gebhart/patrepeval huggingface dataset:
Improving heart rate estimation in preterm infants with bivariate point process analysis of heart rate and respiration (2016)

Accurate estimation of heart rate dynamics in preterm infants is important for predicting recurrent episodes of severe bradycardia. We hypothesize that estimation of heart rate can be improved by including respiration as a state variable, based on mechanisms that underlie cardio-respiratory coherence. For ten preterm infants, we demonstrate that including respiration as a covariate improves estimation accuracy by an average of 11% across bradycardia severity, and reduces the maximum error by 8%. We also find that cardio-respiratory coherence increases in low frequency content just prior to severe bradycardia. Thus, incorporating respiratory information may improve models of heart rate dynamics and narrow potential features for bradycardia prediction.
W versus Co–Al as Gate Fill-Metal for Aggressively Scaled Replacement High-k/Metal Gate Devices for (Sub-)22 nm Technology Nodes (2013)

In this work we provide a comprehensive evaluation of a novel, low-resistance Co–Al alloy vs W to fill aggressively scaled gates with high aspect-ratios [gate height ( H gate ) ∼50–60 nm, gate length ( L gate ) ≥20–25 nm]. We demonstrate that, with careful liner/barrier materials selection and tuning, well-behaved devices are obtained, showing: tight gate resistance ( R gate ) distributions down to L gate ∼20 nm, low threshold voltage ( V T ) values, comparable DC and bias temperature instability (BTI) behavior, and improved RF response. The impact of fill-metals intrinsic stress, including the presence of occasional voids in narrow W-gates, on devices fabrication and performance is also explored.
Silicon Oxycarbides in Hard-Carbon Microstructures and Their Electrochemical Lithium Storage (2013)

Silicon oxycarbide (Si–O–C) glasses have been obtained by pyrolysis of powdery blends, composed of polysiloxane resin and phenol aralkyl resin, to 1000°C. Chemical and structural analyzes were conducted to investigate the characteristics of Si–O–C glass networks and disordered graphitic components. In the completely amorphous nature of the Si–O–C glasses, the carbon content largely increased with increasing the blend ratio of phenol aralkyl resin in a way contrary to the silicon content. The Si–O–C glasses have been evaluated as a negative electrode material for rechargeable lithium-ion batteries. Electrochemical measurements showed that delithiation capacities linearly increased to >800 mA h g−1 with increasing the silicon content in these Si–O–C glasses. Interestingly, the carbon-rich Si–O–C glasses had delithiation capacities of up to 580 mA h g−1 with good cyclability. 7Li NMR analyzes indicated that the carbon-rich Si–O–C glasses have more hard carbon-like features and that at least two electrochemically active sites store lithium species.
Triple, Mutually Orthogonal Bioorthogonal Pairs through the Design of Electronically Activated Sulfamate-Containing Cycloalkynes (2020)

Interest in mutually exclusive pairs of bioorthogonal labeling reagents continues to drive the design of new compounds that are capable of fast and predictable reactions. The ability to easily modify S-, N-, and O-containing cyclooctynes (SNO-OCTs) enables electronic tuning of various SNO-OCTs to influence their cycloaddition rates with Type I–III dipoles. As opposed to optimizations based on just one specific dipole class, the electrophilicity of the alkynes in SNO-OCTs can be manipulated to achieve divergent reactivities and furnish mutually orthogonal dual ligation systems. Significant reaction rate enhancements of a difluorinated SNO-OCT derivative, as compared to the parent scaffold, were noted, with the second-order rate constant in cycloadditions with diazoacetamides exceeding 5.13 M–1 s–1. Computational and experimental studies were employed to inform the design of triple ligation systems that encompass three orthogonal reactivities. Finally, polar SNO-OCTs are rapidly internalized by mammalian cells and remain functional in the cytosol for live-cell labeling, highlighting their potential for diverse in vitro and in vivo applications.
Mononuclear Phagocytic System (2001)

Abstract The mononuclear phagocyte system is made up of blood monocytes and their precursors, and two differentiated cell populations derived from them: macrophages and dendritic cells. The former are professional phagocytes whose main role is to take up particulate material, while the latter are specialized to process and present antigens to T cells.
A compact photonic resonator absorption microscope for point of care digital resolution nucleic acid molecular diagnostics (2021)

