gebhart/patrepeval huggingface dataset:
OP04.07: Diagnostic correlation between 2D and 3D ultrasound at 20–22 weeks in fetal evaluation. Preliminary results (2008)

The aim of this study is to asses the feasibility of 3D ultrasound for fetal evaluation at 20–22 weeks. A cross-sectional study was designed in order to evaluate the correlation between 2D standard ultrasound and 3D multiplanar mode by means of a General Electric Voluson 730 Expert. 35 women were scanned at 20–22 weeks of gestation. A standard anatomical ultrasound was performed in each pacient. Also six volumes of each fetus were obtained (axial head, coronal face, chest, abdominal, upper extremities and lower extremities). Observer A analysed off line the 18 cases obtained by observer B, using 4D view program. Reversaly, observer B analysed the volumes obtained by observer A in 17 pacients. A third observer C also analysed the volumes obteined by A and B in order to evaluate the interobserver reproducibility in a second step. A check list of landmarks (31)was used to study the complete fetal anatomy in both ultrasound methods. For measurements, the intraclass correlation coefficient was calculated between both techniques. While with 2D standard ultrasound 99% of landmarks were identified, it was 94% with 3D off line examination. Grouping by view regions : head and face 97%, 94% respectively; heart : four-chamber 100%, three vassels and trachea wiew 97%, outflow tracts 74%; abdominal structures 100% unless both kidneys 89%; both arms 89%, both hands 57%, both legs 97% and both feet 80%. Spine was completly seen in 85%. One choroid plexus cyst was seen in 2D/3D, one foot with equino-varus position was not satisfactory visualized using 3D and it was two cases of sex error. Intraclass correlation coefficient was almost perfect for biparietal diameter, cephalic circunference and femoral length, and very good for abdominal circunference. 3D ultrasound seems to allow a good anatomical assesment and yield reliable mesurements at 20–22 weeks of gestation. Hands, cardiac outflow tracts and feet are, by now, structures poorly assesed by 3D standard multiplanar mode
Semi-Discrete Matrix Transforms (SDD)for Image and Video Compression (2020)

A wide variety of matrix transforms have been used for compression of image and video data. Transforms have also been used for motion estimation, quantization, and image classification. One such transform, that is frequently used to reduce dimensionality of underlying data is the singular-value decomposition (SVD), which relies on low rank approximations for computational and storage efficiency. In this paper, we describe the performance and use of a variant of SVD in image and video compression. This variant, first proposed by Peleg and O’Leary [5], called semi-discrete decomposition (SDD), restricts the elements of the outer product vectors to 0/1/-1. Thus approximations of much higher rank can be stored for the same amount of storage. We demonstrate the superiority of SDD over SVD for a variety of compression schemes. We also show that DCT-based compression is still superior to SDD-based schemes in terms of compression ratios. However, reconstruction from compressed vectors is much faster in the case of SDD compressed images. Furthermore, SDD can be used for fast and accurate pattern matching and motion estimation; thus presenting excellent opportunities for improved compression.
Analysis of Amino Acid Isotopomers Using FT-ICR MS (2007)

Fluxes through known metabolic pathways and the presence of novel metabolic reactions are often determined by feeding isotopically labeled substrate to an organism and then determining the isotopomer distribution in amino acids in proteins. However, commonly used techniques to measure the isotopomer distributions require derivatization prior to analysis (gas chromatography/mass spectrometry (GC/MS)) or large sample sizes (nuclear magnetic resonance (NMR) spectroscopy). Here, we demonstrate the use of Fourier transform-ion cyclotron resonance mass spectrometry with direct infusion via electrospray ionization to rapidly measure the amino acid isotopomer distribution in a biomass hydrolysate of the soil bacterium Desulfovibrio vulgaris Hildenborough. By applying high front-end resolution for the precursor ion selection followed by sustained off-resonance irradiation collision-induced dissociation, it was possible to determine exactly and unambiguously the specific locations of the labeled atoms in the amino acids, which usually requires a combination of 2-D 13C NMR spectroscopy and GC/MS. This method should be generally applicable to all biomass samples and will allow more accurate determination of metabolic fluxes with less work and less sample.
Ionizing radiation induces femtosecond time scale modulations of a material’s optical properties (2018)

