gebhart/patrepeval huggingface dataset:
A Mechanistic Study of Chemically Modified Inorganic Membranes for Gas and Liquid Separations (2011)

This final report will summarize the progress made during the period August 1, 1993 - October 31, 2010 with support from DOE grant number DE-FG03-93ER14363. The objectives of the research have been to investigate the transport mechanisms in micro- and mesoporous, metal oxide membranes and to examine the relationship between the microstructure of the membrane, the membrane surface chemistry, and the separation performance of the membrane. Examples of the membrane materials under investigation are the microporous silica hollow fiber membrane manufactured by PPG Industries, chemically modified mesoporous oxide membranes, and polymer membranes containing microporous oxides (mixed matrix membranes). Analytical techniques such as NMR, FTIR and Raman spectroscopy, thermal analysis, and gas adsorption were used to investigate membrane microstructure and to probe the chemical interactions occurring at the gas-membrane interface.
Mutations in a novel serine protease PRSS56 in families with nanophthalmos. (2011)

PRSS56 is a good candidate for the causal gene for nanophthalmos in our families.
<title>Multicomponent micropatterned sol-gel materials by capillary molding</title> (1997)

A physically and chemically benign method for patterning multiple sol-gel materials onto a single substrate is described. Structures are demonstrated for potential micro- optical chemical sensor, biosensor, and waveguiding applications. Fabrication is based on the micro molding in capillaries (MIMIC) approach. A novel mold design allows several sols to be cast simultaneously. Closely spaced, organically modified silica ridges containing fluorescent dyes are demonstrated. Ridges have cross sectional dimensions from one to 50 micrometers and are centimeters in length. Processing issues, particularly those related to mold filling, are discussed in detail. Because sol-gel MIMIC avoids the harsh physical and chemical environments normally associated with patterning, the approach allows full exploitation of sol- gel processing advantages, such as the ability to entrap sensitive organic dopant molecules in the sol-gel matrix.
Explanatory Diagnosis of an Ontology Stream via Reasoning About Actions (2016)

Explanatory diagnosis of an ontology stream aims to explain the changes hidden in the ontology stream by a sequence of actions. In this paper, we present a framework for explanatory diagnosis of an ontology stream, which allows the actions to be uncertain. In order to capture the semantics of actions, we introduce a new update operator and effect-guided bold-repair. By combining these operators with a query mechanism of description logicssupporting inconsistency-tolerant semantics, we present a formal definition for the explanatory diagnosis problem of ontology streams.
Clinical Evaluation of Eye Movements in Spinocerebellar Ataxias (2014)

Prospective data from a large cohort of patients with SCAs 1, 2, 3, and 6 provide statistical validation that the SCAs exhibit distinct eye movement abnormalities that are useful in identifying the genotypes. Many of the abnormalities correlate with greater disease severity measures.
Designed hydrophilic and charge mutations of the fibronectin domain: towards tailored protein biodistribution (2012)

Engineered proteins are attractive affinity scaffolds for molecular imaging and drug delivery. Although exquisite binding specificity and affinity can be engineered, many proteins exhibit off-target uptake, particularly in the kidneys and liver, from physiologic effects. We quantified the ability to alter renal and hepatic uptake via hydrophilic and charge mutations. As a model protein, we used the 10th type III domain of human fibronectin, which has been engineered to bind many targets and has been validated for molecular imaging. We screened rational mutants, identified by structural and phylogenetic analyses, to yield eight mutations that collectively substantially increase protein hydrophilicity. Mutation of two parental clones yielded four domains with a range of hydrophilicity. These proteins were labeled with (64)Cu, injected intravenously into nu/nu mice (n = 3-5 each) and evaluated by positron emission tomography. Renal uptake strongly correlated with hydrophilicity (Pearson's correlation coefficient = 0.97), ranging from 29 ± 11 to 100 ± 22% ID/g at 1 h. Hepatic uptake inversely correlated with hydrophilicity (Pearson's correlation coefficient = -0.92), ranging from 30 ± 7 to 3 ± 1% ID/g. Thus, renal and hepatic uptake are directly tunable through hydrophilic mutation, identifiable by structural and phylogenetic analyses. To investigate charge, we mutated acidic and basic residues in both parental clones and evaluated (64)Cu-labeled mutants in nu/nu mice (n = 5-7). Selected charge removal reduced kidney signal: 78 ± 13 to 51 ± 8%ID/g (P < 0.0001) for the hydrophilic clone and 32 ± 10 to 21 ± 3 (P = 0.0005) for the hydrophobic clone. Elucidation of hydrophilicity and charge enabled modulation of background signal thereby enhancing the utility of protein scaffolds as translatable targeting agents for molecular imaging and therapy.
Prenatally detected paternal uniparental chromosome 13 isodisomy (1998)

