gebhart/patrepeval huggingface dataset:
Signaling pathways in early cardiac development (2010)

Cardiomyocyte differentiation is a complex multistep process requiring the proper temporal and spatial integration of multiple signaling pathways. Previous embryological and genetic studies have identified a number of signaling pathways that are critical to mediate the initial formation of the mesoderm and its allocation to the cardiomyocyte lineage. It has become clear that some of these signaling networks work autonomously, in differentiating myocardial cells whereas others work non-autonomously, in neighboring tissues, to regulate cardiac differentiation indirectly. Here, we provide an overview of three signaling networks that mediate cardiomyocyte specification and review recent insights into their specific roles in heart development. In addition, we demonstrate how systems level, 'omic approaches' and other high-throughput techniques such as small molecules screens are beginning to impact our understanding of cardiomyocyte specification and, to identify novel signaling pathways involved in this process. In particular, it now seems clear that at least one chemokine receptor CXCR4 is an important marker for cardiomyocyte progenitors and may play a functional role in their differentiation. Finally, we discuss some gaps in our current understanding of early lineage selection that could be addressed by various types of omic analysis.
Partial Discharge Signatures of Defects in Insulation Systems Consisting of Oil and Oil-impregnated Paper (2012)

Partial discharge measurement is a common method for monitoring and diagnostics of power transformers, and can detect insulation malfunctions before they lead to failure. Different parameters extra ...
CRS5 encodes a metallothionein-like protein in Saccharomyces cerevisiae. (1994)

Protection from copper toxicity in the bakers' yeast Saccharomyces cerevisiae involves the action of a copper binding metallothionein encoded by the CUP1 locus. To identify additional factors contributing to copper ion homeostasis and detoxification, we screened a genomic library for genes that confer high levels of copper resistance to yeast strains lacking CUP1. This screen led to the identification of the CRS5 (copper-resistant suppressor) gene. By sequence analyses, CRS5 encodes a small molecular weight cysteine-rich protein with an amino acid sequence bearing all the features of a eukaryotic metallothionein. The CRS5 polypeptide exhibits a striking similarity to a number of mammalian and invertebrate metallothioneins, yet shares surprisingly little homology with CUP1. In yeast, CRS5 is expressed as a 0.5-kilobase mRNA that is regulated both by copper ions and by oxidative stress, and expression is dependent upon ACE1, a copper and DNA binding transcription factor also known to regulate CUP1. Deletion of the chromosomal CRS5 locus was found to increase cellular sensitivity to copper, but not cadmium, toxicity. These studies support an important role for the CRS5 metallothionein-like protein in copper homeostasis and detoxification.
Morphologic Changes in the Peritoneal Membrane of Patients with Renal Disease (2002)

This study examined the morphologic features of the parietal peritoneal membranes of 130 patients undergoing peritoneal dialysis (PD) and compared them with the features of the peritoneal membranes of normal individuals, uremic predialysis patients, and patients undergoing hemodialysis. The median thickness of the submesothelial compact collagenous zone was 50 microm for normal subjects, 140 microm for uremic patients, 150 microm for patients undergoing hemodialysis, and 270 microm for patients undergoing PD (P < 0.001 for all versus normal subjects). Compact zone thickness increased significantly with the duration of PD therapy [0 to 24 mo, 180 microm (n = 58); 25 to 48 mo, 240 microm (n = 24); 49 to 72 mo, 300 microm (n = 13); 73 to 96 mo, 750 microm (n = 16); >97 mo, 700 microm (n = 19)]. Vascular changes included progressive subendothelial hyalinization, with luminal narrowing or obliteration. These changes were absent in samples from normal subjects but were present in 28% of samples from uremic patients and 56% of biopsies from patients undergoing PD. In the PD group, the prevalence of vasculopathy increased significantly with therapy duration (P = 0.0001). The density of blood vessels per unit length of peritoneum was significantly higher for patients with membrane failure and was correlated with the degree of fibrosis (P = 0.01). For the first time, a comprehensive cross-sectional analysis of the morphologic changes in the peritoneal membranes of patients undergoing PD is provided. The infrequency of fibrosis in the absence of vasculopathy suggests that vasculopathy may predispose patients to the development of fibrosis. This study provides a sufficiently large cohort of samples to allow structure-function relationships to be established, as well as providing a repository of tissue for further studies.
SCANMail (2001)

