gebhart/patrepeval huggingface dataset:
In vitro and in vivo studies on biocompatibility of carbon fibres (2010)

In the present study we focused on the in vitro and in vivo evaluation of two types of carbon fibres (CFs): hydroxyapatite modified carbon fibres and porous carbon fibres. Porous CFs used as scaffold for tissues regeneration could simultaneously serve as a support for drug delivery or biologically active agents which would stimulate the tissue growth; while addition of nanohydroxyapatite to CFs precursor can modify their biological properties (such as bioactivity) without subsequent surface modifications, making the process cost and time effective. Presented results indicated that fibre modification with HAp promoted formation of apatite on the fibre surface during incubation in simulated body fluid. The materials biocompatibility was determined by culturing human osteoblast-like cells of the line MG 63 in contact with both types of CFs. Both tested materials gave good support to adhesion and growth of bone-derived cells. Materials were implanted into the skeletal rat muscle and a comparative analysis of tissue reaction to the presence of the two types of CFs was done. Activities of marker metabolic enzymes: cytochrome c oxidase (CCO) and acid phosphatase were examined to estimate the effect of implants on the metabolic state of surrounding tissues. Presented results evidence the biocompatibility of porous CFs and activity that stimulates the growth of connective tissues. In case of CFs modified with hydroxyapatite the time of inflammatory reaction was shorter than in case of traditional CFs.
Avances del programa conjunto de marcado - recaptura de Gatuzo (Mustelus shcmitti). (2018)

La utilización de marcas en peces es una herramienta útil para evaluar diversos aspectos ecológicos de las especies. En el marco de la Comisión Técnica Mixta del Frente Marítimo (CTMFM) se elaboró el primer Programa Conjunto de Marcado-Recaptura de Gatuzo (PCMG), entre Argentina y Uruguay, con el objetivo de estudiar los movimientos del tiburón gatuzo (Mustelus schmitti) dentro del área del Tratado del Río de la Plata y su Frente Marítimo, y aguas adyacentes. Este documento hace especial énfasis en las experiencias de marcado durante las campañas conjuntas costeras a bordo del B/I Aldebarán en los años 2016 y 2017. A su vez, se presentan los primeros resultados del PCMG, referidos a recapturas de gatuzo, así como consideraciones y perspectivas futuras del programa. En total fueron marcados 937 gatuzos (27-93 cm largo total). A la fecha, se han recapturado cinco ejemplares luego de un tiempo en libertad de entre 139 y 547 días, recorriendo distancias mínimas de entre 41 y 156 km. Ninguno de los ejemplares recapturados mostró indicios de infección producto de las marcas, por lo que es posible afirmar que las mismas son apropiadas para el estudio de esta especie. La continuidad del programa, en conjunto con una adecuada campaña de divulgación, permitirá la recolección de información de gran utilidad para la evaluación y conservación de este recurso pesquero.
Mitochondrial dysfunction and autophagy activation are associated with cardiomyopathy developed by extended methamphetamine self-administration in rats (2022)

The recent rise in illicit use of methamphetamine (METH), a highly addictive psychostimulant, is a huge health care burden due to its central and peripheral toxic effects. Mounting clinical studies have noted that METH use in humans is associated with the development of cardiomyopathy; however, preclinical studies and animal models to dissect detailed molecular mechanisms of METH-associated cardiomyopathy development are scarce. The present study utilized a unique very long-access binge and crash procedure of METH self-administration to characterize the sequelae of pathological alterations that occur with METH-associated cardiomyopathy. Rats were allowed to intravenously self-administer METH for 96 h continuous weekly sessions over 8 weeks. Cardiac function, histochemistry, ultrastructure, and biochemical experiments were performed 24 h after the cessation of drug administration. Voluntary METH self-administration induced pathological cardiac remodeling as indicated by cardiomyocyte hypertrophy, myocyte disarray, interstitial and perivascular fibrosis accompanied by compromised cardiac systolic function. Ultrastructural examination and native gel electrophoresis revealed altered mitochondrial morphology and reduced mitochondrial oxidative phosphorylation (OXPHOS) supercomplexes (SCs) stability and assembly in METH exposed hearts. Redox-sensitive assays revealed significantly attenuated mitochondrial respiratory complex activities with a compensatory increase in pyruvate dehydrogenase (PDH) activity reminiscent of metabolic remodeling. Increased autophagy flux and increased mitochondrial antioxidant protein level was observed in METH exposed heart. Treatment with mitoTEMPO reduced the autophagy level indicating the involvement of mitochondrial dysfunction in the adaptive activation of autophagy in METH exposed hearts. Altogether, we have reported a novel METH-associated cardiomyopathy model using voluntary drug seeking behavior. Our studies indicated that METH self-administration profoundly affects mitochondrial ultrastructure, OXPHOS SCs assembly and redox activity accompanied by increased PDH activity that may underlie observed cardiac dysfunction.
Supplementary Figure 1 from Therapeutic Implications of a Human Neutralizing Antibody to the Macrophage-Stimulating Protein Receptor Tyrosine Kinase (RON), a c-MET Family Member (2023)

