gebhart/patrepeval huggingface dataset:
The cytoprotective protein MANF promotes neuronal survival independently from its role as a GRP78 cofactor (2021)

Mesencephalic astrocyte-derived neurotrophic factor (MANF) is an endoplasmic reticulum (ER)-stress-regulated protein exhibiting cytoprotective properties through a poorly understood mechanism in various in vitro and in vivo models of neuronal and non-neuronal damage. Although initially characterized as a secreted neurotrophic factor for midbrain dopamine neurons, MANF has recently gained more interest for its intracellular role in regulating the ER homeostasis, including serving as a cofactor of the chaperone glucose-regulated protein 78 (GRP78). We aimed for a better understanding of the neuroprotective mechanisms of MANF. Here we show for the first time that MANF promotes the survival of ER-stressed neurons in vitro as a general unfolded protein response (UPR) regulator, affecting several UPR pathways simultaneously. Interestingly, MANF does not affect naïve neurons. We hypothesize that MANF regulates UPR signaling toward a mode more compatible with neuronal survival. Screening of MANF interacting proteins from two mammalian cell lines revealed a conserved interactome of 15 proteins including several ER chaperones such as GRP78, GRP170, protein disulfide isomerase family A member 1, and protein disulfide isomerase family A member 6. Further characterization confirmed previously published finding that MANF is a cofactor of GRP78 interacting with its nucleotide binding domain. Using microscale thermophoresis and nuclear magnetic resonance spectroscopy, we discovered that MANF is an ATP binding protein and that ATP blocks the MANF-GRP78 interaction. Interestingly, functional analysis of the antiapoptotic properties of MANF mutants in cultured neurons revealed divergent roles of MANF as a GRP78 cofactor and as an antiapoptotic regulator of UPR. We conclude that the co-factor type interaction with GRP78 is dispensable for the survival-promoting activity of MANF in neurons.
Pancreaticoduodenectomy for the Management of Pancreatic or Duodenal Metastases from Primary Sarcoma (2018)

To our knowledge, this is the largest series of patients with pancreatic metastases of sarcoma treated with surgical resection. Despite optimal resection with R0 margins, in the absence of effective adjuvant systemic therapies, the benefit of such an approach in metastatic disease remains unclear.
Structural and biophysical characterization of Nodamura virus (1994)

The correlation between virus structure and viral stability and assembly is poorly understood. The following studies were undertaken to gain insight into this relationship. The nodaviruses are a useful model system for studying virus structure and assembly because of their simple architecture and genome. They are assembled as a T = 3 provirion with 180 copies of coat protein and the bipartite RNA genome. Provirions mature by autoproteolytic cleavage of the coat protein. Maturation imparts stability to the capsid and is required for infectivity. The type member of the family, Nodamura virus (NOV), has a broader host range, including mammals and insects, and is less stable to denaturants and high salt than other nodaviruses. Monoclinic crystals of NOV contained four virus particles per unit cell, arranged with pseudo-rhombohedral symmetry. The pseudo symmetry generated novel difficulties in the structure determination. The 4.2 A resolution structure of NOV has several unique features. Most notable was weak density corresponding to 24 base pairs of ordered RNA extending $\sim$70 A in a groove between icosahedral threefold axes. The "peptide in the groove," at the ends of the groove, has many interactions with ordered RNA; this sequence is more basic in NOV than in other nodaviruses. Other changes in the NOV structure include surface loops which correlate with differences in host range. A mechanism was proposed for autoproteolytic maturation in the nodavirus family. Aspartic acid 75, buried at the cleavage site during capsid assembly, activates the scissile bond by a mechanism which resembles general acid catalyzed hydrolysis; mutation of ASP75 prevents maturation. Analysis of cleavage kinetics suggests that maturation is driven by the instability of the provirion; the rate is proportional to the extent of cleavage. Capsid dissociation by urea was observed by turbidity and electron microscopy. Disassembly was an equilibrium process. A formalism developed to describe equilibrium assembly of polyhedral protein complexes allowed further analysis of these studies. The presence of disassembly intermediates, in some conditions, suggests that capsid assembly involves generation of intersubunit strain. Disruption of the capsid breaks some associative interactions between subunits but allows relaxation of this strain energy.
Novel Synthesis of (Butatriene)hexacarbonyldiiron Complexes. Stereochemical Aspects and an X-ray Crystal Structure Determination (1996)

