gebhart/patrepeval huggingface dataset:
Mechanisms Controlling Embryonic Stem Cell Self-Renewal and Differentiation (2006)

Embryonic stem (ES) cells are pluripotent cells with indefinite replication potential and ability to differentiate into all types of cells. An understanding of the regulatory mechanisms responsible for pluripotency in ES cells is critical for realizing their potential in regenerative medicine and science. Cross-species studies on ES cells have identified pathways and networks that are either fundamental to or species-specific for self-renewal and differentiation. Although pluripotency as an essential function in multicellular organisms is conserved through evolution, mechanisms primed for differentiation contribute substantially to the differences among stem cells derived from different tissues or species. Transcriptome mapping analysis has determined the chromosomal domains of gene coexpression patterns specific to the ES state and demonstrated that regulation of ES cell development is operative at both the local chromosomal domain level and global level. Combinatorial signals from multiple pathways regulate the expression of key intrinsic factors critical for ES cell fate determination. The regulatory core formed by Oct4, Sox2, and Nanog, in particular, activates genes critical for self-renewal and represses genes initiating differentiation, controlling ES cell pluripotency. Here, we review recent findings on mechanisms controlling ES cell development. By integrating data from different sources, we present a global picture of how ES cells reach the decision of self-renewal or differentiation.
MR-proADM (2017)

Mid regional pro-adrenomedullin (MR-proADM) has been used as a marker of sepsis, but its dynamics and role in a burn injury setting has not been tested. In a prospective observational study, we included 42 consecutive patients with >15% TBSA. Daily blood specimens collected over the initial 20 days of treatment were submitted for laboratory analysis of MR-proADM and procalcitonin (PCT) via immunoluminometric sandwich assay (Kryptor, BRAHMS, Berlin, Germany). In patients with an absence of sepsis, an initial increase in MR-proADM and PCT levels was noted post-burn injury, peaking on the second day postadmission and thereafter demonstrated a continued decline in MR-proADM and PCT levels. In those patients who went on to develop sepsis (n = 27, 64.3%), the levels of MR-proADM and PCT were significantly higher (P < .001) on days categorized as septic, than on days categorized as nonseptic. The increase in PCT levels was noted on the first day to be categorized as septic. In contrast, the MR-proADM levels demonstrated an increase one day earlier. The optimal relationship between the specificity and sensitivity of MR-proADM and PCT for the detection of sepsis was an increase of 31% and at least 0.015 nmol/L (area under curve 0.76) or of >39% and at least 0.15 µg/L (area under the curve 0.83), respectively. Burn injury is associated with increased levels of MR-proADM. Subsequent increases may be considered as diagnostic of sepsis onset. In this context, PCT displayed higher specificity and sensitivity, while MR-proADM may be more suitable for the early recognition of sepsis (ClinicalTrials.gov number, NCT01055587).
Sequence-based estimation of minisatellite and microsatellite repeat variability (2007)

Variable tandem repeats are frequently used for genetic mapping, genotyping, and forensics studies. Moreover, variation in some repeats underlies rapidly evolving traits or certain diseases. However, mutation rates vary greatly from repeat to repeat, and as a consequence, not all tandem repeats are suitable genetic markers or interesting unstable genetic modules. We developed a model, "SERV," that predicts the variability of a broad range of tandem repeats in a wide range of organisms. The nonlinear model uses three basic characteristics of the repeat (number of repeated units, unit length, and purity) to produce a numeric "VARscore" that correlates with repeat variability. SERV was experimentally validated using a large set of different artificial repeats located in the Saccharomyces cerevisiae URA3 gene. Further in silico analysis shows that SERV outperforms existing models and accurately predicts repeat variability in bacteria and eukaryotes, including plants and humans. Using SERV, we demonstrate significant enrichment of variable repeats within human genes involved in transcriptional regulation, chromatin remodeling, morphogenesis, and neurogenesis. Moreover, SERV allows identification of known and candidate genes involved in repeat-based diseases. In addition, we demonstrate the use of SERV for the selection and comparison of suitable variable repeats for genotyping and forensic purposes. Our analysis indicates that tandem repeats used for genotyping should have a VARscore between 1 and 3. SERV is publicly available from http://hulsweb1.cgr.harvard.edu/SERV/.
KIAA1199 and its biological role in human cancer and cancer cells (Review) (2014)