Supplementary Figure 1 from Therapeutic Implications of a Human Neutralizing Antibody to the Macrophage-Stimulating Protein Receptor Tyrosine Kinase (RON), a c-MET Family Member
Abstract B05: mEAK-7 supports self-renewal and radioresistance in metastatic cancer (2020)

Abstract Mammalian EAK-7, or MTOR associated protein, eak-7 homolog, (mEAK-7) functions as a crucial regulator of mTOR signaling. Dysregulation of mTOR signaling contributes to the pathogenicity of human carcinomas, so we sought to clarify the role of mEAK-7 in tumorigenesis and metastasis. Bioinformatics analysis revealed that MEAK7 mRNA or gene copy number amplification was observed in a multitude of human carcinomas, including non-small cell lung carcinoma (NSCLC). Tissue microarrays containing sections of primary NSCLC tumors, noncancerous adjacent tissue, and metastatic lymph tissue were used to quantify mEAK-7 and mTOR signaling. Our analyses revealed high mEAK-7 expression and mTOR signaling in metastasized lymph nodes. NSCLC cell lines H1299 and H1975 were used for all in vitro experiments. To examine the role mEAK-7 may play in cancer stem cell (CSC) self-renewal, NSCLC cells were FACS sorted into two groups: CD44+/CD90+ CSCs and non-CSCs. CSCs expressing CD44+/CD90+ demonstrated higher mEAK-7 expression and mTOR activation than non-CSCs, suggesting a role for mEAK-7 in cancer self-renewal and radiation resistance. Following X irradiation-induced DNA damage, 2D clonogenicity and 3D spheroid assays were used to further examine mEAK-7's role in clonogenic potential and self-renewal, respectively. These assays revealed that mEAK-7 is essential for the clonogenic potential and self-renewal of cancer cells in response to DNA damage. Comet assays were used to quantify the DNA damage response, and immunoblot and immunoprecipitation analysis confirmed that mEAK-7 is required for promoting radiation stress. Similarly, siRNA-mediated knockdown of mEAK-7 resulted in reduced DNA damage repair and enhanced cellular apoptosis following genotoxic stress. To do so, mEAK-7 may be interacting with components of the DNA damage response, such as DNA-PK. Immunoprecipitation and mass spectrometry analyses identified that mEAK-7 interacts with DNA-PK, and this interaction is strengthened following treatment with genotoxic stress. Further, DNA-PK interacts with mEAK-7 to regulate S6K2, a crucial target of the mTOR. This suggests crosstalk between the DNA-PK and PI3K pathways, since mEAK-7 interacts with DNA-PK to impact the DNA damage response in human cancer cells. Therefore, DNA-PK inhibitors may be utilized to regulate mEAK-7 and mTOR signaling in specific human carcinomas. Thus, mEAK-7 is a novel marker for NSCLC metastasis; overexpressed in both NSCLC and CSCs; and required for clonogenic potential, spheroid formation, and radiation resistance. Citation Format: Joe T. Nguyen, Fatima S. Haidar, Alexandra L. Fox, Connor Ray, Daniela B. Mendonça, Jin K. Kim, Paul H. Krebsbach. mEAK-7 supports self-renewal and radioresistance in metastatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Targeting PI3K/mTOR Signaling; 2018 Nov 30-Dec 8; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(10_Suppl):Abstract nr B05.
Adenosine A2A Receptor Antagonists and Parkinson’s Disease (2011)

