gebhart/patrepeval huggingface dataset:
Chip-scale atomic magnetometer with improved sensitivity by use of the Mx technique (2007)

The fabrication and performance of a miniature optically pumped atomic magnetometer constructed with microfabricated components are discussed. This device measures the spin precession frequency of Rb87 atoms to determine the magnetic field by use of the Mx technique. It has a demonstrated sensitivity to magnetic fields of 5pT∕Hz1∕2 for a bandwidth from 1to100Hz, nearly an order of magnitude improvement over our previous chip-scale magnetometer. The 3dB bandwidth has also been increased to 1kHz by reconfiguring the miniature vapor cell heater.
Recombinantly expressed gas vesicles as nanoscale contrast agents for ultrasound and hyperpolarized MRI (2018)

Ultrasound and hyperpolarized magnetic resonance imaging enable the visualization of biological processes in deep tissues. However, few molecular contrast agents are available to connect these modalities to specific aspects of biological function. We recently discovered that a unique class of gas-filled protein nanostructures known as gas vesicles could serve as nanoscale molecular reporters for these modalities. However, the need to produce these nanostructures via expression in specialized cultures of cyanobacteria or haloarchaea limits their broader adoption by other laboratories and hinders genetic engineering of their properties. Here, we describe recombinant expression and purification of <i>Bacillus megaterium</i> gas vesicles using a common laboratory strain of <i>Escherichia coli</i>, and characterize the physical, acoustic and magnetic resonance properties of these nanostructures. Recombinantly expressed gas vesicles produce ultrasound and hyperpolarized <sup>129</sup>Xe MRI contrast at sub-nanomolar concentrations, thus validating a simple platform for their production and engineering.
A rapid method of reconstituting human erythrocyte sugar transport proteins (1984)

A rapid reconstitution procedure for human erythrocyte hexose transfer activity is described. The procedure (reverse-phase evaporation) avoids exposure of the isolated proteins to detergent, organic solvent, sonication, or freeze-thaw steps during insertion into synthetic membranes and may be effected within 15 min. The so-formed vesicles are unilamellar structures with a large encapsulated volume, narrow size range, and low passive permeabilities. Contamination by carry-through of endogenous (red cell) lipids is less than 1%. Reconstituted hexose transfer activity was examined by using unfractionated proteins (bands 3, 4.5, and 6) and purified proteins (bands 4.5 and 3). With unfractionated proteins, hexose transport activity is low [0.34 mumol X (mg of protein)-1 X min-1], is inhibited by cytochalasin B, and increases monotonically with protein concentration. Kinetic analysis indicates that Vmax values for both influx and efflux of D-glucose are identical. Reconstitution of the cytochalasin B binding protein (band 4.5) results in hexose transport with high specific activity [5 mumol X (mg of protein)-1 X min-1] and symmetry in transfer kinetics. Band 3 proteins also appear to mediate cytochalasin B sensitive D-glucose transport activity.
Classical diffusion of a quantum particle in a noisy environment (2009)

We study the spreading of a quantum-mechanical wave packet in a tight-binding model with a noisy potential and analyze the emergence of classical diffusion from the quantum dynamics due to decoherence. We consider a finite correlation time of the noisy environment and treat the system by utilizing the separation of fast (dephasing) and slow (diffusion) processes. We show that classical diffusive behavior emerges at long times and we calculate analytically the dependence of the classical diffusion coefficient on the noise magnitude and correlation time. This method provides a general solution to this problem for arbitrary conditions of the noisy environment. The calculation can be done in any dimension, but we demonstrate it in one dimension for clarity of representation. The results are relevant to a large variety of physical systems, from electronic transport in solid-state physics to light transmission in optical devices, diffusion of excitons, and quantum computation.
A soft decision helper data algorithm for SRAM PUFs (2009)

In this paper we propose the idea of using soft decision information in helper data algorithms (HDA). We derive and verify a distribution for the responses of SRAM-based physically unclonable functions (PUFs) and show that soft decision information becomes available without loss in min-entropy of the fuzzy secret. This significantly improves the implementation overhead of using an SRAM PUF + HDA for cryptographic key generation compared to previous constructions.
Toward connectomic deep brain stimulation (2016)

