gebhart/patrepeval huggingface dataset:
Selective Generation of Dopaminergic Precursors from Mouse Fibroblasts by Direct Lineage Conversion (2015)

Degeneration of midbrain dopaminergic (DA) neurons is a key pathological event of Parkinson's disease (PD). Limited adult dopaminergic neurogenesis has led to novel therapeutic strategies such as transplantation of dopaminergic precursors (DPs). However, this strategy is currently restrained by a lack of cell source, the tendency for the DPs to become a glial-restricted state, and the tumor formation after transplantation. Here, we demonstrate the direct conversion of mouse fibroblasts into induced DPs (iDPs) by ectopic expression of Brn2, Sox2 and Foxa2. Besides expression with neural progenitor markers and midbrain genes including Corin, Otx2 and Lmx1a, the iDPs were restricted to dopaminergic neuronal lineage upon differentiation. After transplantation into MPTP-lesioned mice, iDPs differentiated into DA neurons, functionally alleviated the motor deficits, and reduced the loss of striatal DA neuronal axonal termini. Importantly, no iDPs-derived astrocytes and neoplasia were detected in mouse brains after transplantation. We propose that the iDPs from direct reprogramming provides a safe and efficient cell source for PD treatment.
Characteristics of minute T1 colorectal cancer in relevance to pathology and treatment (2020)

Minute T1 CRC is significantly associated with flat type, right-sided cancers, as well as with the absence of BGA and LNM. These results suggested the minute T1 CRC lesions are often aggressive and are likely to be missed during colonoscopy.
High Accuracy Tracking Control Based on Trajectory Prediction (2003)

In this paper, we address the problem of predicting the trajectory of the moving target, in order to compensate the time delay. The goal is to achieve the high accuracy tracking control in visual servo system. Since the dynamics of the target are assumed to be unknown, based on the available information on the target polynomial trend model is constructed to predict the future position on the target. The well-known least squares method is used to estimate the model parameters. We propose the method for real-time selecting the optimal order. To demonstrate the effectiveness of the prediction, real-time experiments in the system consist of 3 DOF manipulator and fixed stereovision configuration are presented. As a result, by predicting the trajectory of target using the proposal technique showed that a tracking error decreased.
Laparoscopic Radical Prostatectomy in the Canine Model (1996)

The purpose of this study was to determine the feasibility of performing laparoscopic radical prostatectomy in a canine model. Laparoscopic radical prostatectomy was performed on six adult male canines. A new endoscopic needle driver was used to construct a secure vesicourethral anastomosis. Average operative time required to complete the procedure was 304 min (range 270-345 min). Dissection of the prostate gland took an average of 67 min (range 35-90 min), and construction of the vesicourethral anastomosis took 154 min (rage 80-240 min). There were no intraoperative complications and only one postoperative complication (anastomotic leak). Five of the six animals recovered uneventfully from the procedure, and their foley catheters were removed 10-14 days postoperatively after a retrograde cystourethrogram demonstrated an intact vesicourethral anastomosis. Four (80%) of the surviving animals were clinically continent within 10 days after catheter removal. Post mortem examination confirmed that the vesicourethral anastomosis was intact with no evidence of urine extravasation. These data demonstrate the feasibility of laparoscopic radical prostatectomy in a canine model, and suggest that additional work with this technique should be continued to develop its potential clinical application.
Transparent amorphous oxide semiconductors: Materials design, electronic structure, and device applications (2017)

In 1995, I presented a materials design concept for transparent amorphous oxide semiconductors with a large electron mobility (TAOS) at the 16' <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">h</sup> International conference on amorphous semiconductors along with concrete example materials of TAOS and the paper was published in 1996 [1[. The basic concept of TAOS is that large electron mobility should be retained even in amorphous materials if the conduction band minimum is mainly composed of spatially large spread of metal ns-orbitals. <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> The validity of this design concept was demonstrated by analysis of electronic structure using photoemission experiments combined with calculations based on X-ray structural analysis[2].
Single-Tube Method for Nucleic Acid Extraction, Amplification, Purification, and Sequencing (2004)

