gebhart/patrepeval huggingface dataset:
Biological reactions to reconstructive materials (2020)

Breast reconstructive techniques have been highly reliant on use of non-autologous materials for augmentation purposes. Although these avoid the problems of donor site morbidity, there are potential issues of durability due to innate biological reactions of the host to foreign materials. Biologic scaffolds such as acellular dermal matrix have the potential to undergo “constructive remodeling,” whereby cellular migration into the matrix, recruitment and differentiation of stem cells, along with blood vessel and nerve ingrowth can create new functional tissue for reconstructive purposes. Incorporation of the biologic is a key determinant of reconstructive success, as failure to do so is the root cause of a number of reconstructive complications. The decellularization process involves a balance between the competing aims of complete removal of antigenic cellular material and preserving the structure of extracellular matrix, such that it provides an optimal substrate for regeneration of functional host tissues.
Functional analysis of N-linking oligosaccharyl transferase enzymes encoded by deep-sea vent proteobacteria (2015)

Bacterial N-linking oligosaccharyl transferases (OTase enzymes) transfer lipid-linked glycans to selected proteins in the periplasm and were first described in the intestinal pathogen Campylobacter jejuni, a member of the ε-proteobacteria-subdivision of bacteria. More recently, orthologues from other ε-proteobacterial Campylobacter and Helicobacter species and a δ-proteobacterium, Desulfovibrio desulfuricans, have been described, suggesting that these two subdivisions of bacteria may be a source of further N-linked protein glycosylation systems. Whole-genome sequencing of both ε- and δ-proteobacteria from deep-sea vent habitats, a rich source of species from these subdivisions, revealed putative ORFs encoding OTase enzymes and associated adjacent glycosyltransferases similar to the C. jejuni N-linked glycosylation locus. We expressed putative OTase ORFs from the deep-sea vent species Nitratiruptor tergarcus, Sulfurovum lithotrophicum and Deferribacter desulfuricans in Escherichia coli and showed that they were able to functionally complement the C. jejuni OTase, CjPglB. The enzymes were shown to possess relaxed glycan specificity, transferring diverse glycan structures and demonstrated different glycosylation sequon specificities. Additionally, a permissive D. desulfuricans acceptor protein was identified, and we provide evidence that the N-linked glycan synthesized by N. tergarcus and S. lithotrophicum contains an acetylated sugar at the reducing end. This work demonstrates that deep-sea vent bacteria encode functional N-glycosylation machineries and are a potential source of biotechnologically important OTase enzymes.
An ultraviolet photoelectron spectroscopic study of BF3–donor complexes (1989)

He i spectra of strong n–v type adducts of BF3 with H2O, CH3OH, (C2H5)2O, and CH3CN as well as of weak complexes of BF3 with NO and H2S are reported along with assignments based on MO calculations. The energy of the fluorine orbitals of BF3 is shown to be shifted in proportion to the strength of the donor–acceptor interaction. BF3 seems to form a contact pair with CS2.
Protein-Mimikry: eine neue Dimension für Peptide als Leitstrukturen? (1998)

Ein kurzes Peptid als Mimeticum für den 165 Aminosäuren langen Blutbildungsfaktor Erythropoetin konnte mit Peptidbibliotheken auf Phagenoberflächen (Phagen-Display-Bibliotheken) identifiziert werden. Die Kristallstruktur eines Peptiddimers im Komplex mit zwei Erythropoetin-Rezeptoren (siehe rechts) liefert einen Einblick in die molekulare Grundlage dieser Protein-Mimikry.
Collider in the Sea: Vision for a 500 TeV World Laboratory (2017)