Deep brain stimulation (DBS) is an established and highly efficacious treatment option in idiopathic Parkinson’s disease, dystonia and essential tremor. In the past, the clinical effects of DBS were explained as local effects within the target structure of the DBS electrode. Nowadays, this concept is only considered part of the explanation of the mechanism of action of DBS. Rather, the concept has been extended by additive effects mediated via structural and functional connectivity of the target area to different other areas of the whole brain, namely the so-called cortex basal ganglia cerebellar loop. The analysis of whole brain connectivity is a discipline of the so- called connectomic neuroscience. The goal of the three studies that make up this dissertation was the establishment of a so ware-framework which combines the two fields of research – DBS and connectomic neuroscience – to allow for connectomic DBS research in future studies. The aims of the three studies were as follows: In the first study (Horn et al. 2013), a combined structural- functional whole brain connectivity analysis between forty-thousand points within the gray matter of the brain was performed in 19 healthy subjects. Using this novel observer- independent approach, it could be shown that regions forming part of the so-called default mode network exhibit the highest similarity in their structural and functional connectivity to the rest of the brain. In the second study (Horn et al. 2016), a structural group connectome was estimated by using di usion-weighted data from 169 subjects. This novel dataset allows estimating fiber tracking results within a standardized stereotactic space. Last, in the third study (Horn et al. 2015), a software package was developed that i) can be used to exactly localize DBS electrodes based on postoperative CT-/MR-Imaging and ii) integrates the methods and data estimated in the first two studies into a joint analysis framework. This software package was released as open source to the scientific community under the name of ‘Lead DBS’ and facilitates studies in the fields of DBS, connectomic neuroscience and a combination of both.
Clustering of Stimuli on Single-Walled Carbon Nanotube Bundles Enhances Cellular Activation (2009)

Functionalized single-walled carbon nanotube bundles (f-bSWNT) adsorbed with T-cell-stimulating antibodies are shown to enhance both the kinetics and magnitude of T cell stimulation compared to the same concentration of free antibodies in solution. This enhancement is unique to f-bSWNT compared to other artificial substrates with high surface area and similar chemistry. We explored the origins of this enhanced activity with FRET microscopy and found the preferential formation of large antibody stimuli clusters (5 to 6 microm) on the surface of functionalized versus untreated nanotubes. This highlights the important aspect that antigen clusters can be formed on f-bSWNT, impacting the potency of the T cell stimulus. Clustering of T cell antigens on artificial substrates impacts the avidity of interaction with cells facilitating rapid stimulation dynamics and an overall greater magnitude of response. These findings support the use of chemically treated nanotube bundles as an efficient substrate for the presentation of antigens and point to their potential in clinical applications involving artificial antigen-presentation for ex vivo T cell expansion in adoptive immunotherapy.
Clonal culturing of human embryonic stem cells on laminin-521/E-cadherin matrix in defined and xeno-free environment (2014)

Lack of robust methods for establishment and expansion of pluripotent human embryonic stem (hES) cells still hampers development of cell therapy. Laminins (LN) are a family of highly cell-type specific basement membrane proteins important for cell adhesion, differentiation, migration and phenotype stability. Here we produce and isolate a human recombinant LN-521 isoform and develop a cell culture matrix containing LN-521 and E-cadherin, which both localize to stem cell niches in vivo. This matrix allows clonal derivation, clonal survival and long-term self-renewal of hES cells under completely chemically defined and xeno-free conditions without ROCK inhibitors. Neither LN-521 nor E-cadherin alone enable clonal survival of hES cells. The LN-521/E-cadherin matrix allows hES cell line derivation from blastocyst inner cell mass and single blastomere cells without a need to destroy the embryo. This method can facilitate the generation of hES cell lines for development of different cell types for regenerative medicine purposes.
PapD chaperone function in pilus biogenesis depends on oxidant and chaperone-like activities of DsbA. (1994)