Rapid, sensitive, and selective detection of nucleic acid biomarkers for health diagnostic applications becomes feasible for point of care scenarios when the detection instrument is inexpensive, simple, and robust. Here, we report the design, implementation, and characterization of a point of care instrument for photonic resonator absorption microscopy (PRAM) that takes advantage of resonant optical coupling between plasmonic gold nanoparticle tags and a photonic crystal (PC) surface. Matching the PC resonant wavelength to the gold nanoparticle’s surface plasmon wavelength generates localized and efficient quenching of the PC resonant reflection intensity, resulting in the ability to clearly detect and count individual gold nanoparticles when they are captured on the PC surface. Surface-captured nanoparticles are observed by illuminating the PC at normal incidence with polarized light from a low-intensity red LED, and recording of PC reflected intensity on an inexpensive CMOS image sensor. A contrast limited adaptive histogram equalization (CLAHE) image processing algorithm was applied to derive counts of captured nanoparticles. The instrument is utilized in the context of an activate capture + digital counting (AC + DC) assay for a specific miRNA sequence, using nucleic acid toehold probes applied to gold nano-urchin (AuNU) nanoparticles to achieve 160 aM detection limits in a 30 min. assay.
Graphs, Algorithms, and Optimization (2017)

Graph theory offers a rich source of problems and techniques for programming and data structure development, as well as for understanding computing theory, including NP-Completeness and polynomial reduction. A comprehensive text, Graphs, Algorithms, and Optimization features clear exposition on modern algorithmic graph theory presented in a rigorous yet approachable way. The book covers major areas of graph theory including discrete optimization and its connection to graph algorithms. The authors explore surface topology from an intuitive point of view and include detailed discussions on linear programming that emphasize graph theory problems useful in mathematics and computer science. Many algorithms are provided along with the data structure needed to program the algorithms efficiently. The book also provides coverage on algorithm complexity and efficiency, NP-completeness, linear optimization, and linear programming and its relationship to graph algorithms.Written in an accessible and informal style, this work covers nearly all areas of graph theory. Graphs, Algorithms, and Optimization provides a modern discussion of graph theory applicable to mathematics, computer science, and crossover applications.
A phase II study of everolimus in patients with aggressive RAI refractory (RAIR) thyroid cancer (TC). (2013)

6023 Background: We present results of an open label phase II study of the mTOR inhibitor Everolimus in patients (pts) with RAIR TC. Methods: Pts with metastatic, incurable RAIR TC who had shown radiographic progression within 6 months prior to enrollment received Everolimus 10mg orally once daily. Responses were monitored by CT's every two months. The primary endpoint was progression free survival. Sequential biopsies were obtained in selected pts. Results: Enrollment to the differentiated TC (DTC) cohort finished in Jan 2013 and included 33 pts, among them 11 with Hurthle cell TC. Exploratory cohorts enrolled 10 pts with medullary [MTC] and 5 with anaplastic [ATC] with 2 added openings remaining for ATC. For the DTC cohort, median time on study to date is 10 months (mo) (&lt;1-23+). 31 pts are evaluable at this time. PFS in the DTC cohort by Kaplan-Meier (K-M) analysis is 16.0 mo (95%CI 10-NR). Currently, disease stability for 6 and 12 mo or more was achieved in 18 and 10/31 pts, respectively, 11 pts remain on study. Median OS was not reached but 1 year survival by K-M analysis was 76%. One pt achieved a PR. 3 pts with DTC underwent sequential biopsies which revealed activation of autophagy while markers for apoptosis were not detected. Among 10 MTC pts, one achieved a PR and 9 pts had stable disease for 6 mo or more (6-33+). Among 5 ATC pts, 3 progressed, one has ongoing disease stability for 5 mo. One patient achieved a complete response that lasted for 18 mo and whole exome sequencing revealed somatic loss of function mutation affecting the Tuberous Sclerosis 2 (TSC2) protein, a negative regulator of mTOR activity [TSC2 (Q1178*) and FLCN (R17fs)]. Most common treatment-related adverse events were as anticipated and included fatigue, stomatitis and infections. Grade (gr) 3 events included infection 5, weight loss 3, leukopenia 3, thrombocytopenia 3, fatigue 3, hypophosphatemia 2, stomatitis 2, pneumonitis 1 and thrombosis 1pts. One pt had gr 4 hypercholesterinemia and one pt had gr 4 leukopenia. Conclusions: Everolimus has significant anti-tumor activity in pts with advanced TC. Activation of autophagy could account for high rate of disease stability. Sequencing may identify mechanistic basis and predictive markers for treatment response. Clinical trial information: NCT00936858.
A superconducting transistorlike device having good input-output isolation. (2009)