In this work, we continue the study of an optical based method for annihilation photon detection with the potential for a dramatic improvement in time resolution for time-of-flight positron emission tomography (ToF-PET). Previous work has shown that the refractive index of materials such as bismuth silicon oxide (BSO) and cadmium telluride (CdTe) can be modulated by the charge cloud created by annihilation photon interactions, though the ultrafast nature of the index modulation process remains untested. At the Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory, the arrival time of X-ray pulses with photon energies between 0.5–10 keV is routinely detected with femtosecond scale time resolution. The ionizing interactions alter the local band structure in optically transparent insulators, changing the refractive index. Using a frequency chirped visible continuum probe pulse for a monotonic wavelength-to-time mapping, we measured the induced refractive index modulation, with interferometric sensitivity, and a sub-picosecond time resolution. In this work, we show that femtosecond scale resolution can be achieved for photon arrival time measurement using the refractive index modulation mechanism. This new detection concept has the potential to also achieve significantly improved timing capability for ToF-PET.
The Effect of Physical Activity Bout Patterns on Metabolic Syndrome Risk Factors in Youth: National Health and Nutrition Examination Survey 2003–2006 (2018)

Longer continuous bouts of MVPA had beneficial effects on body anthropometrics and weight status, although these effects may be moderated by total MVPA.
Surface energetics, pit formation, and chemical ordering in InGaN alloys (1999)

We present first-principle calculations of the structure and energetics of the GaN(101_1) surface, and present models for the reconstructions. A strong preference for In surface segregation and occupation of specific surface sites is demonstrated. We argue that inverted pyramid defect formation is enhanced by segregation of In on (101_1) facets. We propose that the chemical ordering recently observed in InGaN alloys is driven by the preference for In incorporation at the sites of reduced N coordination present at step edges during growth on the (0001) and (0001_) surfaces.
Dipyridamole Tl-201 SPECT in Hypertrophic Cardiomyopathy with Asymmetric Septal Hypertrophy:Characteristics of Perfusion Abnormality and Correlation with Clinical Parameters (1999)

Background and Objectives:Exercise myocardial perfusion scans in patients with hypertrophic cardiomyo- pathy have shown reversible perfusion abnormalities with unknown clinical significance. We performed this study to characterize dipyridamole Tl-201 SPECT imaging and correlate with clinical findings in patients with hypertrophic cardiomyopathy. Methods:Tl-201 SPECT was performed in 25 patients of hypertrophic cardiomyopathy with asymmetric septal hypertrophy and 20 normal controls after dipyridamole infusion (0.56 mg/kg. Myocardial wall was divided into 8 segments. Tl-201 uptake and relative washout rate were calculated. Results:Tl-201 SPECT showed significantly lower Tl-201 uptake in basal septal (81.3±3.4% vs 78.2±6.4%, p<0.05 and apical septal wall on stress (88.2±4.7% vs 83.9±6.5%, p<0.05 and higher apical septal (86.6±5.2% vs 89.2±3.1%, p<0.05 and apical anterior wall uptake (88.7%±4.0% vs 91.4±4.9%, p<0.05 on redistribution images in patients with hypertrophic cardiomyopathy. Basal lateral wall uptake of hypertrophic cardiomyopathy was significantly lower than normal control on both stress (84.7±3.5% vs 81.2 ±7.3%, p<0.05 and redistribution images (85.0±5.8% vs 76.8±7.2%, p<0.0001. The septum/lateral uptake ratio of patients on rest image was significantly higher than that of normal controls (0.98±0.07 vs 1.07±0.10, p<0.001. There was no difference in age, sex, symptom, cardiac medication and the parameters of 2D-echo including left ventricular outflow obstruction between subgroups of normal vs abnormal washout in patients with hypertrophic cardiomyopathy. Conclusion:Dipyridamole Tl-201 myocardial SPECT shows reduced
The Power of Composition: Abstracting a Multi-Device SDN Data Path Through a Single API (2019)