(Butatriene)hexacarbonyldiiron complexes with various substituents at either end of the triene ligand were prepared in good yields from 2-butyne-1,4-diols and enneacarbonyldiiron. For (2,5-dimethyl-2,3,4-hexatriene)hexacarbonyldiiron an X-ray crystal structure was obtained.
Integrating Single Domain Antibodies into Field-Deployable Rapid Assays (2022)

Single domain antibodies (sdAb) are the recombinant variable heavy domains derived from camelid heavy-chain antibodies. While they have binding affinities equivalent to conventional antibodies, sdAb are only one-tenth the size and possess numerous advantages such as excellent thermal stability with the ability to refold following denaturation, and inexpensive production in <i>Escherichia coli</i> or yeast. However, their small size does have drawbacks, one being that they can lose activity upon attachment or adsorption to surfaces, or may fail to adsorb efficiently, as they are highly soluble. This can make the transition from using conventional antibodies to sdAb nontrivial for assay development. Specifically, it is often necessary to re-optimize the protocols and tailor the recombinant sdAb through protein engineering to function efficiently in handheld assays, which currently are utilized for point of care testing and field applications. This work focuses on optimizing the integration of sdAb into rapid vertical flow assays. To achieve this goal, we engineered sdAb-based constructs and developed general protocols for the attachment of the sdAb to both gold nanoparticles and a support membrane. We achieved a limit of detection of 0.11 µg/mL for toxins staphylococcal enterotoxin B and ricin, both potential biothreat agents. Additionally, we demonstrated the ability to detect the nucleocapsid protein of SARS-CoV-2, a common target of antigen tests for COVID-19.
A lightweight encryption and authentication scheme for wireless sensor networks (2006)

The research of Wireless Sensor Networks (WSNs) has recently received a strong boost from IEEE 802.15.4 task group, which focuses on the specifications for low rate wireless personal area networks. Another important driving force of WSNs is the ZigBee Alliance, an industrial alliance concentrating on WSNs. This paper addresses the security of WSNs with respect to the protocol stack defined by IEEE 802.15.4 and the ZigBee Alliance. Some security problems are identified and remedies are suggested. A new security architecture based on a lightweight public key scheme, called Derivable Public Key (DPK), is proposed. The DPK scheme significantly simplifies the public key operations and reduces the related cost by eliminating the need for distributing and storing public keys other than the one from the trust centre. It makes possible to support authentications for multicast/broadcast communications in WSNs, which are not available and account for many attacks so far.
The Airborne Multiangle SpectroPolarimetric Imager (AirMSPI): a new tool for aerosol and cloud remote sensing (2013)

Abstract. The Airborne Multiangle SpectroPolarimetric Imager (AirMSPI) is an eight-band (355, 380, 445, 470, 555, 660, 865, 935 nm) pushbroom camera, measuring polarization in the 470, 660, and 865 nm bands, mounted on a gimbal to acquire multiangular observations over a ±67° along-track range. The instrument has been flying aboard the NASA ER-2 high altitude aircraft since October 2010. AirMSPI employs a photoelastic modulator-based polarimetric imaging technique to enable accurate measurements of the degree and angle of linear polarization in addition to spectral intensity. A description of the AirMSPI instrument and ground data processing approach is presented. Example images of clear, hazy, and cloudy scenes over the Pacific Ocean and California land targets obtained during flights between 2010 and 2012 are shown, and quantitative interpretations of the data using vector radiative transfer theory and scene models are provided to highlight the instrument's capabilities for determining aerosol and cloud microphysical properties and cloud 3-D spatial distributions. Sensitivity to parameters such as aerosol particle size distribution, ocean surface wind speed and direction, cloud-top and cloud-base height, and cloud droplet size is discussed. AirMSPI represents a major step toward realization of the type of imaging polarimeter envisioned to fly on NASA's Aerosol-Cloud-Ecosystem (ACE) mission in the next decade.
Quantum communications in space (2004)