A single-tube nucleic acid extraction-to-sequencing method, which requires less time and labor than conventional methods, generates HCV sequence data that are equivalent to conventional methods and can be used to genotype HCV.
Evaluation of Various Electrode Materials for Detection of Oxidized Low-Density Lipoproteins (2013)

Measurement of oxidized low-density lipoprotein (LDL) generated by oxidative stress of various kinds might be useful for evaluating the risk of cardiovascular disease. We evaluated some electrode materials to detect oxidized LDL electrochemically. Some carbon nanotube dispersions were studied as electrode materials. Native LDL was isolated from normal human serum using ultracentrifugation. Oxidized LDL was prepared by treating the native LDL with CuSO4. Electrodes were fabricated by depositing the nanotube dispersion on a gold electrode, with subsequent drying. The potential change of the electrode against a reference electrode was monitored before and after adding native LDL or oxidized LDL. Only acid-treated carbon nanotubes were able to discriminate both LDL preparations, perhaps because of the carboxylic acid groups introduced on the nanotube by acid treatment.
Inhibitory effect of dihydroxyacetone onGluconobacter oxydans: Kinetic aspects and expression by mathematical equations (1993)

Microbial conversion of glycerol into dihydroxyacetone (DHA) by Gluconobacter oxydans was subjected to inhibition by excess substrate. Comparison of cultures containing increasing initial DHA contents (0 to 100 g 1 1) demonstrated that DHA also inhibited this fermentation process. The first effect was on bacterial growth (cellular development stopped when DHA concentration reached 67 g I-1), and then on oxidation of glycerol (DHA synthesis only occurred when the DHA concentration in the culture medium was lower than 85 g 1-1). Productivity, specific rates and, to a lesser extent, conversion yields decreased as initial concentrations of DHA increased. The changes in the specific parameters according to increasing initial DHA contents were described by general equations. These formulae satisfactorily express the concave aspect of the curves and the reduction in biological activity when the cells were in contact with DHA concentrations of up to 96 g 1-1.
Potent Nonpeptide Antagonists of the Bradykinin B1 Receptor:  Structure−Activity Relationship Studies with Novel Diaminochroman Carboxamides (2007)

The bradykinin B1 receptor is induced following tissue injury and/or inflammation. Antagonists of this receptor have been studied as promising candidates for treatment of chronic pain. We have identified aryl sulfonamides containing a chiral chroman diamine moiety that are potent antagonists of the human B1 receptor. Our previously communicated lead, compound 2, served as a proof-of-concept molecule, but suffered from poor pharmacokinetic properties. With guidance from metabolic profiling, we performed structure-activity relationship studies and have identified potent analogs of 2. Variation of the sulfonamide moiety revealed a preference for 3- and 3,4-disubstituted aryl sulfonamides, while bulky secondary and tertiary amines were preferred at the benzylic amine position for potency at the B1 receptor. Modifying the beta-amino acid core of the molecule lead to the discovery of highly potent compounds with improved in vitro pharmacokinetic properties. The most potent analog at the human receptor, compound 38, was also active in a rabbit B1 receptor cellular assay. Furthermore, compound 38 displayed in vivo activity in two rabbit models, a pharmacodynamic model with a blood pressure readout and an efficacy model of inflammatory pain.
Consistent causal effect estimation under dual misspecification and implications for confounder selection procedures (2012)

In a previously published article in this journal, Vansteeland et al. [Stat Methods Med Res. Epub ahead of print 12 November 2010. DOI: 10.1177/0962280210387717] address confounder selection in the context of causal effect estimation in observational studies. They discuss several selection strategies and propose a procedure whose performance is guided by the quality of the exposure effect estimator. The authors note that when a particular linearity condition is met, consistent estimation of the target parameter can be achieved even under dual misspecification of models for the association of confounders with exposure and outcome and demonstrate the performance of their procedure relative to other estimators when this condition holds. Our earlier published work on collaborative targeted minimum loss based learning provides a general theoretical framework for effective confounder selection that explains the findings of Vansteelandt et al. and underscores the appropriateness of their suggestions that a confounder selection procedure should be concerned with directly targeting the quality of the estimate and that desirable estimators produce valid confidence intervals and are robust to dual misspecification.
3D stacking cobalt and nickel microbumps and kinetics of corresponding IMCs at low temperatures (2017)