This Review summarizes and updates the work on adenosine A(2A) receptor antagonists for Parkinson's disease from 2006 to the present. There have been numerous publications, patent applications, and press releases within this time frame that highlight new medicinal chemistry approaches to this attractive and promising target to treat Parkinson's disease. The Review is broken down by scaffold type and will discuss the efforts to optimize particular scaffolds for activity, pharmacokinetics, and other drug discovery parameters. The majority of approaches focus on preparing selective A(2A) antagonists, but a few approaches to dual A(2A)/A(1) antagonists will also be highlighted. The in vivo profiles of compounds will be highlighted and discussed to compare activities across different chemical series. A clinical report and update will be given on compounds that have entered clinical trials.
A Short Synthesis of the Erythrina Skeleton and of (±)-α-Lycorane (2002)

[reaction: see text] A new nonchain 5-endo radical cyclization starting with xanthates was exploited in a short synthesis of (+/-)-alpha-lycorane and the erythrina ring system.
Electromagnetic constraints on a melt region beneath the central Mariana back‐arc spreading ridge (2012)

An electrical resistivity profile across the central Mariana subduction system shows high resistivity in the upper mantle beneath the back‐arc spreading ridge where melt might be expected to exist. Although seismic data are equivocal on the extent of a possible melt region, the question arises as to why a 2‐D magnetotelluric (MT) survey apparently failed to image any melt. We have run forward models and inversions that test possible 3‐D melt geometries that are consistent with the MT data and results of other studies from the region, and that we use to place upper bounds on the possible extent of 3‐D melt region beneath the spreading center. Our study suggests that the largest melt region that was not directly imaged by the 2‐D MT data, but that is compatible with the observations as well as the likely effects of melt focusing, has a 3‐D shape on a ridge‐segment scale focused toward the spreading center and a resistivity of 100 Ω‐m that corresponds to ∼0.1–∼1% interconnected silicate melt embedded in a background resistivity of ∼500 Ω‐m. In contrast to the superfast spreading southern East Pacific Rise, the 3‐D melt region suggests that buoyant mantle upwelling on a ridge‐segment scale is the dominant process beneath the slow‐spreading central Mariana back‐arc. A final test considers whether the inability to image a 3‐D melt region was a result of the 2‐D survey geometry. The result reveals that the 2‐D transect completed is useful to elucidate a broad range of 3‐D melt bodies.
ChemInform Abstract: Selective Reduction of Carboxylic Acids to Aldehydes Catalyzed by B(C6F5)3. (2013)

Abstract A protocol for the selective reduction of carboxylic acids to aldehydes via intermediate disilyl acetals is presented.
Observation of resonant modes of coupled domain walls (2014)

The authors discuss the dynamics of domain walls in thin permalloy magnetic nanowires through the anisotropic magnetoresistance effect. Upon the introduction of a single DW into the magnetic nanowire, only one resonant mode was observed. Two resonant modes were found in coupled DWs.
Cervical Disc Replacement—Porous Coated Motion Prosthesis (2003)

There are two basic types of total knee replacements, posterior cruciate ligament-preserving and posterior cruciate ligament-sacrificing designs. In the cervical spine, an analogous situation exists biomechanically depending on whether the posterior longitudinal ligament needs to be removed in its entirety as part of the spinal cord decompression part of the procedure--it may be helpful to conceptually differentiate between posterior longitudinal ligament-preserving and posterior longitudinal ligament-sacrificing total cervical disc replacements.
Supplementary Information Supplementary Figures 1-3, Supplemental Table 1, Supplemental Figure and Table Legends from Identification of an “Exceptional Responder” Cell Line to MEK1 Inhibition: Clinical Implications for MEK-Targeted Therapy (2023)

&lt;p&gt;Characteristics of the 21 lung cancer cell lines assayed in the Project Achilles data set (8). NSCLC = non-small cell lung cancer, LCLC = large cell lung cancer, SCLC = small cell lung cancer. S1. Each data point represents the normalized gene-level scores for ABL1 (ATARiS gene solution 2) in the 30 hematopoietic and lymphoid cell lines tested (8). The three most sensitive lines (indicated by red circles) are the only lines within this data set known to harbor the BCR-ABL1 translocation. S2. (A) Trametinib dose response curve after 6 days. Cell viability normalized to DMSO treated controls. (B) Refametinib dose response curve after 6 days. Cell viability normalized to DMSO treated controls. (C) PD0325901 dose response curve after 6 days. Cell viability normalized to DMSO treated controls. (D) Immunoblot of protein levels after 4-hour treatment with DMSO or 10 nM trametinib in each cancer cell line. S3. Xenograft tumor growth after NCI-H1437 subcutaneous injection in nude mice. Mice were treated daily with either vehicle 5% DMSO or 0.3mg/kg trametinib. For each tumor, the volume was normalized to its size at the start of drug treatment. Supplemental Table 1. Characteristics of the 21 lung cancer cell lines assayed in the Project Achilles data set (8). NSCLC = non-small cell lung cancer, LCLC = large cell lung cancer, SCLC = small cell lung cancer.&lt;/p&gt;
Photo-on-Demand Phosgenation Reactions with Chloroform for Selective Syntheses of N-Substituted Ureas and Isocyanates (2022)