Some of the detailed designs of a system exchanging a key to a low earth orbit satellite and remaining technical challenges to be overcome are discussed.
Gene expression profiling of two related maize inbred lines with contrasting root-lodging traits (2001)

To assist breeding for increased resistance to root lodging in maize, an attempt was made to identify genes that are associated with root lodging by profiling mRNA expression from two inbreds with contrasting root-related traits. These two inbreds were derived from a common F(2) pool, selfed for several generations and showed 75% relatedness based on 106 genetic markers. Under field conditions, the two inbreds exhibited significant differences in root morphology and resistance to root lodging. Whole root tissue was collected at two developmental stages from inbred 100 and 101 grown in 2 years. RNA was isolated from both the V8 and V12 stages, a few weeks prior to flowering. The RNA samples from the 1997 growing season were analysed by GeneCalling analysis, an open-ended mRNA profiling method. From over 13 500 cDNA fragments detected from each of the V8- and V12-stage samples, 229 and 325 cDNA fragments, respectively, showed greater than 2-fold differences between the two inbred lines. A total of 69 cDNA fragments that showed 2-fold or greater differences for both inbred lines were observed at both developmental stages. The gene identity and expression differences of several cDNA fragments were determined and confirmed by RNA gel blot analysis. Two genes out of five identified were homologous to a cytochrome P450 and the impedance-induced protein, both showing high levels of expression in the roots of lodging resistant lines and low levels in the sensitive lines. These data provide the first clues of genes expressed in the roots during the formative stages of root development associated with root-lodging resistance.
Design Considerations of MASH ΔΣ Modulators with GRO-based Quantization (2018)

A gated ring oscillator (GRO) based multi-stage noise-shaping ΔΣ modulator (ΔΣM) is presented in this paper. Loop-filter integrators followed by a digitally implemented GRO make the proposed architecture suitable for scaling-friendly implementations. Quantization noise of the first stage is represented in the time domain and it eases the quantization error extraction with a simple digital circuitry. The GRO offers inherent dynamic element matching, and hence no extra circuitry is needed to linearize the DACs in the feedback path. Time-domain behavioral simulations are shown to study of main GRO non-idealities considering a discrete-time MASH 3-1 topology, featuring a SNDR of 94 dB for an OSR of 16 over a 2-MHz signal bandwidth.
An evaluation of binary xml encoding optimizations for fast stream based xml processing (2004)

This paper provides an objective evaluation of the performance impacts of binary XML encodings, using a fast stream-based XQuery processor as our representative application. Instead of proposing one binary format and comparing it against standard XML parsers, we investigate the individual effects of several binary encoding techniques that are shared by many proposals. Our goal is to provide a deeper understanding of the performance impacts of binary XML encodings in order to clarify the ongoing and often contentious debate over their merits, particularly in the domain of high performance XML stream processing.
ChemInform Abstract: Chiral Separation by Enantioselective Liquid—Liquid Extraction (2011)

Abstract Review: 168 refs.
Nucleating Acicular Ferrite with Galaxite (Al2O3MnO) and Manganese Oxide (MnO2) in FeMnAlC steels (2012)

