gebhart/patrepeval huggingface dataset:
Spatially Adaptive Bayesian Penalized Splines With Heteroscedastic Errors (2007)

AbstractPenalized splines have become an increasingly popular tool for nonparametric smoothing because of their use of low-rank spline bases, which makes computations tractable while maintaining accuracy as good as smoothing splines. This article extends penalized spline methodology by both modeling the variance function nonparametrically and using a spatially adaptive smoothing parameter. This combination is needed for satisfactory inference and can be implemented effectively by Bayesian MCMC. The variance process controlling the spatially adaptive shrinkage of the mean and the variance of the heteroscedastic error process are modeled as log-penalized splines. We discuss the choice of priors and extensions of the methodology, in particular, to multivariate smoothing. A fully Bayesian approach provides the joint posterior distribution of all parameters, in particular, of the error standard deviation and penalty functions. MATLAB, C, and FORTRAN programs implementing our methodology are publicly available.Key Words: HeteroscedasticityMCMCMultivariate smoothingRegression splinesSpatially adaptive penaltyThin-plate splinesVariance functions
Field Implementation of a Novel Solids-Free System to Minimize Fluid Loss during Overbalanced Workover Operations (2010)

Abstract Controlling fluid loss into the formation is of critical importance during overbalanced workover operations to minimized near-wellbore damage invasion by the completion fluid, which can yield problems associated with poor wellbore cleanout and loss of hydrocarbon reserves. In addition, fluid loss can increase costs associated with rig time and treatments devoted to restore the initial condition of the formation. Traditional techniques to minimize fluid loss use solids or viscous pills, although it has been amply documented that these systems can damage the formation if not properly removed after the treatment. This paper presents the laboratory development and validation of a novel solids-free fluid-loss (SFFL) system used during overbalanced workover operations. This system relies on an ionic polymer that decreases matrix permeability to aqueous fluids, limiting leakoff into treated zones. This polymer immediately adsorbs to the surface of the rock, eliminating the need to shut the well in. In addition, this system does not require the use of breakers, which eliminates negative impact on post-stimulation well productivity. Laboratory test data show the capability of the material to control fluid leakoff and achieve high levels of regained permeability to hydrocarbons. To date, about 60 jobs have been performed with this novel SFFL system. The paper discusses field results from the application of this system during overbalanced workover operations and other applications where maintenance of a hydrostatic column is necessary for well control. This system has been proposed for solving partial and total loss to full circulation in overbalanced operations such as: (1) lost-circulation events occurring during cementing, fracturing, and drilling, (2) well intervention cleanouts by coiled tubing (CT) and hydraulic workover (HWO), (3) gravel packing, (4) replacement of artificial lift equipment (i.e., electrical submersible pumps), and (5) overbalanced tubing-conveyed perforating (UTCP), among others.
Distinct roles of KLF4 in mesenchymal cell subtypes during lung fibrogenesis (2021)

During lung fibrosis, the epithelium induces signaling to underlying mesenchyme to generate excess myofibroblasts and extracellular matrix; herein, we focus on signaling in the mesenchyme. Our studies indicate that platelet-derived growth factor receptor (PDGFR)-β<sup>+</sup> cells are the predominant source of myofibroblasts and Kruppel-like factor (KLF) 4 is upregulated in PDGFR-β<sup>+</sup> cells, inducing TGFβ pathway signaling and fibrosis. In fibrotic lung patches, KLF4 is down-regulated, suggesting KLF4 levels decrease as PDGFR-β<sup>+</sup> cells transition into myofibroblasts. In contrast to PDGFR-β<sup>+</sup> cells, KLF4 reduction in α-smooth muscle actin (SMA)<sup>+</sup> cells non-cell autonomously exacerbates lung fibrosis by inducing macrophage accumulation and pro-fibrotic effects of PDGFR-β<sup>+</sup> cells via a Forkhead box M1 to C-C chemokine ligand 2-receptor 2 pathway. Taken together, in the context of lung fibrosis, our results indicate that KLF4 plays opposing roles in PDGFR-β<sup>+</sup> cells and SMA<sup>+</sup> cells and highlight the importance of further studies of interactions between distinct mesenchymal cell types.
An extended solvation theory for electrolyte osmotic and activity coefficients. Application to 1:1, 1:2, 1:3, 1:4, 2:1, 2:2, 3:1, 3:2 and 4:1 aqueous electrolyte solutions (2022)