Adhesive P pili of uropathogenic Escherichia coli were not assembled by a strain that lacks the periplasmic disulfide isomerase DsbA. This defect was mostly attributed to the immunoglobulin-like pilus chaperone PapD, which possesses an unusual intrasheet disulfide bond between the last two beta-strands of its CD4-like carboxyl-terminal domain. The DsbA-dependent formation of this disulfide bond was critical for PapD's proper folding in vivo. Interestingly, the absence of the disulfide bond did not prevent PapD from folding in vitro or from forming a complex with the pilus adhesin in vitro. We suggest that DsbA maintains nascently translocated PapD in a folding-competent conformation prior to catalyzing disulfide bond formation, acting both as an oxidant and in a chaperone-like fashion. Disulfide bond formation in pilus subunits was also mediated by DsbA even in the absence of PapD. However, the ability of pilus subunits to achieve native-like conformations in vivo depended on PapD. These results suggest that a productive folding pathway for subunits requires sequential interactions with DsbA and the PapD chaperone.
Four highly stable eukaryotic mRNAs assemble 3′ untranslated region RNA–protein complexes sharing cis and trans components (1997)

Assembly of a sequence-specific RNA-protein complex on the 3' untranslated region (3'UTR) of human alpha-globin mRNA (alpha-complex) correlates with mRNA stabilization. Here we map a limited segment of the alpha-globin 3'UTR that is both necessary and sufficient for alpha-complex formation. The sequence of this binding region identifies three additional, highly stable mRNAs that share closely related, pyrimidine-rich cis-motifs in their respective 3'UTRs. Each mRNA assembles a sequence-specific ribonucleoprotein complex at this conserved region. These complexes are structurally related, and each contains a 39-kDa cytoplasmic poly(C) binding protein previously demonstrated to be essential to formation of the alpha-complex. These observations indicate the existence of a general determinant for stabilization of eukaryotic mRNAs.
Detection of inflammable gas in the atmosphere by new type of photo-acoustic Raman spectroscopy (1996)

Summary form only given. We propose a new type of photo-acoustic Raman spectroscopy (PARS) without a tunable laser for inflammable gas detection. The system is composed of a fixed-frequency laser and a Raman shifter filled with the high-pressure gas to be detected. Detection of H/sub 2/ at atmospheric pressure is demonstrated using a Q-switched Nd:YAG laser.
Upper-Airway Stimulation for Obstructive Sleep Apnea (2014)

Strollo, Patrick J. JR*; Soose, Ryan J.†; Maurer, Joachim T.‡; de Vries, Nico§; Cornelius, Jason‖; Froymovich, Oleg¶; Hanson, Ronald D.#; Padhya, Tapan A.**; Steward, David L.††; Boyd Gillespie, M.‡‡; Woodson, Tucker§§; Van de Heyning, Paul H.‖‖; Goetting, Mark G.¶¶; Vanderveken, Oliver M.‖‖; Feldman, Neil##; Knaack, Lennart***; STROHL, Kingman P.††† for the STAR (Stimulation Therapy for Apnea Reduction) Trial Group Author Information
Streptococcus suisBacterin and Subunit Vaccine Immunogenicities and Protective Efficacies against Serotypes 2 and 9 (2008)