Two new reaction processes involving the <i>in situ</i> oxidative photochemical conversion of CHCl<sub>3</sub> to COCl<sub>2</sub> allowed selective syntheses of N-substituted ureas and isocyanates from amines. (I) A CHCl<sub>3</sub> solution containing an amine and an organic base under O<sub>2</sub> bubbling provided the urea derivative under exposure to UV light generated from a low-pressure mercury lamp at 20-40 °C. (II) A two-step reaction involving the oxidative photodecomposition of CHCl<sub>3</sub> at lower temperatures and subsequent sequential injections of an amine and organic base into the sample solution provided the isocyanate in high yield. The reaction processes of (I) and (II) capitalize on the solution conditions of [COCl<sub>2</sub>] < [amine] and [COCl<sub>2</sub>] > [amine], respectively, to result in 1:2 and 1:1 reactions. In general, isocyanates, especially aromatic and haloalkyl ones, readily undergo hydrolysis in the presence of an organic base. However, with the advantage of synthesizing the isocyanates in CHCl<sub>3</sub> solvent, direct addition of monoalcohols and diols to the as-prepared sample solution containing the diisocyanate allowed the one-pot syntheses of biscarbamates and polyurethanes, respectively. The reactions developed in this study are simple, safe, and inexpensive methods of synthesizing N-substituted ureas and isocyanates, and derivatives of isocyanates such as carbamates and polyurethanes. The present new methods can replace current synthetic methods using COCl<sub>2</sub> in both academia and industry.
Brain tubutin and actin cDNA sequence: isolation of recombinant plasmids (1980)

Rat brain mRNA enriched for tubulin and actin sequences was used to prepare double stranded cDNA. A library of recombinant clones was constructed by inserting the dsDNA into the Pst1 site of pBR322 plasmid and transformation of E. coli chi 1776 host. Clones bearing sequences coding for tubulin and actin were identified and characterized.
TD methods applied to mixture of experts for learning 9×9 Go evaluation function (2003)

The temporal difference (TD) method is applied on a committee of neural network experts to learn the board evaluation function for the oriental board game Go. The game has simple rules but requires complex strategies to play well, and the conventional tree search algorithm for computer games makes a poor Go program. Thus, the game Go is an ideal problem domain for exploring machine learning algorithms. Here, the neural networks learned a board evaluation function for Go played on 9/spl times/9 board sizes. Two learning algorithms, e.g., hybrid mixture of experts (HME) and Meta-Pi, are used to train the neural network experts. Both algorithms learned good Go evaluation functions and the neural network based Go engines were able to defeat a public domain rule-based program more than 50% of the times. The performances of the mixture networks are compared with that of a single feedforward network trained similarly.
Glucose-regulated Protein 78 Is an Intracellular Antiviral Factor against Hepatitis B Virus (2009)