This paper describes SCANMail, a system that allows users to browse and search their voicemail messages by content through a GUI. Content based navigation is realized by use of automatic speech recognition, information retrieval, information extraction and human computer interaction technology. In addition to the browsing and querying functionalities, acoustics-based caller ID technology is used to proposes caller names from existing caller acoustic models trained from user feedback. The GUI browser also provides a note-taking capability. Comparing SCANMail to a regular voicemail interface in a user study, SCANMail performed better both in terms of objective (time to and quality of solutions) as well as subjective objectives.
Characteristics of charged networks under an electric stimulus (1994)

Abstract The electrokinetic phenomena of poly(2‐acrylamido‐2‐methyl‐1‐propane sulfonic acid‐co‐ n ‐butylmethacrylate) were examined to investigate physical changes of the gel under an applied electric current. When an electrical stimulus was applied to a piece of the gel, without being in contact with an electrode, reversible gel bending was observed. The bending degree was directly proportional to the intensity of the applied electric stimulus. This was explained by ‘depletion polarization’ of ionic species under the stimulus. The swelling of the gel surface facing the anode increased, due to the decreased ionic strength of the boundary layer upon electric stimulation, while gel shrinking occurred at the cathode. When the gel is in direct contact with electrodes, deswelling of the gel was observed at the anode side, while water seepage occurred at the cathode side. This observation was attributed to the electro‐osmosis inside the gel, combined with local pH changes around the electrodes resulting from electrochemical reactions, particularly water electrolysis. © 1994 John Wiley & Sons, Inc.
Low Concentrations of Trifluoperazine Arrest the Cell Division Cycle of Saccharomyces cerevisiae at Two Specific Stages (1988)

Low concentrations of trifluoperazine (TFP) reversibly inhibited vegetative growth of Saccharomyces cerevisiae. The cell cycle was analysed by flow cytometry using haploid a cells synchronized by alpha-factor arrest and several temperature-sensitive cell division cycle mutants (cdc). Cells were pulse-labelled with fluorescein-labelled concanavalin A (ConA-FITC) to determine cell division or stained with propidium iodide to determine the stage of cell cycle arrest by TFP. Cell growth was estimated from the changes in the relative intensity of scattered light, and budding was determined microscopically. When TFP was added before Start on release from alpha-factor arrest, after release of cdc28-arrested cells, and at transition from stationary phase to vegetative growth, cell growth, budding and DNA synthesis were inhibited. When TFP was added after execution of spindle pole body duplication, cell growth, bud emergence and DNA synthesis were not inhibited but cell division was inhibited and the cells arrested with buds at G2M Using cdc mutants, the second stage of arrest by TFP was determined to be just before medial-nuclear division.
The Zincke Reaction (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Towards an Integration of Low-Level Timing Analysis and Model-Based Code Generation (2006)

Software developers in the automotive sector must achieve high quality objectives. Many design and implementation errors are avoided by synthesizing code from model-based software specifications using automatic code generators such as ETAS' ASCET. To verify non-functional properties of the implementation, model-based design processes should be complemented with static program analysis tools like Abslnt's StackAnalyzer and timing analyzer aiT. ASCET, StackAnalyzer and aiT can be integrated in a way that the analysis results for code generated by ASCET are conveniently accessible from within the ASCET development environment. This gives ASCET users a direct feedback on the effects of their design decisions on resource usage, allowing to select more efficient designs and implementation methods. In the paper, we present the tools, the experimental integration, preliminary results and plans for further tool integration.
Melanoma patient-derived xenografts accurately model the disease and develop fast enough to guide treatment decisions (2014)