In this work, we have used two models (DH-MS and PDH-MS) based upon the extended solvation theory to correlate osmotic and activity coefficients of electrolyte aqueous solutions. These models contain the long-range term of the Debye-Hückel (DH) theory or the Pitzer-Debye-Hückel (PDH) modification and a short-range term based upon a modified solvation (MS) theory. We have used literature experimental data of mean ionic activity and osmotic coefficients of 338 aqueous solutions. The electrolytes included in this work are type 1:1, 1:2, 1:3, 1:4, 2:1, 2:2, 3:1, 3:2, and 4:1 at 298.15 K. The results show that the DH-MS and PDH-MS models effectively correlate the experimental data within an average absolute percentage deviation of 0.588% and 0.688%, respectively. We have compared our results with those obtained from the Archer model. This model agrees within 0.769% with the literature data.
ChemInform Abstract: REACTIONS OF ALKOXYCARBONYLCARBENOIDS WITH IMIDAZOLE; AN IMPROVED PREPARATION OF ETHYL IMIDAZOLE‐1‐YLACETATE AND THE FIRST SYNTHESIS OF DIETHYL IMIDAZOLE‐1‐YLMALONATE (1981)

Abstract Die Umsetzungen von Imidazol (I) mit den Diazoestern (II) und (IV) in Gegenwart von Kupferbronze wird untersucht.
A Flexible, Microfluidic, Dispensing System for Screening Drug Combinations (2020)

It is known that in many cases a combination of drugs is more effective than single-drug treatments both for reducing toxicity and increasing efficacy. With the advent of organoid screens, personalised medicine has become possible for many diseases. Automated pipetting to well plates is the pharmaceutical industry standard for drug screening, but this is relatively expensive and slow. Here, a rotary microfluidic system is presented that can test all possible drug combinations at speed with the use of droplets. For large numbers of combinations, it is shown how the experimental scale is reduced by considering drug dilutions and machine learning. As an example, two cases are considered; the first is a three-ring and three radii configuration and the second is a four ring and forty-eight radii configuration. Between these two, all other cases are shown to be possible. The proposed commercial instrument is shown to be flexible, the user choosing which wells to fill and which driver-computational sub-routine to select. The major issues addressed here are the programming theory of the instrument and the reduction of droplets to be generated by drug dilutions and machine learning.
Identification of the base-pair substitution responsible for a human acid alpha glucosidase allele with lower "affinity" for glycogen (GAA 2) and transient gene expression in deficient cells. (1990)

The lysosomal enzyme termed acid alpha glucosidase (GAA), or acid maltase, is genetically polymorphic, with three alleles segregating in the normal population. The rarer GAA 2 allozyme has a lower affinity for glycogen and starch but not for lower-molecular-weight substrates. The GAA 2 allozyme can be detected by "affinity" electrophoresis in starch gel, since the lower affinity for the starch matrix results in a more rapid migration to the anode. Previously, we have isolated and sequenced the cDNA for GAA and transiently expressed the cDNA in deficient fibroblasts. In order to determine the molecular basis for the GAA 2 allozyme, we constructed a cDNA and a genomic DNA library from a GAA 2 cell line and determined the nucleotide sequence of the coding region. Only a single base-pair substitution of an A for a G at base-pair 271 was found, resulting in substitution of asparagine for aspartic acid at codon 91. This amino acid substitution is consistent with the more basic pI of the GAA 2 enzyme. The base-pair substitution also abolishes a Taq-I site, predicting the generation of a larger DNA fragment. This larger Taq-I fragment was also seen in two other individuals expressing the GAA 2 allozyme. A 5' fragment containing the base-pair substitution was ligated to the remaining 3' cDNA from a GAA 1 allele and cloned into an expression vector, and the hybrid cDNA was transiently expressed in SV40-transformed GAA-deficient fibroblasts. The enzyme activity exhibited the altered mobility of the GAA 2 allozyme, as demonstrated by electrophoresis in starch gel.(ABSTRACT TRUNCATED AT 250 WORDS)
Supplementary Figure 3 from CUL4A Induces Epithelial–Mesenchymal Transition and Promotes Cancer Metastasis by Regulating ZEB1 Expression (2023)