Software Defined Networking aims to separate network control and data plane by moving the control logic from network elements into a logically-centralized controller. Using a well-defined, unified control-channel protocol, such as OpenFlow, the controller is able to configure the forwarding behavior of data plane devices. Here, the OpenFlow protocol is translated to vendor- and device-specific instructions that, for instance, manipulate the flow table entries of a switch. In practice, SDN-enabled switches often feature different hardware capabilities and configurations with respect to the number of flow tables, their implementation, and which kind of data plane features they support. This leads to device heterogeneity within the SDN landscape, thereby obstructing the increased scalability and flexibility promised by the SDN paradigm. To overcome this challenge we propose TableVisor, a transparent proxy-layer for the SDN control channel that enables the flexible abstraction of heterogeneous data plane devices into a single emulated data plane switch. In this paper, we extend our previous work by introducing features to integrate modern P4 devices into an existing SDN environment and perform a detailed performance evaluation to quantify the overhead induced by our approach.
Inspecting Twin 42” Reinforced Concrete Pipes with Pipe Penetrating Radar Supplemented by LiDAR (2021)

In the midst of a renovation project set to convert an old field house into a recreational centre, concerns were raised about the feasibility of the project due to the structural integrity of the pipes running under the building. The project entailed converting an old Campbell soup factory into a recreational cold storage facility for the residents of Worthington, MN. The issue involved two 80+-year-old 42 in. reinforced concrete pipes with unknown conditions that lay beneath the building. Without proper inspection of the pipes, the consultants could not allow the project to continue. A condition assessment was called for, in order to continue the project, but the consultants were not convinced either CCTV or LiDAR alone was the solution, so they contacted SewerVUE Technology and inquired about their patented pipe penetrating radar (PPR) technology. PPR is the in-pipe application of ground penetrating radar. GPR antennas are taken inside the pipe and are used to scan the inner wall. With this method, PPR surveys can see remaining wall thickness, rebar cover, delamination, and detect the presence of voids developing outside the pipe. PPR, supplemented by LiDAR, were assets in coming up with the appropriate design approach for the project.
Generalization Bounds for Ranking Algorithms via Algorithmic Stability (2009)

The problem of ranking, in which the goal is to learn a real-valued ranking function that induces a ranking or ordering over an instance space, has recently gained much attention in machine learning. We study generalization properties of ranking algorithms using the notion of algorithmic stability; in particular, we derive generalization bounds for ranking algorithms that have good stability properties. We show that kernel-based ranking algorithms that perform regularization in a reproducing kernel Hilbert space have such stability properties, and therefore our bounds can be applied to these algorithms; this is in contrast with generalization bounds based on uniform convergence, which in many cases cannot be applied to these algorithms. Our results generalize earlier results that were derived in the special setting of bipartite ranking (Agarwal and Niyogi, 2005) to a more general setting of the ranking problem that arises frequently in applications.
Bio-organic-inorganic Hybrid Soft Materials: Photoelectric Conversion Systems Based on Photosystem I and II with Molecular Wires (2021)

This review discusses methods for increasing the efficiency of photoelectric conversion systems using photosystem I (PSI) and photosystem II (PSII) isolated from thermophilic cyanobacteria. The structure and electron transfer pathways for PSI and PSII are described, followed by a description of a new type of photoelectric conversion system and its application in light-sensing devices using PSI or PSII. Photoelectron transfer is demonstrated by spectroscopic and electrochemical measurements. A strategy to enhance photocurrent intensity is described, involving wiring photosynthetic reaction centers onto a self-assembled monolayer on an electrode. We review the fundamental concept behind these semi-artificial photosynthetic systems, as well as representative examples from published papers, including those from our laboratory. This review discusses methods for increasing the efficiency of photoelectric conversion systems using photosystem I (PSI) and photosystem II (PSII) isolated from thermophilic cyanobacteria. Fabrication of photoelectric conversion systems and their applications in light-sensing devices using PSI or PSII are described. A strategy to enhance photocurrent intensity is also described, involving wiring photosynthetic reaction centers onto a self-assembled monolayer on an electrode.
Fabrication of Radio-Opaque and Macroporous Injectable Calcium Phosphate Cement (2022)