KIAA1199 is a gene included in the Human Unidentified Gene-Encoded (HUGE) large protein database which contains more than 2,400 members identified in the Kazusa cDNA sequencing project. Early studies described KIAA1199 as an inner ear-specific protein in which 3 point mutations were found to be associated with non‑syndromic hearing loss. Recently, KIAA1199 has been found to play a central role in hyaluronan binding and depolymerisation, and a small number of studies indicate its senescence/apoptosis-promoting role. An increasing body of evidence suggests its involvement in cancer progression, metastasis and poor prognosis of patients with cancer as determined in clinical studies. It has also been shown, in vitro, that KIAA1199 influences the proliferation, adhesion, motility, invasiveness and epithelial-to-mesenchymal transition of cancer cells. Pathway signalling analysis found that KIAA1199 is a likely target gene of the Wnt/β-catenin signalling pathway. Therefore, KIAA1199 may be a new and prospective target for cancer therapy, although further in vitro and in vivo investigations are required.
Films of Silicon Nitride-Silicon Dioxide Mixtures (1968)

Amorphous films of silicon nitride‐silicon dioxide mixtures have been deposited on silicon substrates by the pyrolysis of silane in ammonia‐oxygen mixtures in a gas flow system. The properties of these films such as composition, density, dissolution rate, dielectric constant, refractive index, infrared absorption, etc., were determined as a function of the reactant composition. MIS (metal‐insulator‐silicon) and MIOS (metal‐insulator‐oxide‐silicon) structures were prepared by using silicon nitride‐silicon dioxide mixtures as the insulator, and their capacitance‐voltage behavior compared with that of MNS (metal‐nitride‐silicon) and MNOS (metal‐nitride‐oxide‐silicon) structures. Similar to MNS structures, the MIS structures under study are characterized by high charge densities in the silicon‐insulator interface region and by the ease of charge transfer across the interface. These effects are considerably reduced in MIOS structures; however, MIOS structures are less stable than MNOS structures under electrical and thermal stresses.
Application of STM Nanometer-Size Oxidation Process to Planar-Type MIM Diode (1995)

Ultra fine oxidized titanium (Ti) lines 18 nm wide and 3 nm high have been formed on the surface of a 4 nm Ti layer on a SiO 2 /Si substrate using the scanning tunneling microscope [STM] tip as a selective anodization electrode. The dependence of the size of the oxidized titanium line on the various parameters is investigated. The formed oxidized titanium line has resistivity of 2×10 4 ohm cm, which is a value seven orders of magnitude higher than that of the deposited Ti layer. The oxidized Ti line is used in the planar type metal-insulator-metal [MIM] diode, and works as an energy barrier for the electron. The energy barrier height of the oxidized Ti line is found to be δ E g =0.25 eV.
Evaluating the use of profiling by a region-based register allocator (2002)

In a region-based compilation framework, the compiler builds regions to provide the best compilation unit for scheduling and optimization. The compiler uses execution frequency information gained from profiling to place frequently executed blocks in the same region. This paper investigates the use of profiling in a region-based compilation framework and measures its impact on the register allocation phase. The profiling information can be used by the register allocator to assign values to physical registers based on the execution frequency of the regions. Register allocation can be performed on the most frequently executed regions first so that any spilling that occurs causes memory accesses in less frequently executed regions. The experimental study indicates that profile assisted region formation and register allocation can result in code that executes faster than the code that was compiled without using profiling information and the amount of spill code executed can be reduced significantly.
Photoelectric Methods in Analytical Chemistry (1939)