To improve the performance of 3D electronic chips, dense I/O and interconnects are required. Increasing the density of interconnects requires smaller pitch micro-bumps. However, when scaling down microbumps several challenges have to be taken into account. Lithography of dense and high aspect ratio bump, wet etching of seed and barrier layer, solder volume and intermetallics (IMC) formation are some of the challenges that needs to be addressed. With reducing bump dimensions, solder volume decreases as well, converting Sn to complete IMC during the Thermo-Compression-Bonding (TCB) process. Full IMC formation increases stress in the joint, leading to crack formation and a brittle connection. Beside concerns about the IMC layer, the UBM (under bump metallization) consumption by the solder has to be addressed as well. Therefore, it is important to select the right UBM and solder to have enough Sn and UBM left in the joint for the time the product is working at a specific temperature. In this paper, the kinetics and solid state inter-diffusion behavior of the intermetallic compound is studied at temperatures below 180 °C for Cu, Co and Ni as UBM, ECD Ni, ELD Cu and ELD NiB as diffusion barriers, and Sn as solder. For this study, wafers with 50 μm diameter pillar structures, were aged at 3 different temperatures (80, 100 and 120°C) for 6 weeks. The IMC thickness was measured before and after aging, and IMC growth rate parameters like activation energy, power factor and inter-diffusion coefficient were extracted.
Molecular probes for two-photon excited fluorescence and second harmonic generation imaging of biological membranes (2002)

Novel microscopies based on nonlinear optical (NLO) phenomena are attracting increasing interest in the biology community owing to their potentialities in the area of real-time, non-damaging imaging of biological systems. In particular, second-harmonic generation (SHG) and two-photon excited fluorescence (TPEF) are NLO phenomena that scale with excitation intensity squared, and thus give rise to an intrinsic 3-dimensional resolution when used in microscopic imaging. In this perspective, we have implemented a molecular engineering approach toward NLO-probes specifically designed for SHG and/or TPEF imaging of cellular membranes. We have designed nanoscale rod-like fluorophores showing very large TPEF cross-sections in the visible red, outperforming standard fluorophores such as fluorescein by up to two orders of magnitude. Bolaamphiphilic derivatives combining high TPEF cross-sections and affinity for cellular membranes were prepared. Their incorporation into model or cell membranes can be monitored by TPEF microscopy. Amphiphilic push-pull chromophores showing both high TPA and SHG cross-sections in the near-IR region were designed as NLO-probes for imaging of biological membranes by simultaneous SHG and TPEF microscopy. These NLO-phores offer intriguing potentialities for imaging of fundamental biological processes such as adhesion, fusion or for reporting of membrane electrical potentials.
Primary Structure of the Human Platelet Serotonin Uptake Site: Identity with the Brain Serotonin Transporter (1993)

A cDNA encoding the human platelet serotonin (5-HT) uptake site was isolated and sequenced using the PCR. The cDNA represents a approximately 3.1-kb mRNA transcript and contains an open reading frame encoding a hydrophobic polypeptide of 630 amino acids with 12 membrane-spanning segments, a calculated molecular mass of 70,320 Da, and an estimated isoelectrical point of 5.84. The human platelet 5-HT uptake site is identical with the human brain 5-HT transporter and approximately 92% homologous to the rat protein. Hydropathicity analysis indicates 12 membrane-spanning segments with two putative glycosylation sites within the second extracellular loop. The human platelet 5-HT uptake site contains two intraplasmatic consensus phosphorylation sites for cyclic AMP-dependent protein kinase recognition located in the cytoplasmatic N-terminal region and three potential protein kinase C phosphorylation sites. The identity of the human platelet 5-HT uptake site and the brain 5-HT transporter indicates that both proteins are encoded by the same single-copy gene, which has been assigned to the human chromosome 17. Our findings are likely to facilitate molecular pharmacologic and genetic investigations of the 5-HT transporter in psychiatric disorders.
Polymorphism of DNA/Multi-cationic Lipid Complexes Driven by Temperature and Salts (2001)