A 13q isodisomy in a balanced karyotype: 45,XY,-13,-13, + i(13)(q10) was found in cultured amniocytes studied because of advanced maternal age. The isochromosome was monocentric and a new mutation as both parents had normal chromosomes. Fetal blood was studied to exclude 13-trisomy mosaicism. All (100) lymphocytes studied had the same karyotype with i(13)(q10) as the amniocytes. To determine the origin of the isochromosome, six microsatellite markers from 13q were analysed: D13S175, D13S166, D13S162, AC224, COLAC1 and D13S122. The results indicated that the i(13)(q10) was of paternal origin and isodisomic. The father had a risk of 1/20 for being a carrier for an autosomal recessive, progressive brain disorder, variant late infantile neuronal ceroid lipofuscinosis (CLN5). The risk for the fetus for this disorder of chromosome 13 was excluded by haplotype analysis. A healthy child was born at week 40 of pregnancy, supporting the idea that there are no paternally imprinted genes on chromosome 13q. Analysis of extra embryonal tissue (four samples studied) revealed the same balanced karyotype with the i(13)(q10)pat chromosome. According to the cytogenetic and molecular studies, the origin of the isochromosome 13 could be a transverse centromere cleavage at the paternal meiosis II or at an early mitosis.
A Continuous Cell-Free Protein Synthesis System for Coupled Transcription-Translation1 (1991)

A continuous cell-free protein synthesis system [Spirin et al. (1988) Science 242, 1162-1164] was modified so as to be suitable for coupled transcription-translation, a process useful for obtaining products of cloned genes or cDNAs. A reaction chamber equipped with an ultrafiltration membrane was newly designed and an HPLC pump was used to supply a low molecular weight substrate solution at a constant rate to the viscous reaction mixture in the chamber. By using an Escherichia coli S30 extract in this modified flow system (1 ml), coupled transcription-translation could be continuously performed for 17 h, the synthesized chloramphenicol acetyltransferase (congruent to 0.1 mg) being subsequently eluted through the chamber's membrane and then purified.
Timing of Heparin Addition to the Biomolecular Corona Influences the Cellular Uptake of Nanocarriers (2019)

Few studies have considered the interaction of nanocarriers with drugs and the implications for their individual efficiency. Here, we demonstrate that heparin, a common anticoagulant, interacts with nanocarriers. Hence, nanocarriers, precoated with heparin and plasma in different conditions, were incubated with cancer cells, as well as primary cells from human blood. The relation between the timing of the heparin's addition to the nanocarrier and the cellular uptake extent was assessed by flow cytometry. Through proteomics the effect of heparin on the biomolecular corona composition was determined. We found that HeLa cells, monocytes and macrophages reacted differently to the presence of heparin: the uptake of the precoated nanocarriers decreased for HeLa and primary monocytes, while it increased for macrophages. Heparin induced no obvious change in the protein corona composition; thus, we suggest that heparin itself, through its adsorption on the nanocarrier, was responsible for the change of uptake.
Provenance-Based Analytics Services for Access Control Policies (2017)

Successful collaborations require information and resource sharing and thus adequate access control policy management systems that control sharing among the collaborating entities. Such management systems need to be flexible in order to adapt to different environments and thus be able to support access control policy evolution. However, when dealing with large sets of evolving policies it is critical that policies meet certain "policy quality requirements". Specifically, policies of interest must be up-to-date, complete, free of inconsistencies, relevant. In this paper, we propose an approach to analyze policies in order to determine whether policies meet such requirements. Our approach is based on the use of provenance techniques that collect comprehensive data about actions executed by users in the context of workflows, that is, sets of tasks executed according to some ordering by users. Provenance data are used by services that support various types of analysis to determine whether the policies of interest verify the quality requirements.
Detection of DNA Rearrangement in Rice Using a Cosmid Library (1997)