ADVERTISEMENT RETURN TO ISSUEArticleNEXTPhotoelectric Methods in Analytical ChemistryRalph MullerCite this: Ind. Eng. Chem. Anal. Ed. 1939, 11, 1, 1–17Publication Date (Print):January 1, 1939Publication History Published online1 May 2002Published inissue 1 January 1939https://pubs.acs.org/doi/10.1021/ac50129a001https://doi.org/10.1021/ac50129a001research-articleACS PublicationsRequest reuse permissionsArticle Views147Altmetric-Citations21LEARN 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 options Get e-Alerts
Micropatterning of Poly(Ethylene Glycol) Diacrylate Hydrogels with Biomolecules to Regulate and Guide Endothelial Morphogenesis (2008)

Angiogenesis, which is morphogenesis undertaken by endothelial cells (ECs) during new blood vessel formation, has been traditionally studied on natural extracellular matrix proteins. In this work, we aimed to regulate and guide angiogenesis on synthetic, bioactive poly(ethylene glycol)-diacrylate (PEGDA) hydrogels. PEGDA hydrogel is intrinsically cell nonadhesive and highly resistant to protein adsorption, allowing a high degree of control over presentation of ligands for cell adhesion and signaling. Since these materials are photopolymerizable, a variety of photolithographic technologies may be applied to spatially control presentation of bioactive ligands. To manipulate EC adhesion, migration, and tubulogenesis, the surface of PEGDA hydrogels was micropatterned with a cell adhesive ligand, Arg-Gly-Asp-Ser (RGDS), in desired concentrations and geometries. ECs cultured on these RGDS patterns reorganized their cell bodies into cord-like structures on 50-microm-wide stripes, but not on wider stripes, suggesting that EC morphogenesis can be regulated by geometrical cues. The cords formed by ECs were reminiscent of capillaries with cells participating in the self-assembly and reorganization into multicellular structures. Further, endothelial cord formation was stimulated on intermediate concentration of RGDS at 20 microg/cm(2), whereas it was inhibited at higher concentrations. This work has shown that angiogenic responses can be tightly regulated and guided by micropatterning of bioactive ligands and also demonstrated great potentials of micropatterned PEGDA hydrogels for various applications in tissue engineering, where vascularization prior to implantation is critical.
Dinosaur Tracks At The Fourth Crossing Of The Paluxy River Near Glen Rose, Texas (1937)

Erosion has laid bare at least eight localities in Somervell County, Texas, showing dinosaur tracks in the Glen Rose limestone. It is with keen regret that this article records the disappearance of one of the most notable of these exhibits, the well known track locality at the fourth crossing of the Paluxy River, about four miles west of the town of Glen Rose. Stream erosion, which brought to view there a superb collection of tracks, continued its work too well and wiped out the exhibit as an eraser wipes out a school­boy's blackboard drawing.
Recursive Optical Flow Estimation—Adaptive Filtering Approach (1998)

This paper presents a new approach based on the differential framework proposed by Horn and Schunck, to the problem of recursive optical flow estimation from image sequences. The original method of Horn and Schunck is applicable only to the problem of estimating the optical flow between a pair of images from an image sequence. When we aim at estimating the optical flow for long image sequences recursively, the question is whether and how can we gain from previous estimates. In this paper we show that gain is achieved from both computational and accuracy points of view. Incorporation of the time axis into the estimation process is done by assuming temporal smoothness of the optical flow, resulting in simplified spatial–temporal models. The obtained models permit incorporation of the constrained weighted least squares (CWLS) estimator. This estimator is shown to yield RLS and LMS adaptive filter versions for recursive optical flow estimation in time. An interesting and desirable property of the proposed estimation algorithms is their flexibility with respect to performance versus computational requirements. By a simple choice of a parameter these algorithms can be modified to exploit the available time to improve their performance with respect to estimation error. The convergence properties of these estimation algorithms are analyzed. Simulations for various image sequences support the analysis and demonstrate the performance of the estimation algorithms.
Crystal structure of ribonuclease A.d(ApTpApApG) complex. Direct evidence for extended substrate recognition. (1994)