Streptococcus suis causes numerous diseases in pigs, most importantly, meningitis, arthritis, septicemia, and bronchopneumonia. One of the major problems in modern swine production is the lack of a vaccine protecting against more than one S. suis serotype. The objective of this study was to determine the protective efficacy of a serotype 2 murein-associated protein (MAP) fraction subunit vaccine in comparison to that of a bacterin against experimental challenge with serotype 2 (containing muramidase-released protein [MRP], extracellular factor, and suilysin [SLY]) and serotype 9 (containing MRP variant MRP* and SLY) strains. MAP was shown to include different surface-associated proteins, such as the MRP and surface antigen one (SAO) expressed by both pathotypes used for challenge. The results of this study demonstrated that the serotype 2 bacterin induced protective immunity against homologous challenge. In contrast, the protective efficacy of the MAP subunit vaccine was low, though MAP immunization resulted in high serum immunoglobulin G2 titers against MRP and SAO. Importantly, immunization with bacterin but not with MAP induced opsonizing antibody titers against the serotype 2 strain, and these antibody titers were found to correlate with protection. However, after absorption with a nonencapsulated isogenic mutant, the sera from bacterin-immunized piglets failed to facilitate neutrophil killing, indicating that antibodies directed against capsule may not have been essential for opsonophagocytosis. Furthermore, induction of opsonizing antibodies against serotype 9 was not detectable in the group receiving bacterin or in the group receiving the MAP vaccine. In agreement, protection against the heterologous serotype 9 strain was low in both groups. Thus, identification of an antigen protecting against these two important S. suis pathotypes remains an important goal of future studies.
Production of haloperidol-loaded PLGA nanoparticles for extended controlled drug release of haloperidol (2005)

This study developed an emulsion-solvent evaporation method for producing haloperidol-loaded PLGA nanoparticles with up to 2% (wt/wt. of polymer) drug content, in vitro release duration of over 13 days and less than 20% burst release. The free haloperidol is removed from the nanoparticle suspension using a novel solid phase extraction technique. This leads to a more accurate determination of drug incorporation efficiency than the typical washing methods. It was discovered that PLGA end groups have a strong influence on haloperidol incorporation efficiency and its release from PLGA nanoparticles. The hydroxyl-terminated PLGA (uncapped) nanoparticles have a drug incorporation efficiency of more than 30% as compared to only 10% with methyl-terminated PLGA (capped) nanoparticles. The in vitro release profile of nanoparticles with uncapped PLGA has a longer release period and a lower initial burst as compared to capped PLGA. By varying other processing and materials parameters, the size, haloperidol incorporation and haloperidol release of the haloperidol-loaded PLGA nanoparticles were controlled.
Torsade de pointes in a patient receiving intravenous vasopressin (1988)

A patient experienced hypertension, bradycardia, QT prolongation, and multiple episodes of torsade de pointes while receiving an iv vasopressin infusion. The dysrhythmias were attributed to vasopressin, but may have been potentiated by hypomagnesemia. Upon vasopressin discontinuation, ECG findings returned to normal before magnesium supplementation. Vasopressin may contribute to the development of torsade de pointes.
Mammalian cell growth proteins. I. Growth stimulation of fetuin. (1968)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Substrate Noise Coupling in Analog/RF Circuits (2010)

This practical resource offers you detailed guidance on the impact of substrate noise on a wide range of circuits operating from baseband frequencies up to mm-wave frequencies. This unique book presents case studies to illustrate that careful modeling of the assembly characteristics and layout details is required to bring simulations and measurements into agreement. You learn how to use a proper combination of isolation structures and circuit techniques to make analog/RF circuits more immune to substrate noise.
In silico studies on the comparative characterization of the interactions of SARS‐CoV‐2 spike glycoprotein with ACE‐2 receptor homologs and human TLRs (2020)

Abstract Coronavirus disease‐2019 (COVID‐19) outbreak due to novel coronavirus or severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection has come out as a major threat for mankind in recent times. It is continually taking an enormous toll on mankind by means of increasing number of deaths, associated comorbidities, and socioeconomic loss around the globe. Unavailability of chemotherapeutics/vaccine has posed tremendous challenges to scientists and doctors for developing an urgent therapeutic strategy. In this connection, the present in silico study aims to understand the sequence divergence of spike protein (the major infective protein of SARS‐CoV‐2), its mode of interaction with the angiotensin‐converting enzyme‐2 receptor (ACE2) receptor of human and related animal hosts/reservoir. Moreover, the involvement of the human Toll‐like receptors (TLRs) against the spike protein has also been demonstrated. Our data indicated that the spike glycoprotein of SARS‐CoV‐2 is phylogenetically close to bat coronavirus and strongly binds with ACE2 receptor protein from both human and bat origin. We have also found that cell surface TLRs, especially TLR4 is most likely to be involved in recognizing molecular patterns from SARS‐CoV‐2 to induce inflammatory responses. The present study supported the zoonotic origin of SARS‐CoV‐2 from a bat and also revealed that TLR4 may have a crucial role in the virus‐induced inflammatory consequences associated with COVID‐19. Therefore, selective targeting of TLR4‐spike protein interaction by designing competitive TLR4‐antagonists could pave a new way to treat COVID‐19. Finally, this study is expected to improve our understanding on the immunobiology of SARS‐CoV‐2 and could be useful in adopting spike protein, ACE2, or TLR‐guided intervention strategy against COVID‐19 shortly.
Familiar Music Listening with Binaural Beats for Older People with Depressive Symptoms in Retirement Homes (2017)