The aim of this work was the development of injectable radio-opaque and macroporous calcium phosphate cement (CPC) to be used as a bone substitute for the treatment of pathologic vertebral fractures. A CPC was first rendered radio-opaque by the incorporation of zirconium dioxide (ZrO<sub>2</sub>). In order to create macroporosity, poly lactic-<i>co</i>-glycolic acid (PLGA) microspheres around 100 μm were homogeneously incorporated into the CPC as observed by scanning electron microscopy. Physicochemical analyses by X-ray diffraction and Fourier transform infrared spectroscopy confirmed the brushite phase of the cement. The mechanical properties of the CPC/PLGA cement containing 30% PLGA (wt/wt) were characterized by a compressive strength of 2 MPa and a Young's modulus of 1 GPa. The CPC/PLGA exhibited initial and final setting times of 7 and 12 min, respectively. Although the incorporation of PLGA microspheres increased the force necessary to inject the cement and decreased the percentage of injected mass as a function of time, the CPC/PLGA appeared fully injectable at 4 min. Moreover, in comparison with CPC, CPC/PLGA showed a full degradation in 6 weeks (with 100% mass loss), and this was associated with an acidification of the medium containing the CPC/PLGA sample (pH of 3.5 after 6 weeks). A cell viability test validated CPC/PLGA biocompatibility, and in vivo analyses using a bone defect assay in the caudal vertebrae of Wistar rats showed the good opacity of the CPC through the tail and a significant increased degradation of the CPC/PLGA cement a month after implantation. In conclusion, this injectable CPC scaffold appears to be an interesting material for bone substitution.
Prospects for high power Linac Coherent Light Source (LCLS) development in the 1000{angstrom} {minus} 1{angstrom} wavelength range (1994)

Electron bunch requirements for single-pass saturation of a Free-Electron Laser (FEL) operating at full transverse coherence in the Self-Amplified Spontaneous Emission (SASE) mode include: (1) a high peak current, (2) a sufficiently low relative energy spread, and (3) a transverse emittance {var_epsilon}[r-m] satisfying the condition {var_epsilon} {le} {lambda}A/4{pi}, where {lambda}[m] is the output wavelength of the FEL. In the insertion device that induces the coherent amplification, the prepared electron bunch must be kept on a trajectory sufficiently collinear with the amplified photons without significant dilution of its transverse density. In this paper we discuss a Linac Coherent Light Source (LCLS) based on a high energy accelerator such as, e.g., the 3km S-band structure at the Stanford Linear Accelerator Center (SLAC), followed by a long high-precision undulator with superimposed quadrupole (FODO) focusing, to fulfill the given requirements for SASE operation in the 1000{Angstrom}--1{Angstrom} range. The electron source for the linac, an RF gun with a laser-excited photocathode featuring a normalized emittance in the 1--3 mm-mrad range, a longitudinal bunch duration of the order of 3 ps, and approximately 10{sup {minus}9} C/bunch, is a primary determinant of the required low transverse and longitudinal emittances. Acceleration of the injected bunch to energies in the 5--25 GeV range is used to reduce the relative longitudinal energy spread in the bunch, as well as to reduce the transverse emittance to values consistent with the cited wavelength regime. Two longitudinal compression stages are employed to increase the peak bunch current to the 2--5 kA levels required for sufficiently rapid saturation. The output radiation is delivered, via a grazing-incidence mirror bank, to optical instrumentation and a multi-user beam line system. Technological requirements for LCLS operation at 40{Angstrom}, 4.5{Angstrom}, and 1.5{Angstrom} are examined.
A unique PDZ domain and arrestin-like fold interaction reveals mechanistic details of endocytic recycling by SNX27-retromer (2014)

The sorting nexin 27 (SNX27)-retromer complex is a major regulator of endosome-to-plasma membrane recycling of transmembrane cargos that contain a PSD95, Dlg1, zo-1 (PDZ)-binding motif. Here we describe the core interaction in SNX27-retromer assembly and its functional relevance for cargo sorting. Crystal structures and NMR experiments reveal that an exposed β-hairpin in the SNX27 PDZ domain engages a groove in the arrestin-like structure of the vacuolar protein sorting 26A (VPS26A) retromer subunit. The structure establishes how the SNX27 PDZ domain simultaneously binds PDZ-binding motifs and retromer-associated VPS26. Importantly, VPS26A binding increases the affinity of the SNX27 PDZ domain for PDZ- binding motifs by an order of magnitude, revealing cooperativity in cargo selection. With disruption of SNX27 and retromer function linked to synaptic dysfunction and neurodegenerative disease, our work provides the first step, to our knowledge, in the molecular description of this important sorting complex, and more broadly describes a unique interaction between a PDZ domain and an arrestin-like fold.
Opportunistic Spectrum Access in Fading Channels Through Collaborative Sensing (2007)