The crystal structure of the complex between ribonuclease A and d(ApTpApApG) has been solved by x-ray crystallography using the molecular replacement method. The model includes, besides the enzyme, the d(ApTpApA) 5'-segment (A1T2A3A4) and 68 solvent molecules. The R-factor for the strongest 87% of the measured data that partially extends to 2.3-A resolution is 0.207. The A1 position is well defined; the 5'-O of the deoxyribose establishes a hydrogen bond with a solvent molecule that is, in turn, bonded to the epsilon-amino group of Lys66. The base (B0 site) is well ordered; it interacts with a symmetry-related enzyme molecule. In the crystal, the phosphate group at the p0 site has no direct charge compensation. However, Lys66 is not too far, and, in solution, it could bind to it. The T2 (R1B1p1) site is occupied as in other complex structures, and it is defined by very good electron density. The A3 site shows that the adenine moiety interacts with Asn71 and Gln69 and that the phosphate at p2 forms a salt bridge with Lys7. The most consistent model for the base of A4 (B3), both in terms of electron density and stereochemistry, shows that it forms a hydrogen bond with Gln69 and a g-g- array with the base at B2. The stacking of B2 and B3 may be a general feature of the binding of polyribonucleotides to ribonuclease A. The side chains of Gln69, Asn71, and Glu111 may thus constitute a malleable binding site capable of establishing various hydrogen bonds depending on the nature of the stacked bases. There is no evidence for the 3' G5 site in the electron density map.
Using eye-tracking to identify pedestrians’ critical visual tasks, Part 1. Dual task approach (2014)

This paper investigates the critical visual tasks of pedestrians, the first step in a review of design guidance for lighting in residential roads. Eye tracking was used to record pedestrians’ visual fixations when walking outdoors in daytime and after dark with a concurrent dual task to better understand which fixations were critical. Fixations at critical instances, these being shown by slow reactions to the secondary task, were categorised into one of eight groups. Of these, the path and other people were the most frequent items, with people more likely to be fixated at a far distance and the path at a near distance. After dark the path was more likely to be fixated and other people less likely to be fixated compared with daylight.
Down-regulation of p63 is required for epidermal UV-B-induced apoptosis. (2000)

In the epidermis, p53 plays an important role in UV-B protection that led us to examine the role, if any, that p63, a p53 homologue highly expressed in the basal layer of the epidermis, might play in the epidermal UV-B response. One p63 isoform, deltaNp63alpha, decreased dramatically in normal keratinocytes or newborn epidermis at both the protein and RNA levels after UV-B irradiation. In an attempt to further investigate the significance of the UV-B-induced decrease of this p63 isoform as well as further delineate the function of p63 in the epidermis, we generated transgenic mice that constitutively express deltaNp63alpha in the mouse epidermis using the loricrin promoter (ML.deltaNp63alpha). The ML.deltaNp63alpha mouse epidermis developed normally, with no overt phenotype and an unaltered proliferation rate. When challenged by UV-B exposure, the ML.deltaNp63alpha mice exhibited a 40-45% decrease in the number of apoptotic cells in the epidermis as compared with nontransgenic littermates. These results suggest that aberrant expression of deltaNp63alpha altered the UV-B-induced apoptotic pathway in the transgenic epidermis, proving that down-regulation of deltaNp63alpha in response to UV-B is important to epidermal apoptosis. The forced overexpression of deltaNp63alpha may act via a dominant negative effect on the endogenous p53 transcriptional activity required for UV-B-induced apoptosis.
Enhancement of merocyanine 540-mediated phototherapy by salicylate. (1993)