Previously we reported the migration and rearrangement of a chloroplast gene cluster into mitochondria. The exact genomic locations of the clusters, modes of the gene rearrangement and mechanisms of the interorganellar migration of the clusters have yet to be understood. The detailed analysis needs to include a larger region of DNA surrounding each cluster. To study DNA rearrangement and migration in more detail a cosmid library was constructed using the total rice genomic DNA including nuclear, chloroplast and mitochondrial DNA. From this cosmid library, a sub-library was obtained by selecting the clones hybridized to various regions of chloroplast DNA. According to the hybridization pattern 136 clones from the sub-library were classified into 29 groups. Detailed analysis of these clones revealed that in addition to authentic chloroplast DNA, the clones contain its homologs resulted from rearrangement and mutation. We analyzed two clones in detail, which contain different rp12 homologs resulted from rearrangement and/or migration, respectively.
A Miniaturized High Temperature Superconducting Bandpass Filter Using CPW Quarter-Wavelength Spiral Resonators (2006)

A novel compact high temperature superconducting BPF is developed by using coplanar waveguide quarter-wavelength spiral resonators. The filter is a 5-pole Chebyshev BPF with a midband frequency of 5.0GHz and an equal-ripple fractional bandwidth of 3.2%. The CPW spiral resonator is made as small as 1.02times2.1mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . As a result, the 5-pole filter occupies an area of only 7.65x2.11mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , less than one-third that of a newly reported CPW interdigital filter. The filter is fabricated by using 0.5mum YBCO film deposited on an MgO substrate. No bond-wire air-bridges are used and no post-tuning is made in the experiment. The measured filtering characteristics agree well with EM simulations and show low passband insertion losses in spite of the small size of the filter
Lipid-Specific β-Sheet Formation in a Mussel Byssus Protein Domain (2013)

Intrinsically disordered proteins (IDP) or regions (IDR) can adopt multiple conformational states, depending on the interaction partners they encounter. This enables proteins or individual domains to fulfill multiple functions. Here, we analyzed the flank sequences of preCol-NG, one of three collagenous proteins of a mussel byssus thread governing its mechanical performance. preCol-NG comprises a collagen domain and nonrepetitive termini enclosing specific flank regions characterized by tandem repeats known from silk proteins, protein elastomers, and plant cell wall-associated proteins. We recombinantly produced a protein mimicking the M. galloprovincialis preCol-NG C-terminal flank region. The protein was intrinsically unfolded in solution, even at elevated temperatures. However, upon contact with small unilamellar vesicles (SUVs) reversible β-structure formation occurred, reminiscent of partitioning-folding coupling. This behavior of preCol-NG flank domains likely impacts byssogenesis and sheds new light on a distinct mechanism of how fibrous protein materials might be achieved by lipid-induced self-assembly in nature.
FiDo: Ubiquitous Fine-Grained WiFi-based Localization for Unlabelled Users via Domain Adaptation (2020)

To fully support the emerging location-aware applications, location information with meter-level resolution (or even higher) is required anytime and anywhere. Unfortunately, most of the current location sources (e.g., GPS and check-in data) either are unavailable indoor or provide only house-level resolutions. To fill the gap, this paper utilizes the ubiquitous WiFi signals to establish a (sub)meter-level localization system, which employs WiFi propagation characteristics as location fingerprints. However, an unsolved issue of these WiFi fingerprints lies in their inconsistency across different users. In other words, WiFi fingerprints collected from one user may not be used to localize another user. To address this issue, we propose a WiFi-based Domain-adaptive system FiDo, which is able to localize many different users with labelled data from only one or two example users. FiDo contains two modules: 1) a data augmenter that introduces data diversity using a Variational Autoencoder (VAE); and 2) a domain-adaptive classifier that adjusts itself to newly collected unlabelled data using a joint classification-reconstruction structure. Compared to the state of the art, FiDo increases average F1 score by 11.8% and improves the worst-case accuracy by 20.2%.
SDS-PAGE of purified <i>Brugia malayi</i> recombinant proteins, <i>Bm</i>-RAL-2, <i>Bm</i>-103 and <i>Bm</i>-RAL-2—<i>Bm</i>-103 fusion protein. (2016)