// Berglind O. Einarsdottir 1,4 , Roger Olofsson Bagge 1,4 , Joydeep Bhadury 1,4 , Henrik Jespersen 2,4 , Jan Mattsson 1,4 , Lisa M. Nilsson 1,4 , Katarina Truvé 5 , Marcela Dávila López 4,5 , Peter Naredi 1,4 , Ola Nilsson 3,4 , Ulrika Stierner 2,4 , Lars Ny 2,4 and Jonas A. Nilsson 1,4 1 Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden 2 Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden 3 Department of Biomedicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden 4 Sahlgrenska Translational Melanoma Group at the Sahlgrenska Cancer Center, Gothenburg, Sweden 5 The Bioinformatics Core Facility at the University of Gothenburg, Gothenburg, Sweden Correspondence: Jonas Nilsson, email: // Keywords : melanoma, mouse models, patient-derived xenografts Received : August 18, 2014 Accepted : September 07, 2014 Published : September 08, 2014 Abstract The development of novel therapies against melanoma would benefit from individualized tumor models to ensure the rapid and accurate identification of biomarkers of therapy response. Previous studies have suggested that patient-derived xenografts (PDXes) could be useful. However, the utility of PDXes in guiding real-time treatment decisions has only been reported in anecdotal forms. Here tumor biopsies from patients with stage III and IV metastatic malignant melanoma were transplanted into immunocompromised mice to generate PDXes. 23/26 melanoma biopsies generated serially transplantable PDX models, and their histology, mutation status and expression profile resembled their corresponding patient biopsy. The potential treatment for one patient was revealed by an in vitro drug screen and treating PDXes with the MEK inhibitor trametinib. In another patient, the BRAF mutation predicted the response of both the patient and its corresponding PDXes to MAPK-targeted therapy. Importantly, in this unselected group of patients, the time from biopsy for generation of PDXes until death was significantly longer than the time required to reach the treatment phase of the PDXes. Thus, it could be clinically meaningful to use this type of platform for melanoma patients as a pre-selection tool in clinical trials.
Progress and pitfalls: bipolar molecular linkage studies (1998)

This paper reviews the history of molecular genetic linkage studies of bipolar disorder. The topic is introduced with a brief discussion of various genetic concepts, including linkage, lod scores and non-parametric statistics. It is emphasized that criteria for declaring linkage must include independent confirmation by a second group of investigators. Given that the inherited susceptibility for bipolar disorder is most likely explained by multiple genes of small effect, simulations indicate that universal confirmation of valid linkages cannot be expected. With this background, several valid linkages of BP disorder to genomic regions are reviewed. These valid linkages include 18p11, 18q22, 21q21, Xq26 and 4pter. The issue of anticipation and expanding triplet repeats is discussed. Finally, there is a brief section on recommendations for future genetic linkage studies of bipolar disorder.
Frequency and impact of autosomal dominant polycystic kidney disease in the Seychelles (Indian Ocean) (1997)

In the Seychelles, ADPKD clusters in the Caucasian population (possibly a founder effect), is rare in individuals of black descent, and is associated with substantial clinical and survival impact.
Active‐site mobility in human immunodeficiency virus, type 1, protease as demonstrated by crystal structure of A28S mutant (1998)

The mutation Ala28 to serine in human immunodeficiency virus, type 1, (HIV-1) protease introduces putative hydrogen bonds to each active-site carboxyl group. These hydrogen bonds are ubiquitous in pepsin-like eukaryotic aspartic proteases. In order to understand the significance of this difference between HIV-1 protease and homologous, eukaryotic aspartic proteases, we solved the three-dimensional structure of A28S mutant HIV-1 protease in complex with a peptidic inhibitor U-89360E. The structure has been determined to 2.0 A resolution with an R factor of 0.194. Comparison of the mutant enzyme structure with that of the wild-type HIV-1 protease bound to the same inhibitor (Hong L, Treharne A, Hartsuck JA, Foundling S, Tang J, 1996, Biochemistry 35:10627-10633) revealed double occupancy for the Ser28 hydroxyl group, which forms a hydrogen bond either to one of the oxygen atoms of the active-site carboxyl or to the carbonyl oxygen of Asp30. We also observed marked changes in orientation of the Asp25 catalytic carboxyl groups, presumably caused by the new hydrogen bonds. These observations suggest that catalytic aspartyl groups of HIV-1 protease have significant conformational flexibility unseen in eukaryotic aspartic proteases. This difference may provide an explanation for some unique catalytic properties of HIV-1 protease.
Intron-3 Retention/Splicing Controls Neuronal Expression of Apolipoprotein E in the CNS (2008)