The structural polymorphism of DNA/lipopolyamine (multi-cationic lipid) complexes has been studied by X-ray diffraction and cryo-electron microscopy. Monovalent salt and temperature effects have been analyzed. Depending on the treatment applied to the lipidic solution prior to DNA addition, two types of structure can be obtained for identical final conditions: a classical lamellar structure and a more complex structure. The latter was shown to appear when the lipidic solution prepared in high salt condition is vortexed and quenched below the hydrocarbon chain melting temperature, before addition to the DNA solution. It corresponds to some small facetted vesicles. Similar behavior is observed for the poly(styrene-sulfonate)/lipid system.
High Risk Population Isolate Reveals Low Frequency Variants Predisposing to Intracranial Aneurysms (2014)

3% of the population develops saccular intracranial aneurysms (sIAs), a complex trait, with a sporadic and a familial form. Subarachnoid hemorrhage from sIA (sIA-SAH) is a devastating form of stroke. Certain rare genetic variants are enriched in the Finns, a population isolate with a small founder population and bottleneck events. As the sIA-SAH incidence in Finland is &amp;gt;2× increased, such variants may associate with sIA in the Finnish population. We tested 9.4 million variants for association in 760 Finnish sIA patients (enriched for familial sIA), and in 2,513 matched controls with case-control status and with the number of sIAs. The most promising loci (p&amp;lt;5E-6) were replicated in 858 Finnish sIA patients and 4,048 controls. The frequencies and effect sizes of the replicated variants were compared to a continental European population using 717 Dutch cases and 3,004 controls. We discovered four new high-risk loci with low frequency lead variants. Three were associated with the case-control status: 2q23.3 (MAF 2.1%, OR 1.89, p 1.42×10-9); 5q31.3 (MAF 2.7%, OR 1.66, p 3.17×10-8); 6q24.2 (MAF 2.6%, OR 1.87, p 1.87×10-11) and one with the number of sIAs: 7p22.1 (MAF 3.3%, RR 1.59, p 6.08×-9). Two of the associations (5q31.3, 6q24.2) replicated in the Dutch sample. The 7p22.1 locus was strongly differentiated; the lead variant was more frequent in Finland (4.6%) than in the Netherlands (0.3%). Additionally, we replicated a previously inconclusive locus on 2q33.1 in all samples tested (OR 1.27, p 1.87×10-12). The five loci explain 2.1% of the sIA heritability in Finland, and may relate to, but not explain, the increased incidence of sIA-SAH in Finland. This study illustrates the utility of population isolates, familial enrichment, dense genotype imputation and alternate phenotyping in search for variants associated with complex diseases.
Towards Compliance to Safety Objectives Using Data Curation (2023)

Summary and ConclusionsThis paper presents a methodology to show compliance to safety objectives using a new data curation system called RACK. First, we use a bowtie diagram as a lightweight safety analysis to demonstrate the connection between safety assessment and software development process. Once an assurance level is properly assigned, we use a Python script to highlight which DO-178C objectives we are obligated to show compliance to. Next, we present the use of RACK—Rapid Assurance Curation Kit—to find evidence in each of the software development processes. Finally, we present a novel way to concisely visualize traceability and status of compliance to DO-178C objectives via a sunburst. Our finding is that provenance language is embedded in DO-178C and their referenced activities. This makes RACK suitable for demonstrating compliance since its underlying data model is built on provenance classes and relationships. In summary, this paper presents a methodology that automatically generates a visualization to show compliance to DO-178C objectives using RACK to query for evidence that an activity was completed.
272 Long-term monitoring of trait-like characteristics of the sleep electroencephalogram using ear-EEG (2021)