&lt;p&gt;Two μg of each protein was loaded in SDS-PAGE along with SeeBlue pre-stained protein marker (Invitrogen, USA). (A) &lt;i&gt;Bm&lt;/i&gt;-RAL-2; (B) &lt;i&gt;Bm&lt;/i&gt;-103; (C) &lt;i&gt;Bm&lt;/i&gt;-RAL-2—&lt;i&gt;Bm&lt;/i&gt;-103 fusion protein.&lt;/p&gt;
Multiparametric MRI is not sufficient for prostate cancer staging: A single institutional experience validated by a multi-institutional regional collaborative (2023)

Despite enthusiasm for its use, in a real-world setting, mpMRI appears to be a poor staging study for localized CaP and is unreliable as the sole means of staging patients prior to prostatectomy. mpMRI should be used cautiously as a staging tool for CaP, and should be interpreted considering individual patient risk strata.
Leader and Leaderless Multi-Layer Consensus With State Obfuscation: An Application to Distributed Speed Advisory Systems (2017)

Two new distributed speed advisory systems (SASs) are introduced in this paper. The systems implement consensus algorithms that guide a set of vehicles toward a common driving speed. A major innovation is that consensus is achieved over a multi-layer network, in which parallel network topologies of connected vehicles are superimposed. The reason for the use of these parallel networks is that, in this way, the state obfuscation is possible, with the benefit that common driving speed is attained with no vehicle knowing the exact state of other vehicles. Convergence of the SASs is formally proved and two new results for the consensus of multi-layer networks modeled via stochastic differential equations are introduced. The SASs are also validated via simulation and via a hardware-in-the-loop setup, in which a real vehicle interacts with simulated entities.
Supplemental Figure 4 from Somatic Epigenetic Silencing of <i>RIPK3</i> Inactivates Necroptosis and Contributes to Chemoresistance in Malignant Mesothelioma (2023)

&lt;p&gt;Treatment of MM cells with the DNA demethylase 5-aza-2'-deoxycytidine (5-Aza) results in restoration of RIPK3 expression. MM cells lacking RIPK3 protein expression (RIPK3-negative) were treated with 30 µM of 5-Aza for 4 days. Semi-quantitative RT-PCR analysis was performed to analyze RIPK3 transcript levels in the RIPK3-negative cell lines.&lt;/p&gt;
The Affinity of Integrin α4β1 Governs Lymphocyte Migration (2001)

The interaction of integrin alpha(4)beta(1) with endothelial VCAM-1 controls the trafficking of lymphocytes from blood into peripheral tissues. Cells actively regulate the affinity of alpha(4)beta(1) for VCAM-1 (activation). To investigate the biological function of alpha(4)beta(1) activation, we isolated Jurkat T cell lines with defective alpha(4)beta(1) activation. Using these cells, we found that alpha(4)beta(1)-stimulated alpha(L)beta(2)-dependent cell migration was dramatically reduced in cells with defects in alpha(4)beta(1) activation. These cells required 20 times more VCAM-1 to promote alpha(L)beta(2)-dependent cell migration. This defect was at the level of alpha(4)beta(1) affinity as an activating alpha(4)beta(1) Ab rescued alpha(4)beta(1)-stimulated alpha(L)beta(2)-dependent migration. In contrast, migration of alpha(4)beta(1) activation-defective cells on VCAM-1 alone was enhanced at higher VCAM-1 densities. Thus, alpha(4)beta(1) activation determines a set point or threshold at which VCAM-1 can regulate alpha(L)beta(2)-dependent as well as alpha(4)beta(1)-dependent cell migration. Changes in this set point may specify preferred anatomical sites of integrin-dependent leukocyte emigration from the bloodstream.
Design and Electrical Performance of the Kinetic Inductance Detectors of the OLIMPO Experiment (2017)

