrystals.
In Situ Time-Resolved X-ray Scattering Study of Isotactic Polypropylene in Additive Manufacturing (2019)

Using a specially designed apparatus, which collects simultaneous temperature and X-ray scattering data, we performed in situ measurements of the filament during MatEx 3D printing. The data show that the MatEx 3D printing extrusion process provides sufficient shear to form shish-kebab structures, which initially nucleate at the filament surface and spread into the filament core. Time-resolved measurements show that the kebab component near the surface relaxes after deposition of the second filament and enhances chain diffusion across the interface. SEM images indicate near complete interfacial merging of the filaments, which results in excellent mechanical properties.
Modulation of Redox Signaling in Chronic Diseases and Regenerative Medicine (2019)

Over the last decades, major advances in therapeutic strategies for chronic diseases have significantly reduced death rates. Redox signaling is being implicated in the pathophysiology of such diseases, affecting most organs. Proliferation of cancer cells, damage to cardiomyocytes and vascular cells, and exacerbation of inflammation are just a few examples of events importantly controlled by reacting oxygen species (ROS). Physiologic levels of ROS act as signaling molecules and modulate healthy functions, while high levels of ROS can derange the homeostasis of most organs and systems in our body. Hence, fine-tuning the complexity of redox signaling is a very up-to-date field of research
Acute intermittent porphyria: Comorbidity and shared familial risks with schizophrenia and bipolar disorder in Sweden (2015)

Acute intermittent porphyria (AIP) has been associated with schizophrenia in some studies, but prior research is limited by the absence of comparison populations. Here, we linked Swedish registers to examine the risk of schizophrenia and bipolar disorder in 717 individuals diagnosed with AIP and their first-degree relatives, compared with matched individuals without AIP and their first-degree relatives. Individuals with AIP had a fourfold increased risk of schizophrenia or bipolar disorder. Similarly, relatives of individuals with AIP had double the risk of schizophrenia or bipolar disorder, suggesting that these associations may be as a result of common genetic influences.