Hepatitis B virus (HBV) infection is a global public health problem that plays a crucial role in the pathogenesis of chronic hepatitis, cirrhosis, and hepatocellular carcinoma. However, the pathogenesis of HBV infection and the mechanisms of host-virus interactions are still elusive. In this study, two-dimensional gel electrophoresis and mass spectrometry-based comparative proteomics were applied to analyze the host response to HBV using an inducible HBV-producing cell line, HepAD38. Twenty-three proteins were identified as differentially expressed with glucose-regulated protein 78 (GRP78) as one of the most significantly up-regulated proteins induced by HBV replication. This induction was further confirmed in both HepAD38 and HepG2 cells transfected with HBV-producing plasmids by real time RT-PCR and Western blotting as well as in HBV-infected human liver biopsies by immunohistochemistry. Knockdown of GRP78 expression by RNA interference resulted in a significant increase of both intracellular and extracellular HBV virions in the transient HBV-producing HepG2 cells concomitant with enhanced levels of hepatitis B surface antigen and e antigen in the culture medium. Conversely overexpression of GRP78 in HepG2 cells led to HBV suppression concomitant with induction of the positive regulatory circuit of GRP78 and interferon-beta1 (IFN-beta1). In this connection, the IFN-beta1-mediated 2',5'-oligoadenylate synthetase and RNase L signaling pathway was noted to be activated in GRP78-overexpressing HepG2 cells. Moreover GRP78 was significantly down-regulated in the livers of chronic hepatitis B patients after effective anti-HBV treatment (p = 0.019) as compared with their counterpart pretreatment liver biopsies. In conclusion, the present study demonstrates for the first time that GRP78 functions as an endogenous anti-HBV factor via the IFN-beta1-2',5'-oligoadenylate synthetase-RNase L pathway in hepatocytes. Induction of hepatic GRP78 may provide a novel therapeutic approach in treating HBV infection.
Patient-specific computational simulation of coronary artery bypass grafting (2023)

We presented a comprehensive patient-specific computational platform that can simulate the hemodynamic conditions before and after CABG and faithfully reproduce the hemodynamic effects of bypass grafting on the native coronary artery flow. Further clinical studies are warranted to validate this preliminary data.
Intermediate phases in sodium intercalation into MoS2 nanosheets and their implications for sodium-ion batteries (2017)

Alkali metal ion intercalation into layered transition-metal dichalcogenide structures is a promising approach to make next generation rechargeable batteries for energy storage. It has been noted that the number of Na-ions which can be reversibly intercalated and extracted per MoS2 is limited, and the chemical and electrochemical processes/mechanisms remain largely unknown, especially for nano-sized materials. Here, sodiation of MoS2 nanosheets are studied by in-situ electron diffraction and the phase transformations in sodiation are identified with the aid of DFT calculations to reveal the reaction mechanism. Several thermodynamically stable/metastable structures are identified in the sodiation pathway of MoS2 nanosheets, previously unnoticed in bulk MoS2. The gradual reduction of Mo4+ upon Na-ion intercalation leads to a transition of the Mo-S polyhedron from a trigonal prism to an octahedron around 0.375 Na per MoS2 inserted (i.e. Na0.375MoS2). When the intercalated Na-content is larger than 1.75 per MoS2 structural unit (i.e. Na1.75MoS2), the MoS2 layered structure collapses and the intercalation reaction is replaced by an irreversible conversion reaction with the formation of Na2S and metal Mo nanoparticles. The calculated sodiation pathways reproduce the experimental sodiation voltages. The current observations provide useful insights in developing sodium-ion batteries with high cycling stability.
Trading Symmetry for Stereoinduction in Tetradentate, non‐C2‐Symmetric Fe(II)‐Complexes for Asymmetric Catalysis (2023)

A series of stereogenic-at-metal iron complexes comprising a non-C<sub>2</sub> -symmetric chiral topology is introduced and applied to asymmetric 3d-transition metal catalysis. The chiral iron(II) complexes are built from chiral tetradentate N4-ligands containing a proline-derived amino pyrrolidinyl backbone which controls the relative (cis-α coordination) and absolute metal-centered configuration (Λ vs. Δ). Two chloride ligands complement the octahedral coordination sphere. The modular composition of the tetradentate ligands facilitates the straightforward incorporation of different terminal coordinating heteroaromatic groups into the scaffold. The influence of various combinations was evaluated in an asymmetric ring contraction of isoxazoles to 2H-azirines revealing that a decrease of symmetry is beneficial for the stereoinduction to obtain chiral products in up to 99 % yield and with up to 92 % ee. Conveniently, iron catalysis is feasible under open flask conditions with the bench-stable dichloro complexes exhibiting high robustness towards oxidative or hydrolytic decomposition. The versatility of non-racemic 2H-azirines was subsequently showcased with the conversion into a variety of quaternary α-amino acid derivatives.
Genome-wide Studies of Verbal Declarative Memory in Nondemented Older People: The Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium (2020)

Memory performance in older persons can reflect genetic influences on cognitive function and dementing processes. We aimed to identify genetic contributions to verbal declarative memory in a community setting.