Neuronal expression of apolipoprotein (apo) E4 may contribute to the pathogenesis of Alzheimer's disease (AD). In studying how apoE expression is regulated in neurons, we identified a splicing variant of apoE mRNA with intron-3 retention (apoE-I3). ApoE-I3 mRNA was detected in neuronal cell lines and primary neurons, but not in astrocytic cell lines or primary astrocytes, from humans and mice by reverse transcription (RT)-PCR. In both wild-type and human apoE knock-in mice, apoE-I3 was found predominantly in cortical and hippocampal neurons by in situ hybridization. Cell fractionation and quantitative RT-PCR revealed that over 98% of the apoE-I3 mRNA was retained in the nucleus without protein translation. In transfected primary neurons, apoE expression increased dramatically when intron-3 was deleted from a genomic DNA construct and decreased markedly when intron-3 was inserted into a cDNA construct, suggesting that intron-3 retention/splicing controls apoE expression in neurons. In response to excitotoxic challenge, the apoE-I3 mRNA was markedly increased in morphologically normal hippocampal neurons but reduced in degenerating hippocampal neurons in mice; apoE mRNA showed the opposite pattern. This apparent precursor-product relationship between apoE-I3 and apoE mRNA was supported by a transcriptional inhibition study. Thus, neuronal expression of apoE is controlled by transcription of apoE-I3 under normal conditions and by processing of apoE-I3 into mature apoE mRNA in response to injury.
Transplantation of ventral mesencephalic anlagen to hosts with genetic nigrostriatal dopamine deficiency. (1986)

Attempts to reconstruct the damaged nigrostriatal pathway in experimental models of Parkinson disease have thus far been carried out in animals with neurotoxically induced dopamine deficiency. The present study establishes the weaver (wv/wv) mutant mouse as a genetic model of chronic striatal dopamine denervation by demonstrating a marked decrease of tyrosine hydroxylase-immunoreactive neurons in the substantia nigra pars compacta. Moreover, grafts of embryonic ventral mesencephalon taken from genetically normal mice and transplanted into the lateral ventricle of adult weaver mutants can survive and grow in the mutant host environment, express tyrosine hydroxylase immunoreactivity, and reinnervate the target regions of the recipient. These results provide evidence of integration of graft and host tissue and suggest that transplantation of dopamine neurons may be effectively applied to overcome nigrostriatal degeneration of genetic etiology.
Soft Cold EI – approaching molecular ion only with electron ionization (2015)

It was found that an increased nozzle-skimmer distance resulted in a noticeable increase in the abundance ratio of molecular ions to low mass fragment ions. Consequently, Cold EI at low electron energies and a large nozzle-skimmer distance converts EI into Soft Cold EI while further approaching the ideal of a molecular ion only ionization method.
42.1: <i>Invited Paper</i> : Improved Amorphous In‐Ga‐Zn‐O TFTs (2008)

Abstract We review the features of amorphous In‐Ga‐Zn‐O (a‐IGZO) thin‐film transistors (TFTs), as well as circuit operation based on these TFTs. We also report a novel TFT structure which improves environmental stability of the TFT operation by taking full advantage of the a‐IGZO properties, where a conventional PECVD a‐SiN X :H films serve not only as an effective barrier layer but also as a hydrogen source to form the coplanar source and drain.
Three-level neodymium fiber laser incorporating photonic bandgap fiber (2006)

We report a neodymium fiber laser incorporating an all-solid photonic bandgap fiber to suppress the four-level laser transition 4F(3/2)-4I(11/2). We demonstrate lasing at 907 nm on the three-level transition 4F(3/2)-4I(9/2) when pumping at 808 nm. The maximum slope efficiency obtained was 32% with a threshold pump power of 70 mW.
Modeling and Control of a Low-Speed Flywheel Driving System for Pulsed-Load Mitigation in DC Distribution Networks (2016)