&lt;p&gt;PDF file - 293K, Supplemental Figure 3. CUL4A promotes migration and invasion-metastasis of human normal mammary and cancer cells.&lt;/p&gt;
On the feasibility of PV concentrators operating over 1000* (1988)

An analysis of the possibility of increasing the concentration level to over 1000* while keeping or increasing cell efficiency is presented. Si and GaAs cells are discussed, and innovative concentrating approaches permitting multiple-gap cells are presented. A brief analysis of the thermal aspects of the problem is also given. It is concluded that efficiencies of 40% are achievable when these devices are properly combined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
HLA Class II Polymorphism Influences Onset and Severity of Pathology inSchistosoma mansoni-Infected Transgenic Mice (2001)

Genetic factors that might influence susceptibility or resistance in naive individuals and early-stage pathology in schistosomiasis are difficult to study in clinical trials, since in areas where the disease is endemic the first contact with the parasite occurs most often at very early ages. Therefore, four strains (DR1.Abeta degrees, DR2.Abeta degrees, DQ8.Abeta degrees, and DQ6.Abeta degrees ) of major histocompatibility complex class II-deficient mice (Abeta degrees ), transgenic for different HLA alleles, have been used to evaluate the potential role of HLA class II polymorphism in the onset of the infection by Schistosoma mansoni. The survival rates and parasitological and immunological parameters after infection were evaluated and compared against the control values obtained with Abeta degrees mice. All four mouse strains used in this study were able to generate a specific immune response against S. mansoni antigens (cytokine production and antibody production). However, only mice expressing DR alleles survived until the chronic stage of the infection and were able to mount protective granulomatous response avoiding hepatic damage, presenting predominant gamma interferon production. In contrast, strains expressing DQ alleles revealed an impairment in generating effective granulomas, resulting in earlier death, which was associated with an impaired hepatic granulomatous response and liquefactic necrosis, reflecting the influence of HLA polymorphism in the establishment of protective response in the early stage of infection.
Principles of Sustaining Partnerships between Higher Education and their Larger Communities: Perspectives from Engineering Faculty Engaged in Learning through Service (2014)

With the increased focus on community engagement in higher education, engineering faculty members are using Learning through Service (LTS) as a viable way of providing a platform for interactive participatory student learning and involvement in the community. By engaging students to learn in the community, the creation of knowledge shifts from the classroom to the community. This paper explores how LTS engineering practitioners from a diverse range of institutions use LTS to engage community partners in the co-creation of knowledge. Twenty-seven interviews were conducted with these faculty members to identify best practices for mutually beneficial partnership with the communities they serve. Analysis of the interview transcripts reveals six guiding principles of effective and sustainable community partnerships: 1) understand the needs of the community, 2) seek community feedback through direct interaction, 3) engage community partners from an asset-based viewpoint, 4) use cultural intermediaries in international LTS efforts, 5) deliver useful projects, and 6) sustain long-term relationships to improve project outcomes.
Preparation of Poly(N-Msopropylacrylamide)-B-Poly(Ethylene Glycol) and Calorimetric Analysis of Its Aqueous Solution (1994)

Abstract A block copolymer composed of poly(N-isopropylacrylamide) [poly-(NIPAAm)] and a hydrophilic polymer such as poly(ethylene glycol) was prepared. The aqueous solution of the block copolymer exhibited a calorimetric endothermic peak on heating, similar to a poly(NIPAAm) homopolymer, although in a random copolymer composed of NIPAAm and a hydrophilic monomer such as acrylamide, no endothermic peak was observed. This result suggests that it is the NIPAAm sequence length which dominantly affects the LCST phenomenon of the copolymer rather than the content of hydrophilic comonomers.
Supplementary Table 1 from Genome-wide Methylation Analysis Identifies Genes Specific to Breast Cancer Hormone Receptor Status and Risk of Recurrence (2023)

&lt;p&gt;XLS file - 47K&lt;/p&gt;
EUV resist based on low molecular weight PHS (2008)