A multiterminal superconducting device with the S1IS2FIS3 structure (where S, I, and F denote a superconductor, an insulator, and a ferromagnetic material) is fabricated and characterized. Introducing a thin ferromagnetic layer into the middle electrode dramatically reduces parasitic back action of the acceptor junction (S1IS2) bias current on the injector junction (S2FIS3) current-voltage characteristic as compared with that for the formerly reported quiteron, a device exploiting similar operation principle.
Proteases That Can Distinguish among Different Post-translational Forms of Tyrosine Engineered Using Multicolor Flow Cytometry (2009)

We report the isolation of a highly active (k(cat)/K(M) approximately 10(5) M(-1)s(-1)) variant of the E. coli endopeptidase OmpT that selectively hydrolyzes peptides after 3-nitrotyrosine while effectively discriminating against similar peptides containing unmodified tyrosine (160-fold), sulfotyrosine (3600-fold), phosphotyrosine (>8000-fold), and phosphoserine (>8000-fold). The isolation of endopeptidase variants that can discriminate between substrates based on the post-translational modification of Tyr was made possible by implementing a multicolor flow cytometric assay for the screening of large mutant libraries. For the multicolor assay, a desired selection substrate was used simultaneously with multiple counterselection fluorescent substrates to isolate rare enzyme variants that displayed finely tuned substrate specificity. This work demonstrates that enzymes with exquisite selectivity can be isolated from large libraries using appropriate high throughput screening approaches and constitutes a critical step toward the production of a 3-nitrotyrosine-specific protease useful for proteomic applications.
Observation of deep holes using new technique (1993)

We discovered the phenomena in scanning electron microscopy that the bottom of deep holes can be observed clearly when a high energy electron beam is irradiated. In order to utilize this phenomena, we developed a novel instrument that generates a scanning electron probe of 50 to 200 keV with TV-scan rate that enables us to inspect maximum 8 inches diameter wafers. In the past, we could inspect deep holes by observing cross sectional view of a hole milled with a focused ion beam (FIB). Using the novel instrument, we can easily inspect such holes without destroying samples. This observation does not depend on the specimen conditions, such as aspect ratio of holes and specimen charging that often occurs in the case of observing insulators. This instrument enables us to observe inside structures of semiconductor devices. Irradiation damage on semiconductor devices, such as threshold voltage and sub-threshold coefficient deviation of MOS transistors can be recovered, except for the irradiated area by means of hydrogen annealing of 30 minutes with temperature of 450 degree(s)C.
Numerical light dosimetry in murine tissue: analysis of tumor curvature and angle of incidence effects upon fluence in the tissue (2003)

In order to better understand light dosimetry issues for photodynamic therapy (PDT), we have used various tumor and normal tissue geometries to develop a diffusion model of light transport in tissues. We hypothesize that tumor tissues with curved surfaces will have significantly different internal fluence distributions, as compared to tissues with flat surfaces. Using a mouse subcutaneous tumor and rear limb muscle model we compared the internal fluence values within the tissue. In addition, numerical simulations for these corresponding tissue geometries and laser light incidence angles were made. Assuming that the relative photon fluence in the tissue can be accurately modeled by the diffusion equation, we used a finite element approach to approximate the distribution inside the tissue. Meshes with different geometries (flat and curved with different curvatures) were used in this study to mimic the tumor and leg geometries of the murine tumors treated in the lab. Results suggest that tissues surface geometries and incidence angle of light can significantly alter the photon fluence inside the tissue. The photon fluence difference for an 8 mm diameter, curved surface mouse tumor vs. flat muscle tissue can be as high as 20%. In general, the greater the tissues curvature, the greater the potential loss in light fluence is. In summary, our data demonstrates the importance of tissue surface geometry and the incidence angle of light in determining optimal PDT light dosimetry, and indicates that comparisons between tissue geometries must be carried out with attention to differences in the internal optical distribution.
Protective Roles of Eosinophils in <i>Nippostrongylus brasiliensis</i> Infection (1997)