This paper details the modeling and development of an improved controller design for a dc flywheel energy storage system (FESS) driving circuit. The driving system is based on a bidirectional buck-boost converter. The modeling of this converter including the parasitic resistances for all the components was carried out. In this model, the equivalent circuit of the machine was integrated in the converter state-space model for improved accuracy and controllability. The system has two operating modes; when the FESS is charging, the converter operates in the buck mode. A controller was designed to regulate the charging rate through controlling the machine's terminal voltage. In the discharging mode, the converter operates in the boost mode. A current controller takes over to control the injected current from the machine to the dc bus. The detailed design of both control loops was identified. Simulation results show the accuracy of the derived model and the enhanced performance of the FESS. Further, it is shown that the reversal of power-flow direction was performed seamlessly. A hardware prototype of the converter was implemented and the effectiveness of the developed system was experimentally verified. The experimental results are in excellent agreement with the simulation.
Lessons Learned from Implementing a Privacy-Preserving Smart Contract in Ethereum (2018)

Real-world smart contracts which preserve the privacy of both, their users and their data, have barely been proposed theoretically, let alone been implemented practically. In this paper, we are the first to implement a privacy-preserving protocol from the energy domain as a smart contract in Ethereum. We elaborate on and present our implementation as well as our practical findings, including more or less subtle traps and pitfalls. Despite major optimizations to our implementation, we find that while it is currently possible, it is not feasible to implement a privacy-preserving protocol of modest complexity in the Ethereum blockchain due to the high cost of operation and the lack of privacy by design.
Effects of cryopreservation on adipose tissue‐derived microvascular fragments (2017)

Adipose tissue-derived microvascular fragments (ad-MVF) are effective vascularization units for tissue engineering. They rapidly reassemble into new microvascular networks after seeding on scaffolds and subsequent in vivo implantation. Herein, we analyzed whether the vascularization capacity of ad-MVF is affected by cryopreservation. Ad-MVF were isolated from the epididymal fat pads of C57BL/6 mice and cryopreserved for 7 days to compare their morphology, viability, cellular composition, and protein expression with freshly isolated control ad-MVF. Moreover, cryopreserved and control ad-MVF from green fluorescent protein (GFP)<sup>+</sup> donor mice were seeded on collagen-glycosaminoglycan matrices (Integra<sup>®</sup> ), which were implanted into dorsal skinfold chambers of GFP<sup>-</sup> recipient animals to study their vascularization and incorporation using intravital fluorescence microscopy, histology, and immunohistochemistry. Cryopreservation of ad-MVF did not affect vessel morphology and cellular composition. However, cryopreservation was associated with an increased rate of necrotic cells and a significantly reduced number of transplantable ad-MVF. This was compensated by a higher angiogenic activity of the remaining ad-MVF, as indicated by significantly elevated expression levels of pro-angiogenic factors when compared to controls. Accordingly, cryopreserved and control ad-MVF induced a comparable vascularization and incorporation of implanted Integra<sup>®</sup> without differences in microvascular network formation, maturation, and remodeling. Enhanced angiogenic sprouting even resulted in a higher fraction of GFP<sup>+</sup> microvessels within the implants of the cryopreservation group. These findings indicate that cryopreservation of ad-MVF is feasible and, thus, offers the exciting opportunity to build up stocks of readily available vascularization units for future tissue engineering applications.
Lead Time and Overdiagnosis in Prostate-Specific Antigen Screening: Importance of Methods and Context (2009)

The precise definition and the population used to estimate lead time and overdiagnosis can be important drivers of study results and should be clearly specified.
Normal Germ Line Establishment in Mice Carrying a Deletion of the <i>Ifitm/Fragilis</i> Gene Family Cluster (2008)

The family of interferon-inducible transmembrane proteins (Ifitm) consists of five highly sequence-related cell surface proteins, which are implicated in diverse cellular processes. Ifitm genes are conserved, widely expressed, and characteristically found in genomic clusters, such as the 67-kb Ifitm family locus on mouse chromosome 7. Recently, Ifitm1 and Ifitm3 have been suggested to mediate migration of early primordial germ cells (PGCs), a process that is little understood. To investigate Ifitm function during germ cell development, we used targeted chromosome engineering to generate mutants which either lack the entire Ifitm locus or carry a disrupted Ifitm3 gene only. Here we show that the mutations have no detectable effects on development of the germ line or on the generation of live young. Hence, contrary to previous reports, Ifitm genes are not essential for PGC migration. The Ifitm family is a striking example of a conserved gene cluster which appears to be functionally redundant during development.