A design is presented for a hadron collider in which the magnetic storage ring is configured as a circular pipeline, supported in neutral buoyancy in the sea at a depth of ~100 m. Each collider detector is housed in a bathysphere the size of the CMS hall at LHC, also neutral-buoyant. Each half-cell of the collider lattice is ~300 m long, housed in a single pipe that contains one dipole, one quadrupole, a correction package, and all umbilical connections. A choice of ~4 T dipole field, 2000 km circumference provides a collision energy of 700 TeV. Beam dynamics is dominated by synchrotron radiation damping, which sustains luminosity for &gt;10 hours. Issues of radiation shielding and abort can be accommodated inexpensively. There are at least ten sites world-wide where the collider could be located, all near major urban centers. The paper summarizes several key issues; how to connect and disconnect half-cell segments of the pipeline at-depth using remote submersibles; how to maintain the lattice in the required alignment; provisions for the injector sequence.
Performance Comparison of Duobinary Formats for 40-Gb/s and Mixed 10/40-Gb/s Long-Haul WDM Transmission on SSMF and LEAF Fibers (2009)

Duobinary formats are today considered as being one of the most promising cost-effective solutions for the deployment of 40-Gb/s technology on existing 10-Gb/s WDM long-haul transmission infrastructures. Various methods for generating duobinary formats have been developed in the past few years but to our knowledge their respective performances for 40-Gb/s WDM transmission have never been really compared. In this paper, we made an extensive numerical evaluation of the robustness of these different types of duobinary transmitter to accumulation of ASE noise, chromatic dispersion, PMD but also to single-channel and WDM 40-Gb/s transmission impairments on standard single-mode fiber. A numerical evaluation of the ability of duobinary format for mixed 10/40-Gb/s WDM long-haul transmission with 50-GHz channel spacing is also led, on both standard single-mode and LEAF fibers, and compared to DQPSK format. In order to clearly identify the limiting transmission effects on each of these two fiber types, the assessment of the performance of a 50-GHz spaced WDM 40-Gb/s long-haul transmission using either duobinary or DQPSK channels only is implemented at last.
2 mm Radius Loop Antenna and Linear Active Balun for Near Field Measurement of Magnetic Field in MRI-Conditional Testing of Medical Devices (2019)

This paper presents the design and construction of a magnetic field probe with an active balun for conditional testing of medical devices within a magnetic resonance imaging (MRI). The magnetic field probe was designed using a small loop antenna with 2 mm radius to have high spatial resolution and accuracy. It was tuned and matched at a center frequency of 128 MHz, which corresponds to 3 T MRI systems or equivalent radio frequency (RF) exposure systems for MRI-conditional testing of medical devices. An active balun with a differential transistor topology and a passive low-profile transformer were employed to boost the detected magnetic field signal level lead to higher sensitivity. It also has high input impedance that improves the decoupling of the probe to nearby medical devices. The designed magnetic field probe and active balun have been fabricated on a double-sided printed circuit board, FR4 thickness of 1.57 mm and a copper thickness of 35 μm, with overall footprint of 22 mm × 11 mm. A verification test setup was developed to generate a known field and calibrate the probe based upon an analytic calculation of field, FDTD simulation and a 10-mm radius passive tuned/matched loop antenna.
Cysteine-Rich α-Conotoxin SII Displays Novel Interactions at the Muscle Nicotinic Acetylcholine Receptor (2022)

α-Conotoxins that target muscle nicotinic acetylcholine receptors (nAChRs) commonly fall into two structural classes, frameworks I and II containing two and three disulfide bonds, respectively. Conotoxin SII is the sole member of the cysteine-rich framework II with ill-defined interactions at the nAChRs. Following directed synthesis of α-SII, NMR analysis revealed a well-defined structure containing a 3<sub>10</sub>-helix frequently employed by framework I α-conotoxins; α-SII acted at the muscle nAChR with half-maximal inhibitory concentrations (IC<sub>50</sub>) of 120 nM (adult) and 370 nM (fetal) though weakly at neuronal nAChRs. Truncation of α-SII to a two disulfide bond amidated peptide with framework I disulfide connectivity led to similar activity. Surprisingly, the more constrained α-SII was less stable under mild reducing conditions and displayed a unique docking mode at the nAChR.
Nanoscale Probing of Dynamics in Local Molecular Environments (2015)