Two types of EUV resists based on poly(4-hyrdoxystyrene) (PHS) were designed, i.e., PHS-bound sensitizer (PHS-FISS) and PHS/sensitizer blend (PHS/FITS). Imino sulfonate compounds were used as a photosensitizer. A PHS-bound sensitizer resist was prepared by the conventional radical copolymerization of 4-(tertbutyldimethylsilyl)oxystyrene (MSOST) and 9-fluorenilideneimino p-styrenesulfonate (FISS) and subsequent de-silylation of the copolymer. PHS with low molecular weight distribution was obtained by the anionic polymerization of MSOST and followed by de-silylation of the polymer. It was found that both types of resist were negative type and highly sensitive ( 10-20 mJ/cm<sup>2</sup> ) on exposure at 254 nm and 13.5 nm. In the case of blended resist, the sensitivity was dependent on the amounts of sensitizer added and molecular weight of PHS. Outgassing from the present resists on EUV exposure was lower than that observed for MET-2D resist.
State of the Art in Phalloplasty (2005)

Introduction: After Sigmund Freud “opened the bedroom door,” significant shifts in social attitudes, behaviors, and institutional regulations concerning male and female body images and the understanding of human sexuality began to occur. Today, male cosmetic genital enhancement surgery, or phalloplasty, has become the subject of recent surgical achievements that are gaining significant popularity in the United States and abroad. Appropriate methodology and surgical techniques have been developed to fulfill the demand in this field of cosmetic surgery. The objective of this study is to review the state of the art in phalloplasty and provide information about the availability of the techniques to the medical community and the public to inform them of surgical treatments that may improve unsatisfactory sexual performance, relationships, intimacy, and love by increasing the size of a man's penis. Material and Methods: Two surgeons performed phalloplasty on 594 patients at multiple surgical facilities over a 2-year period. Phalloplasty procedures include penile lengthening, penile girth enhancement, dual augmentation (combined lengthening and girth enhancement), penile glanular enhancement, scrotal web resection, and reconstruction. The patients' own satisfaction with the results of their surgeries was analyzed by using the Penis Image Assessment Scale Questionnaire. The assessment was based upon questions related to penis size, satisfaction of sexual experiences, and the psychological perspective of patients regarding their penises before and after phalloplasty. Results: Patient scores on the Penis Image Assessment Scale Questionnaire were higher before surgery (almost twice as high) than they were after surgery, showing an increase in patient satisfaction with penis size and performance after enhancement. Seventeen patients required subsequent surgery to treat local infection. Twenty-nine patients experienced localized swelling 3–7 days after surgery. The results showed enormous patient satisfaction with the cosmetic surgical procedures performed. Discussion: Penis size has always symbolized strength, virility, power, and domination in relationships. Although this subject was taboo some years ago, today many men are interested in learning about how phalloplasty may improve their self-confidence, sexual relationships, and female partners' satisfaction. Consequently, phalloplasty has acquired wide acceptance and tremendous popularity.
Automatic Nonzero Structure Analysis (1999)

The efficiency of sparse codes heavily depends on the size and structure of the input data. Peculiarities of the nonzero structure of each sparse matrix must be accounted for to avoid unsatisfying performance. Therefore, it is important to have an efficient analyzer that automatically determines characteristics of nonzero structures. In this paper, some efficient algorithms are presented that automatically detect particular nonzero structures.
In-vivo and ex-vivo beta-amyloid load detection in Alzheimer’s Disease using R2* and quantitative susceptibility mapping (QSM) at ultra-high magnetic field: comparison to histology (2018)

Poster: ECR 2018 / C-3076 / In-vivo and ex-vivo beta-amyloid load detection in Alzheimer’s Disease using R 2 * and quantitative susceptibility mapping (QSM) at ultra-high magnetic field: comparison to histology by: Tuzzi, G. E. Hagberg, D. Balla, J. Loureiro, M. Neumann, C. Laske, R. Pohmann, K. Scheffler; Tubingen/DE
Synchronization of a single-phase photovoltaic generator with the grid (2011)