Nippostrongylus brasiliensis infection is characterized by blood and tissue eosinophilia induced by interleukin (IL)-5 secreted from CD4+ T cells. However, it is still obscure whether eosinophils play an important role in the protection against N. brasiliensis infection. In this study we attempted to determine whether the in vivo environment of IL-5 transgenic mice, characterized by high eosinophil production, could affect the worm burden after N. brasiliensis infection. Kinetic studies on the infection demonstrated a significantly lower worm recovery from the intestine of IL-5 transgenic mice compared to age-matched background controls. This tendency was also observed at the lung stage of the infection. Furthermore, with respect to elevation of the serum IgE concentration, the peak level was observed at 2 weeks after infection in infected background control mice with four times higher concentrations than those of uninfected mice. In contrast, the increase of IgE concentration in IL-5 transgenic mice was very limited and low. The adoptive transfer of eosinophils from IL-5 transgenic mice into background control animals resulted in the reduction of worm recovery from the lungs, suggesting that eosinophils play a key role in the protection against migrating larvae of N. brasiliensis. These results indicate that the innate high level of eosinophils due to constitutive production of IL-5 augments immunity against N. brasiliensis infection.
Extracting symbolic information from facial images (2003)

A method for automatically extracting symbolic-level information from single facial images is proposed. We combine a 2D Gabor wavelet labelled elastic graph representation with Fisher discriminant analysis. Use of this representation relaxes the requirement for exact normalization of the face. The algorithm is used to extract information about the sex, "race" and emotional expression of the face in the image. A visual interpretation of the discriminant vectors is provided.
Comparative expressed sequence hybridization to chromosomes for tumor classification and identification of genomic regions of differential gene expression (2001)

Altered expression of genes can have phenotypic consequences in cancer development and treatment, developmental abnormalities, and differentiation processes. Here we describe a rapid approach, termed comparative expressed sequence hybridization (CESH), which gives a genome-wide view of relative expression patterns within tissues according to chromosomal location. No prior knowledge of genes or cloning is required, and minimal amounts of tissue can be used. Expression profiles are achieved in a manner similar to the identification of chromosomal imbalances by comparative genomic hybridization analysis. The approach is demonstrated to indicate a chromosomal region that harbors overexpressed genes that may be associated with a drug-resistant phenotype. In addition, known and new regions of differential gene expression in both normal tissues and tumor samples from the soft tissue sarcoma group of rhabdomyosarcoma (RMS) are indicated. These regions included 2p24; overexpression of MYCN at 2p24 was confirmed by quantitative reverse transcription-PCR for all of the alveolar RMS cases and did not necessarily correspond to genomic amplification. Evidence including region specific microarray analysis indicated that overexpression of several genes from a region may be required for detection by CESH. This evidence is consistent with clusters of functionally related genes and mechanisms that affect the expression of a number of genes at a particular genomic location. The distinctive CESH profiles demonstrated in different subtypes of RMS show potential for tumor classification.
Detection of lymphoid leukosis virus infected chickens by testing for group‐specific antigen or virus in feather pulp (1983)

Exogenous lymphoid leukosis virus (LLV) and group-specific antigen (gsa) were detected in feather pulp and other specimens from naturally or experimentally infected chickens by phenotypic mixing or complement fixation tests, respectively. Electron microscopic studies on the calamus of plucked feathers revealed numerous C-type virus particles in intercellular spaces of the epidermis and pulp. LLV and gsa were detected in feather pulp from approximately 90% of 47 newly-hatched chicks that were shown to be congenitally infected. Chicks that were inoculated at 1-day-old or reared as contact controls were positive for gsa in feather pulp at 44 days, whereas at 111 days only the inoculated chicks were positive. Isolated controls were consistently negative. Titres of gsa </= 1 : 32 in feather pulp were found in adult chickens of three strains that tested negative for infection with LLV. In these chickens gsa was presumed to be associated with an endogenous virus infection. In chickens that were positive for exogenous LLV in feather pulp the gsa titres were usually >/= 1 : 64. It was concluded that gsa could be detected in the feather pulp of most chickens actively infected with LLV and that titres would generally be higher in exogenous than in endogenous infections.
Towards a completely implantable, light-sensitive intraocular retinal prosthesis (2005)