Vibrational spectroscopy can provide information about structure, coupling, and dynamics underlying the properties of complex molecular systems. While measurements of spectral line broadening can probe local chemical environments, the spatial averaging in conventional spectroscopies limits insight into underlying heterogeneity, in particular in disordered molecular solids. Here, using femtosecond infrared scattering scanning near-field optical microscopy (IR s-SNOM), we resolve in vibrational free-induction decay (FID) measurements a high degree of spatial heterogeneity in polytetrafluoroethylene (PTFE) as a dense molecular model system. In nanoscopic probe volumes as small as 10(3) vibrational oscillators, we approach the homogeneous response limit, with extended vibrational dephasing times of several picoseconds, that is, up to 10 times the inhomogeneous lifetime, and spatial average converging to the bulk ensemble response. We simulate the dynamics of relaxation with a finite set of local vibrational transitions subject to random modulations in frequency. The combined results suggest that the observed heterogeneity arises due to static and dynamic variations in the local molecular environment. This approach thus provides real-space and real-time visualization of the subensemble dynamics that define the properties of many functional materials.
Protein redesign by learning from data (2014)

Protein redesign methods aim to improve a desired property by carefully selecting mutations in relevant regions guided by protein structure. However, often protein structural requirements underlying biological characteristics are not well understood. Here, we introduce a methodology that learns relevant mutations from a set of proteins that have the desired property and demonstrate it by successfully improving production levels of two enzymes by Aspergillus niger, a relevant host organism for industrial enzyme production. We validated our method on two enzymes, an esterase and an inulinase, creating four redesigns with 5-45 mutations. Up to 10-fold increase in production was obtained with preserved enzyme activity for small numbers of mutations, whereas production levels and activities dropped for too aggressive redesigns. Our results demonstrate the feasibility of protein redesign by learning. Such an approach has great potential for improving production levels of many industrial enzymes and could potentially be employed for other design goals.
Effect of gain saturation on receiver sensitivity in multichannel frequency-shift-keying direct-detection systems using erbium-doped fiber preamplifiers (1991)

Erbium-doped fiber amplifiers (EDFA's) are essential for optical communications applications.1 One advantage of EDFA's is the compensation of splitting loss in frequency-division multiplexing (FDM) star networks.2 However, the effect of gain saturation due to multiple channels decreases the EDFA inversion and the signal-to-noise ratio (SNR). A study of EDFA gain saturation effects on receiver sensitivity, using a single 1 Gb/s [215–1] frequency-shift-keying (FSK) channel, is reported here. The power penalty caused by ΔG = 6 dB gain compression is found to be ~1.5 dB and to increase rapidly for ΔG &gt; 6 dB, in agreement with our theoretical analysis which dearly identifies that such a rise is due to the measured increase in both the spontaneous emission factor, nsp, and relative contribution of the circuit noise.
Multiscale image segmentation using joint texture and shape analysis (2000)

We develop a general framework to simultaneously exploit texture and shape characterization in multiscale image segmentation. By posing multiscale segmentation as a model selection problem, we invoke the powerful framework offered by minimum description length (MDL). This framework dictates that multiscale segmentation comprises multiscale texture characterization and multiscale shape coding. Analysis of current multiscale maximum a posteriori segmentation algorithms reveals that these algorithms implicitly use a shape coder with the aim to estimate the optimal MDL solution, but find only an approximate solution.
The orthopedist as clinical densitometrist: cost- and time-effectiveness. (2007)

We tested the hypothesis that an orthopedic surgeon and his or her staff can efficiently and economically provide a bone densitometry service. This hypothesis reflects a philosophy that orthopedists should take a more active role in identifying patients at risk for osteoporosis. We evaluated the cost- and time-effectiveness of an orthopedic surgeon and his medical assistant in completing reports and related correspondence for dual-energy x-ray absorptiometry scans conducted in an orthopedic subspecialty clinic. Cost analysis showed that completing 14 or 15 reports per month was required to break even and that completing up to 40 reports per month was a highly efficient and economic use of the surgeon's time.
Investigation of Thermal Annealing Process of GaN Layer on Sapphire by Molecular Dynamics (2000)