Objective Depression affect not only older people’ self-care ability and quality of life, but also increase the burden of their families and caregivers as well as health care resources. With consideration of the adverse effects of antidepressant medications and high medical costs of treating depression, it is important to use non-pharmacological interventions for managing depressive symptoms of older people. This study aimed to evaluate the effects of familiar music with alpha binaural beats on blood pressure, heart rate variability, and depression level of older people with depressive symptoms and to assess its feasibility for older people. Methods This study used a one-group pre-test and post-test design. Thirty-five older people residing in a retirement home participated in the study. Each participant listened to 30-minute familiar music with alpha binaural beats via a headphone individually while lying on the chair or bed in the afternoon in a private room. The music compact disk were Taiwanese old songs from the 1950-1970s which was familiar to most of the Taiwanese older people. Results The study results indicated that the participants after listening to 30-minute familiar music with embedded binaural beats of alpha frequencies at 10 Hz had shown immediate effects by a significant reduction on their heart rate, systolic blood pressure, and LF norm of heart rate variability (HRV), and a significant increase on HF norm of HRV indicating that the participants were in a relaxing state after listening to the music. Depression level was significantly decreased after listening to 30-minute familiar music with alpha binaural beats in the afternoon daily for five days. Conclusions Familiar music listening with alpha binaural beats can be a noninvasive and suitable intervention to promote relaxation and alleviate negative emotion in older people with depressive symptoms in long-term care settings.
Three-dimensional structure of potato carboxypeptidase inhibitor in solution. A study using nuclear magnetic resonance, distance geometry, and restrained molecular dynamics (1987)

The solution conformation of potato carboxypeptidase inhibitor (CPI) has been investigated by 1H NMR spectroscopy. The spectrum is assigned in a sequential manner by using two-dimensional NMR techniques to identify through-bond and through-space (less than 5 A) connectivities. A set of 309 approximate interproton distance restraints is derived from the two-dimensional nuclear Overhauser enhancement spectra and used as the basis of a three-dimensional structure determination by a combination of metric matrix distance geometry and restrained molecular dynamics calculations. A total of 11 converged distance geometry structures were computed and refined by using restrained molecular dynamics. The average atomic root mean square (rms) difference between the final 11 structures and the mean structure obtained by averaging their coordinates is 1.4 +/- 0.3 A for residues 2-39 and 0.9 +/- 0.2 A for residues 5-37. The corresponding values for all atoms are 1.9 +/- 0.3 and 1.4 +/- 0.2 A, respectively. The larger values for residues 2-38 relative to those for residues 5-37 arise from the fact that the positions of the N- (residues 1-4) and C- (residues 38-39) terminal tails are rather poorly determined, whereas those of the core of the protein (residues 5-37) are well determined by the experimental interproton distance data. The computed structures are very close to the X-ray structure of CPI in its complex with carboxypeptidase, and the backbone atomic rms difference between the mean of the computed structures and the X-ray structure is only 1.2 A. Nevertheless, there are some real differences present which are evidenced by significant deviations between the experimental upper interproton distance limits and the corresponding interproton distances derived from the X-ray structure. These principally occur in two regions, residues 18-20 and residues 28-30, the latter comprising part of the region of secondary contacts between CPI and carboxypeptidase in the X-ray structure.