This paper presents the architecture of a hybrid phase lock loop circuit topology for synchronizing a single-phase inverter fed from a renewable energy source such as a photovoltaic (PV) generator to the low voltage utility grid. The system uses a digital phase lock loop (DPLL) architecture, which is based on the arctan phase detector, driving a phase lock loop (PLL) to synchronize a PV generator with the grid. The proposed system has been tested by simulation using Simulink/Matlab. The test results, which are also presented, demonstrate the ability of the system to synchronize a PV inverter with the grid and to regain synchronization following a sudden change in the phase of the grid voltage.
Abstract LB-189: Pharmacological reactivation of MYC-dependent apoptosis cooperates with anti-PD1 immunotherapy (2019)

Elevated MYC levels sensitize tumor cells to apoptosis but the therapeutic potential of this mechanism remains unclear. We find, in a model of MYC-driven breast cancer, that pharmacological activation of AMPK dramatically synergizes with BCL-2/BCL-XL inhibitors to activate MYC-dependent apoptosis. We demonstrate the translational potential of an AMPK and BCL- 2/BCL-XL co-targeting strategy in ex vivo and in vivo models of MYC-high breast cancer. Metformin combined with either navitoclax or venetoclax efficiently inhibits tumor growth, confers survival benefits and induces tumor infiltration by immune cells. However, withdrawal of the drugs allowed tumor re- growth with presentation of PD1+/CD8+ T cell infiltrates, suggesting immune escape. A two-step treatment regimen, beginning with neoadjuvant metformin+venetoclax to induce apoptosis and followed by tumor resection and adjuvant metformin+venetoclax+anti-PD1 treatment to overcome immune escape, led to durable antitumor responses even after drug withdrawal. We demonstrate that pharmacological reactivation of MYC-dependent apoptosis is a powerful antitumor strategy involving both tumor cell depletion and immunosurveillance.Citation Format: Heidi M. Haikala, Johanna M. Anttila, Mariel Savelius, Elsa Marques, Tiina Raatikainen, Mette Ilander, Henna Hakanen, Johanna Mattson, Paivi Heikkila, Marjut Leidenius, Heikki Joensuu, Satu Mustjoki, Panu Kovanen, Martin Eilers, Joel D. Leverson, Juha T. Klefström. Pharmacological reactivation of MYC-dependent apoptosis cooperates with anti-PD1 immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-189.
Prognostic factors for lymphomas (2013)

Lymphomas are tumors that have largely benefited from the introduction of cytotoxic chemotherapy. Treatment strategies based on intensive chemotherapy have also demonstrated improved survival of patients with relapsed lymphomas. It is necessary to identify selected populations with adverse prognostic factors that would justify such a strategy. Prognostic indices have been developed both to define therapeutic strategies and compare results of clinical trials. Such indices are usually based on retrospective studies that highlight methodological problems in prospective studies in the monoclonal antibody era. The recent development of technologies analyzing gene expression profiling also gives us new tools for both more accurate diagnosis and prognostic implications. We are also beginning to see the development of indices based on lymphoma-specific biological risk factors. Positron emission tomography using 18F-fluorodeoxyglucose should also improve assessment of tumor response and introduce new prognostic measures.
Strain balancing of MOVPE InAs/GaAs quantum dots using GaAs 0.8 P 0.2 (2016)

MOVPE growth of stacked InAs/&#13;\nGaAs QDs with and without GaAs&#13;\n0.8&#13;\nP&#13;\n0.2&#13;\n strain balancing layers has been &#13;\nstudied. The GaAsP layers reduce the accumulated strain whilst &#13;\nmaintaining the electrical characteristics. This should &#13;\nenable closer stacking of QD layers leading to higher gain and improved laser performance.
Locant (2017)

IUPAC recommendations on source-based nomenclature for single-strand polymers have so far addressed its application mainly to copolymers, non-linear polymers and polymer assemblies, and within generic source-based nomenclature of polymers. In this document, rules are formulated for devising a satisfactory source-based name for a polymer, whether homopolymer or copolymer, which are as clear and rigorous as possible. Thus, the source-based system for naming polymers is presented in a totality that serves as a user-friendly alternative to the structure-based system of polymer nomenclature. In addition, because of their widespread and established use, recommendations for the use of traditional names of polymers are also elaborated.