Molecular dynamics (MD) calculations have been performed to simulate the heteroepitaxial growth process of GaN on sapphire (0001) substrates and the thermal stability of the low-temperature GaN layer during the annealing process has been investigated. The MD simulations indicated that the surface morphology and the crystallinity of GaN thin layers grown on sapphire at low temperature of 800 K was amorphouslike and very rough. The surface atomic morphology of the low-temperature GaN layer was improved after the thermal annealing MD simulations at 1100 and 1200 K and showed atomically hexagonal structures. The crystallinity of the GaN epitaxial layer on the sapphire (0001) substrate is found to be strongly dependent on the temperature of annealing.
ChemInform Abstract: Radionuclide Sensors for Environmental Monitoring: From Flow Injection Solid‐Phase Absorptiometry to Equilibration‐Based Preconcentrating Minicolumn Sensors with Radiometric Detection (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Two‐Photon Fluorescence Imaging and Therapy of Cancer Cells with Anisotropic Gold‐Nanoparticle‐Supported Porous Silicon Nanostructures (2018)

Abstract In this work, we prepared porous silicon (pSi) nanostructures decorated with gold nanoparticles, as probes for cell tissue imaging under two‐photon excitation. We also demonstrated that the Au/pSi nanosystems induced cytotoxicity and phototoxicity under two‐photon excitation.
Supermolecular liquid crystals (2004)

In this article we review recent work on the development and study of the properties of self-organising supermolecular and supramolecular materials, that are in size comparable to small proteins. We take the concept of the creation of dendritic liquid crystals, and apply it to the creation of new materials with single identifiable entities, so that they are monodisperse or are single compounds. We show how functionality can be in-built into such materials so that self-organising functional systems can be created.
Improved MPPT method for rapidly changing environmental conditions (2006)

A well-known limitation of the perturb and observe (P&O) MPPT method is that it can get confused and track in wrong direction during rapidly changing irradiation. The present work offers a simple and effective solution to this problem, by using an additional measurement of the solar array's power in the middle of the MPPT sampling period. The method has been experimentally tested and compared with the traditional P&O method
Reactivities of Silicas with Organometallic Methylating Agents (2000)

The surface of silica gel was modified by a variety of procedures aimed at the introduction of CH3−Si moieties. The formation of these moieties by reactions of either SOCl2-chlorinated silica or SiCl4-modified silica with simple organometallic reagents (methyllithium, methylmagnesium bromide, dimethylzinc, or trimethylaluminum) was examined. Solid-state 29Si and 13C NMR techniques were used to characterize the resulting materials, especially to determine the extent of methylation of the silica surface. It was shown that, for a synthetic pathway that includes a chlorination step, methylmagnesium bromide was the best reagent for simply attaching a methyl group to a surface silicon atom. Methyllithium is very destructive to the silica framework, and trimethylaluminum forms a very small amount of Si−CH3 moieties when allowed to react with silica itself, SOCl2-chlorinated silica, or SiCl4-treated silica. There was no obvious evidence that dimethylzinc reacted with dry silica or with either SOCl2-modified or SiCl4-modified silicas to form Si−CH3 bonds.
Associations of hiatus hernia with CT-based interstitial lung changes: the MESA Lung Study (2022)

HH was associated with more HAAs over time, particularly among <i>MUC5B</i> risk allele carriers, and ILAs in younger adults, and may be a risk factor in the early stages of interstitial lung disease.
Neurotrophic factors for disease-modifying treatments of Parkinson's disease: gaps between basic science and clinical studies (2020)

Gaps in our understanding of underlying disease etiology have hindered our attempts to find treatments able to slow down the progression of PD.
HistoCartography: A Toolkit for Graph Analytics in Digital Pathology (2021)

Advances in entity-graph based analysis of histopathology images have brought in a new paradigm to describe tissue composition, and learn the tissue structure-to-function relationship. Entity-graphs offer flexible and scalable representations to characterize tissue organization, while allowing the incorporation of prior pathological knowledge to further support model interpretability and explainability. However, entity-graph analysis requires prerequisites for image-to-graph translation and knowledge of state-of-the-art machine learning algorithms applied to graph-structured data, which can potentially hinder their adoption. In this work, we aim to alleviate these issues by developing HistoCartography, a standardized python API with necessary preprocessing, machine learning and explainability tools to facilitate graph-analytics in computational pathology. Further, we have benchmarked the computational time and performance on multiple datasets across different imaging types and histopathology tasks to highlight the applicability of the API for building computational pathology workflows.
Sensitivity of summer Lake Superior thermal structure to meteorological forcing (2011)