Spectrum scarcity is becoming a major issue for service providers interested in either deploying new services or enhancing the capacity for existing applications. On the other hand, recent measurements suggest that many portions of the licensed (primary) spectrum remain unused for significant periods of time. This has led the regulatory bodies to consider opening up under-utilized licensed frequency bands for opportunistic access by unlicensed (secondary) users. Among different options, sensing-based access incurs a very low infrastructure cost and is backward compatible with the legacy primary systems. In this paper, we investigate the effect of user collaboration on the performance of sensing-based secondary access in fading channels. In particular, we demonstrate that under independent fading or shadowing, a low-overhead collaboration scheme with a very simple detector as its building block, 1) improves the spectrum utilization significantly, 2) enables the individual users to employ less sensitive detectors, thereby allowing a wider range of devices to access the primary bands, 3) increases the robustness toward noise uncertainty, 4) reduces the time and bandwidth resources required for satisfactory sensing which translates into higher agility and efficiency of the secondary access.
Abstract 321: Synergistic activity of the ATR inhibitor BAY 1895344 in combination with DNA damage inducing and DNA repair compromising therapies in preclinical tumor models (2018)

Abstract The DNA damage response (DDR) system consists of complex signalling pathways that secure the integrity of the genome in eukaryotic cells. DDR pathway activation follows recognition of DNA damage and results in cell cycle arrest, suppression of general translation, induction of DNA repair, cell survival or even cell death. Proteins that directly recognize aberrant DNA structures recruit and activate kinases of the DDR, such as ATR (ataxia telangiectasia and Rad3-related). ATR responds to a broad spectrum of DNA damages, including double-strand breaks (DSB) and lesions derived from interference with DNA replication as well as increased replication stress. Therefore, inhibition of ATR kinase activity could be the basis for a novel anti-cancer therapy in tumors with increased DNA damage, deficiency in DDR or replication stress. The potential of combining ATR kinase inhibitor with DNA damage inducing or DNA repair compromising anti-cancer therapeutics was studied in preclinical tumor models. We assessed the novel ATR kinase inhibitor (ATRi) BAY 1895344 in combination with external beam radiation therapy (EBRT), poly ADP ribose polymerase (PARP) inhibition or anti-androgen (AA) therapy. In cellular anti-proliferation assays as well as in tumor xenograft studies we could demonstrate synergistic activity of BAY 1895344 in combination treatment with the PARP inhibitor AZD-2281 in the homologous recombination (HR) defective breast cancer model MDA-MB-436, and with the non-steroidal AA darolutamide in the hormone-dependent prostate cancer model LAPC-4. Strong synergistic anti-tumor activity of BAY 1895344 could be further demonstrated in combination with EBRT inducing long-lasting tumor growth inhibition in the colorectal cancer xenograft model LOVO. The mechanism-based potential of combining DNA damage induction by EBRT with ATRi BAY 1895344 suggests a potential new treatment option for radiation therapy-resistant patients. Furthermore, the inhibition of parallel DDR pathways, as a combination of ATRi BAY 1895344 with a PARP inhibitor, indicates novel treatment opportunities in breast cancer patients with homologous recombination deficiencies, as does the synergism of BAY 1895344 and AA darolutamide therapy in hormone-dependent prostate cancer patients. BAY 1895344 is currently under clinical investigation in patients with advanced solid tumors and lymphomas (NCT03188965). Citation Format: Antje Margret Wengner, Gerhard Siemeister, Ulrich Luecking, Julien Lefranc, Kirstin Meyer, Eleni Lagkadinou, Bernard Haendler, Pascale Lejeune, Dominik Mumberg. Synergistic activity of the ATR inhibitor BAY 1895344 in combination with DNA damage inducing and DNA repair compromising therapies in preclinical tumor models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 321.