We are going to describe the design and the electrical performance of the horn-coupled lumped element kinetic inductance detectors (LEKIDs) for the OLIMPO experiment. OLIMPO is a balloon-borne mission, devoted to the study of the largest structures in the Universe, by detecting the Sunyaev-Zel'dovich effect of the Cosmic Microwave Background (CMB) photons crossing clusters of galaxies. The multi-band focal planes (centered at 150, 200, 350 and 480 GHz), large aperture telescope (2.6 m), photometric and spectrometer configuration (OLIMPO is equipped with a plug-in differential Fourier transform spectrometer) make OLIMPO able to characaterise all the components of the Sunyaev-Zel'dovich effect with unprecedented precision. The design of the LEKIDs has been optimised to cope with a wide range of optical loadings (corresponding to both photometric and spectrometric configurations). The electrical characterisation of the LEKID arrays was performed in the OLIMPO cryostat, at a temperature around 300 mK and under a constant optical load lower than 500 fW. The readout electronics is a customised ROACH-2 coupled to a MUSIC DAC/ADC board. The averaged responsivities for the arrays, measured from the phase readout, are 1.18x10^11 rad/W for the 150 GHz array, 4.10x10^10 rad/W for the 200 GHz array, 1.09x10^12 rad/W for the 350 GHz array, and 4.41x10^11 rad/W for the 480 GHz array. Therefore, measuring the spectral noise density for each pixels of the arrays, whose average values are 2.5x10^-5 rad/Hz^(1/2) for the 150 GHz array, 3.6x10^-5 rad/Hz^(1/2) for the 200 GHz array, 5.1x10^-5 rad/Hz^(1/2) for the 350 GHz array, and 1.9x10^-5 rad/Hz^(1/2) for the 480 GHz array, we obtained the values of the averaged electrical noise equivalent power (NEP) over all the arrays: 2x10^-16 W/Hz^(1/2), 9x10^-16 W/Hz^(1/2), 5x10^-17 W/Hz^(1/2), and 4x10^-17 W/Hz^(1/2) respectively for the four OLIMPO arrays.
Scarless Wound Closure by a Mussel-Inspired Poly(amidoamine) Tissue Adhesive with Tunable Degradability (2017)

Burn, trauma, and various medical conditions including bacterial infection, diabetes complication, and surgery could lead to an acute cutaneous wound and scar formation. Application of tissue glues instead of sutures could minimize the additional trauma and scar formation. Despite the countless efforts devoted to the development of high-strength tissue glues, little attention has been paid to their influence on the scar formation. Here, we report the development of a new tissue glue with excellent biocompatibility and tunable degradability for scarless wound closure. A series of catechol-containing poly(amidoamine) (CPAA) polymers were synthesized via the one-step Michael addition of dopamine and bisacrylamide. The tertiary amino group in the polymer backbone was used to introduce a zwitterionic sulfobetaine group by one-step ring-opening polymerization. The introduction of the zwitterionic sulfobetaine group could easily tune the hydrophilicity and the degradability of CPAA without influencing the density of the catechol group in the polymer. Lap-shear tests on the porcine skin demonstrated a high adhesion strength of 7 kPa at 1 h, rising to 24 kPa by 12 h. Addition of silica nanoparticles could further enhance the adhesion strength by 50%. In vivo studies further confirmed that the CPAA tissue glue could effectively accelerate the healing process of incisional wounds on the back of Sprague Dawley rats compared with suture and reduce the scar formation.
FastLane: Test Minimization for Rapidly Deployed Large-Scale Online Services (2019)

Today, we depend on numerous large-scale services for basic operations such as email. These services, built on the basis of Continuous Integration/Continuous Deployment (CI/CD) processes, are extremely dynamic: developers continuously commit code and introduce new features, functionality and fixes. Hundreds of commits may enter the code-base in a single day. Therefore one of the most time-critical, yet resource-intensive tasks towards ensuring code-quality is effectively testing such large code-bases. This paper presents FastLane, a system that performs data-driven test minimization. FastLane uses light-weight machine-learning models built upon a rich history of test and commit logs to predict test outcomes. Tests for which we predict outcomes need not be explicitly run, thereby saving us precious test-time and resources. Our evaluation on a large-scale email and collaboration platform service shows that our techniques can save 18.04%, i.e., almost a fifth of test-time while obtaining a test outcome accuracy of 99.99%.