Merocyanine 540 (MC540) is a photosensitizing dye of potential use in the purging of cancer cells from autologous bone marrow explants. Treatment of marrow with MC540, followed by illumination with visible light, selectively kills neoplastic cells while sparing a sufficient number of stem cells to allow marrow engraftment. The photodynamic action of MC540 is thought to be mediated by reactive oxygen species, particularly singlet oxygen. We have previously shown that salicylic acid (SA) scavenges MC540-generated singlet oxygen. In this work, we sought to abrogate MC540-mediated cell killing of murine L1210 and human K562 leukemia cells with salicylate. Paradoxically, the presence of salicylate during illumination in the presence of MC540 appreciably enhanced cell killing. Enhancement was dependent on salicylate concentration in the range 0.1 to 10 mM, with 1.0 mM SA potentiating the MC540-mediated reduction in survival of L1210 and K562 cells by factors of 2.7 and 1.9, respectively. Neither preincubation with SA followed by washing prior to illumination nor addition of SA following illumination altered MC540-mediated cell killing, indicating that potentiation was dependent on the presence of SA during illumination. Illumination in the presence of salicylate alone did not diminish cell viability. In addition to SA, a number of structurally related compounds including dihydroxybenzoic acids, aspirin, and sodium benzoate also enhanced MC540-mediated cell killing. Potentiation of leukemic cell killing by salicylate could provide a basis for enhancing the clinical efficacy of MC540-mediated phototherapy.
Time-resolved imaging of optical coefficients through murine chest cavities (2006)

As small animal optical imaging and tomography are gaining popularity for interrogating functional and molecular events in vivo, it becomes increasingly necessary to gain knowledge of the optical properties of the species investigated to better understand and describe photon propagation through their tissues. To achieve characterization of the spatial variation of average optical properties through murine chest cavities, time- and spatially resolved measurements of femto-second laser pulse transmission are performed through mice using a high-speed gated image intensifier. Application of time-resolved diffusion theory for finite slab geometry is first confirmed on phantoms and then applied to in vivo measurements for spatially resolving and quantifying mouse optical properties. Photon transmission images through mouse chest cavities are further obtained at different time gates to visualize the spatial variation observed and confirm the optical coefficient patterns calculated.
Single pulse switchout system for a passively mode-locked <i>Q</i>-switched Nd:YAG laser (1981)

A new optical switchout device for a passively mode-locked Q-switched laser is presented. This device can switch out a single pulse with energy at a preset level. The stability of the switched out single-pulse energy is greater than the input pulse train. This is achieved by means of a high speed comparator and avalanche transitor chains. A single pulse of ±13% energy stability is obtained from the pulse train of our Nd:YAG laser oscillator with a ±25% fluctuation. The maximum repetition frequency of 2 kHz is sufficient not only for this kind of laser but also for other applications. The life of the avalanche transistors used here is more than one million shots. The possibility of further improvements in output stability is also discussed.
Prediction of nodal metastasis and prognosis in breast cancer: a neural model. (1997)

Although this study considered a relatively small sample of patients, nevertheless it demonstrates that artificial neural networks are capable of providing strong indicators for predicting lymph node involvement. There is no longer a need for axillary dissection with all its implications in patient morbidity and demands on clinical resources. The management of breast cancer and the planning of strategies for adjuvant treatments is also facilitated by the use of neural networks for the long-term prognosis of patients.
Atomic migration in molten and crystalline Ge2Sb2Te5 under high electric field (2009)

Atomic migration under an electric field, electromigration, in molten and crystalline Ge2Sb2Te5 was studied using a pulsed dc stress to an isolated line structure. Under a single pulse (∼10−3 s), Ge2Sb2Te5 was melted by Joule heating, and an electrostatic force-induced drift of Ge and Sb toward the cathode and Te toward the anode was observed. Effective charge numbers were calculated to be 0.28, 0.38, and −0.29 for Ge, Sb, and Te, respectively. Electromigration in the crystalline state was studied by applying a 10 MHz pulsed dc; constituent elements migrated toward the cathode, which suggests a hole wind-force operating in this phase.