We use a one‐dimensional model, forced with realistic meteorological measurements, to determine to first order the sensitivity of summer surface water temperature, heat content, and vertical stratification scale to three forcing variables: air temperature, wind speed, and previous winter ice cover, all three of which have exhibited long‐term trends over the last few decades. Summer‐averaged surface temperature increases with increased air temperature, decreased ice cover, and decreased wind speed. Differences in heat content between model runs with differing initial temperatures (a proxy for winter ice cover) decrease over the course of the season, but significant differences present in late spring persist through the summer season. Interannual variability in wind speed is the predominant driver of variability in the vertical stratification scale.
Gastroendoscopic microwave in treatment of active upper gastrointestinal hemorrhage (2005)

Objective To evaluate the effects of gastroendascopic microwave in treatment of upper gastrointestinal hemorrhage.Methods The patients with active bleeding from upper gastrointestinal tract were randomly divided into two groups.The effects of gastroendoscopic miorowave therapy and traditional medications were comparatively evaluated.Results The therapeutic effects in the treatment group was much better than those in the control group.Emergency operation rate and mortality rate in the treatment group were lower than those in the control group.Average hospital stay in the treatment group was shorter than in the control group.Conclusion Gastroendoscopic microwave therapy is consider as highly effective,safe method in treatment of active upper gastrointestinal hemorrhage.
Bunazosin Reduces Intraocular Pressure in Rabbits by Increasing Uveoscleral Outflow (1998)

The mechanism of the ocular hypotensive effect of bunazosin hydrochloride (an alpha1-adrenergic antagonist) and the possible intermediary role of prostaglandins were studied in New Zealand albino rabbits. Aqueous flow, outflow facility and uveoscleral outflow were determined by fluorophotometry, and intraocular pressure (IOP) was measured by pneumatonometry on the fourth day of twice daily topical treatment with 0.1% bunazosin. Uveoscleral outflow was measured with a tracer infusion technique at 1 to 2 hours after one dose of 0.1% bunazosin. Total outflow facility was measured by a two-level constant-pressure infusion method before and at one hour after one dose of 0.1% bunazosin. The effect of topically applied cyclooxygenase inhibitors, including 0.25% indomethacin and 0.03% flurbiprofen, on the IOP reduction after bunazosin was evaluated. At 3 hours after the seventh consecutive dose given twice-daily, bunazosin significantly (P<0.001) reduced IOP to 13.4+/-0.8 mm Hg (mean +/- SEM) from a baseline of 19.6+/-1.1 mm Hg. Indomethacin significantly inhibited the IOP reduction after one dose of bunazosin, whereas flurbiprofen did not (repeated measures ANOVA). Bunazosin significantly increased uveoscleral outflow (P<0.05) and total outflow facility (P<0.02), but not fluorophotometric outflow facility or aqueous flow. It is concluded that, in rabbits, 0.1% bunazosin reduces IOP predominantly by increasing uveoscleral outflow. The role of prostaglandins in this effect is equivocal.
Channel coding and transmission aspects for wireless multimedia (1999)

Multimedia transmission has to handle a variety of compressed and uncompressed source signals such as data, text, image, audio, and video. On wireless channels the error rates are high and joint source/channel coding and decoding methods are advantageous. Also, the system architecture has to adapt to the bad channel conditions. Several examples of a joint design are given. We especially advocate the use of rate-compatible punctured systematic recursive convolutional (RCPRSC) codes which are show to lead to a straightforward and versatile unequal error protection (UEP) design. In addition, the high-end receiver could use soft outputs and source-controlled channel decoding for even better performance.
Education, socio-economic status and age-related macular degeneration in Asians: the Singapore Malay Eye Study (2008)

Low educational level is associated with a higher prevalence of early AMD signs in our Asian population, independent of age, cardiovascular risk factors and cigarette smoking.