Abstract Introduction Wearable electroencephalogram (EEG) monitoring has a remarkable potential, it is safe, scalable and can track neural signatures for long periods. One such signature is the power spectra of non-rapid-eye-movement (NREM) sleep which has been shown to demonstrate a trait-like characteristic. Changes in personalized signatures has been associated with biomarkers of Alzheimer’s disease and is of great interest for early detection and clinical management. This work investigates monitoring of signatures using a wearable device that records EEG from the ear (ear-EEG) and compares the intra- and inter-individual similarity of the neural signatures with that from central scalp-EEG. Methods We initiated a two phased in-home study, monitoring 20 subjects for 4 nights (A), followed by a delayed but continued monitoring of 10 subjects for 12 nights (B). In A, subjects wore a dry-electrode ear-EEG system and a partial PSG, in B the subjects wore only the ear-EEG system. Subjects were instructed to follow their usual time schedule and lifestyle. Sleep stages were scored manually according to AASM in A and automatically in B. The grand average power spectra of NREM2 sleep were computed and log-transformed prior to calculating the cosine similarity for determination of the intra- and inter-individual similarity. Results The ear-EEG and scalp-EEG analysis showed that mean intra-individual similarity was higher than mean inter-individual similarity. Permutation tests indicate that the observed mean difference is statistically significant p&amp;lt;0.01 for both montages. Comparing the distributions of intra-individual similarities for ear-EEG and scalp-EEG, the observed mean difference is statistically significant p&amp;lt;0.05, in favor of a more stable ear-EEG signature. Comparing ear-EEG signatures between A and B, considering nights from A as reference, all subjects from B were most similar with its own reference signature. Considering signatures from individual nights the accuracy paring subjects from A and B were 88% correct. Conclusion Nocturnal ear-EEG measures trait-like characteristics as reliable as scalp-EEG. The neural signature is stable over time within healthy subjects and demonstrated its ability as a personalized signature. Support (if any):
Synthetic studies on polyether antibiotics. 4. Total synthesis of monensin. 1. Stereocontrolled synthesis of the left half of monensin (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthetic studies on polyether antibiotics. 4. Total synthesis of monensin. 1. Stereocontrolled synthesis of the left half of monensinG. Schmid, T. Fukuyama, K. Akasaka, and Y. KishiCite this: J. Am. Chem. Soc. 1979, 101, 1, 259–260Publication Date (Print):January 1, 1979Publication History Published online1 May 2002Published inissue 1 January 1979https://pubs.acs.org/doi/10.1021/ja00495a064https://doi.org/10.1021/ja00495a064research-articleACS PublicationsRequest reuse permissionsArticle Views4130Altmetric-Citations155LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Secreted Aspartic Proteinase Family of Candida tropicalis (2001)

Medically important yeasts of the genus Candida secrete aspartic proteinases (Saps), which are of particular interest as virulence factors. Like Candida albicans, Candida tropicalis secretes in vitro one dominant Sap (Sapt1p) in a medium containing bovine serum albumin (BSA) as the sole source of nitrogen. Using the gene SAPT1 as a probe and under low-stringency hybridization conditions, three new closely related gene sequences, SAPT2 to SAPT4, encoding secreted proteinases were cloned from a C. tropicalis lambdaEMBL3 genomic library. All bands identified by Southern blotting of EcoRI-digested C. tropicalis genomic DNA with SAPT1 could be assigned to a specific SAP gene. Therefore, the SAPT gene family of C. tropicalis is likely to contain only four members. Interestingly, the SAPT2 and SAPT3 gene products, Sapt2p and Sapt3p, which have not yet been detected in C. tropicalis cultures in vitro, were produced as active recombinant enzymes with the methylotrophic yeast Pichia pastoris as an expression system. As expected, reverse transcriptase PCR experiments revealed a strong SAPT1 signal with RNA extracted from cells grown in BSA medium. However, a weak signal was obtained with all other SAPT genes under several conditions tested, showing that these SAPT genes could be expressed at a basic level. Together, these experiments suggest that the gene products Sapt2p, Sapt3p, and Sapt4p could be produced under conditions yet to be described in vitro or during infection.