A completely implantable, light-sensitive retinal prosthesis must include the capability for both phototransduction and stimulus current generation, two power intensive functions. These devices will be implanted in the eye, creating a significant source of heat that must be dissipated by the ocular tissue without damaging the retina. However, significant technological hurdles remain. The amount of heat that can be safely dissipated by the eye and surrounding head without harming the retina, depends significantly on the position of the heater. Technology for, a high-density electrode array is advancing, but high-quality wires of biocompatible material in dimensions usable for a retinal prosthesis material have yet to be achieved.
Inhibition of the TGF-β Receptor I Can Stimulate Hematopoiesis in Primary Myelodysplastic Syndrome Progenitors as Well as in TGF-β Driven Transgenic Mouse Model of Bone Marrow Failure. (2007)

Abstract Myelodysplastic syndromes (MDS) are characterized by ineffective hematopoiesis that leads to peripheral cytopenias. TGF-β is a myelosuppressive cytokine that has been indirectly linked to the pathogenesis of some subsets of MDS and acute leukemias. We demonstrate by immunohistochemistry that smad2, a component of the TGF-β signaling pathway, is constitutively activated in MDS bone marrows. This activation was seen in both low and high grade cases of MDS when compared to anemic controls and provides the first direct evidence of activation of TGF-β signaling in MDS. To demonstrate the functional role of TGF-β signaling in MDS, a GFP expressing lentiviral siRNA construct was designed to knockdown TGF receptor I (TBRI) expression. Stable expression of this lentivirus in a variety of hematopoietic cells resulted in &gt;70% inhibition of TBRI mRNA by qPCR. Lentiviral siRNA Knockdown of TBRI in primary CD34+ cells resulted in an increase in GFP+ erythroid colony formation, indicating an inhibitory role of TGF-β in human hematopoiesis. To further test the efficacy of TBRI inhibition in stimulating hematopoiesis, we used a specific and potent inhibitor of TBRI (ALK5) kinase, SD-208. SD-208 was effectively able to inhibit TGF-β mediated activation of smad-2 and potently inhibit TGF-β mediated gene expression in bone marrow stromal cells. SD-208 treatment also led to reversal of TGF-β induced inhibition of primary CD34 cell proliferation and both erythroid and myeloid colony formation in short term assays. Most importantly, treatment with SD-208 led to significant dose dependent increases in erythroid and myeloid colony formation from primary MDS bone marrow derived hematopoietic progenitors. Furthermore, we tested the efficacy and specificity of SD-208 in a TGF-overexpressing transgenic mouse. This mouse constitutively expresses TGF-β through an albumin promoter, develops progressive anemia and dysplasia and thus serves as a novel model of human bone marrow failure. Treatment with SD-208 by oral lavage at 30mg/kg/d for two weeks led to significant increases in both myeloid and erythroid colony formation from murine bone marrows and led to a trend of increasing hemoglobin and hematocrit. Taken together, these studies demonstrate a role of TBRI inhibition in stimulating hematopoiesis in human bone marrow failure and should lead to future studies with SD-208 and other inhibitors of TGF signaling pathways in MDS.
Thin‐film‐transistor‐ and diode‐addressed AMLCDs on polymer substrates (1997)

Abstract— Amorphous‐silicon‐rich nitride (αSiN x :H) thin‐film diodes (TFDs) have been fabricated on glass, polyethersulphone (PES), polyacrylate (PAR), and polyethelyenenaphthalate (PEN) substrates at temperatures of 150–200°C, and a TFD‐addressed TN‐LCD fabricated on polyethersulphone is presented. Furthermore, poly‐Si thin‐film‐transistors (TFTs) have been fabricated on glass, polyimide (PI), and polyethersulphone at temperatures of 200–275°C, and active‐matrix arrays with drive circuitry have been realized. This work is an important step leading to a compact, lightweight, robust, system on a panel.
Titanium miniplates or stainless steel wire for cranial fixation: a prospective randomized comparison (2002)

Titanium miniplate cranial fixation provides more accurate and rigid reapproximation of the bone edges, with results that are significantly better on close inspection or palpation. The additional cost of miniplate fixation may thus be justified in many cases.