Effectiveness of galaxite (Al2O3MnO) and manganese oxide (MnO2) in nucleating acicular ferrite was demonstrated in a steel with composition of Fe-13.92Mn-4.53Al-1.28Si-0.11C. The hot rolled and quenched steel had a duplex microstructure of delta-ferrite and partially transformed austenite. Thermal treatments were used to manipulate the concentration and type of oxides and the ferrite plate density was found to correlate with inclusions of low misfit. Both bainitic and acicular ferrite were observed and the prior austenite had a grain diameter of 16.5 micrometers. Upon tensile testing the retained austenite transformed to alpha-martensite. Ultimate tensile strength and elongation were 970 MPa and 40 percent. The yield strength was found to be dependent on the ferrite plate size, which varied linearly with the strength of the austenite. Ductility decreased as the strength disparity between delta-ferrite and deformation-induced alpha-martensite increased.
Correlated self-heterodyne method for ultra-low-noise laser linewidth measurements (2020)

Narrow-linewidth lasers are important to many applications spanning precision metrology to sensing systems. Characterization of these lasers requires precise measurements of their frequency noise spectra. Here we demonstrate a correlated self-heterodyne (COSH) method capable of measuring frequency noise as low as 0.01 Hz$^2$/Hz at 1 MHz offset frequency. The measurement setup is characterized by both commercial and lab-built lasers, and features low optical power requirements, fast acquisition time and high intensity noise rejection.
Effect of Sodium on HCl Hydrate Diffusion in Ice:  Evidence for Anion−Cation Trapping (2002)

The effects of sodium (Na) on hydrogen chloride (HCl) hydrate diffusion in ice were investigated using infrared laser resonant desorption depth-profiling (LRD) techniques. By exciting the O−H stretching vibration in H2O, LRD was used to depth-profile into ice sandwich multilayers containing either an HCl or a Na/HCl interlayer. Diffusion coefficients for HCl were determined by measuring the relaxation of the HCl concentration gradient versus time. The HCl hydrate diffusion coefficient at 190 K in pure ice was D = 5.1(±1.7) × 10-11 cm2/s and lower for the Na/HCl interlayers. The HCl diffusion coefficients varied from D = 1.2(±0.5) × 10-11 cm2/s to D ≤ 9.0 × 10-13 cm2/s for initial interlayer molar ratios of Na/Cl = 0.04 to Na/Cl = 0.5, respectively. The effect of Na on HCl hydrate diffusion in ice is attributed to anion−cation trapping. Similar trapping interactions may influence the distribution of species in ice cores used to interpret the historical record of Earth's atmosphere.
Resource Constrained CVD Classification Using Single Lead ECG On Wearable and Implantable Devices (2021)

Electrocardiogram (ECG) is one of the fundamental markers to detect different cardiovascular diseases (CVDs). Owing to the widespread availability of ECG sensors (single lead) as well as smartwatches with ECG recording capability, ECG classification using wearable devices to detect different CVDs has become a basic requirement for a smart healthcare ecosystem. In this paper, we propose a novel method of model compression with robust detection capability for CVDs from ECG signals such that the sophisticated and effective baseline deep neural network model can be optimized for the resource constrained micro-controller platform suitable for wearable devices while minimizing the performance loss. We employ knowledge distillation-based model compression approach where the baseline (teacher) deep neural network model is compressed to a TinyML (student) model using piecewise linear approximation. Our proposed ECG TinyML has achieved ~156x compression factor to suit to the requirement of 100KB memory availability for model deployment on wearable devices. The proposed model requires ~5782 times (estimated) less computational load than state-of-the-art residual neural network (ResNet) model with negligible performance loss (less than 1% loss in test accuracy, test sensitivity, test precision and test F1-score). We further feel that the small footprint model size of ECG TinyML (62.3 KB) can be suitably deployed in implantable devices including implantable loop recorder (ILR).
A Non-Through Silicon Via 1000+ IO Package On Package Solution For Wide IO Applications (2013)

We are developing a new solution for wide I/O package on package applications, which is Bond Via Array (BVA) technology. The prototype vehicle built in this study has 1020 I/O's at a pitch of 0.24 mm with a high aspect ratio of approximately 10:1 and is ≤1.4 mm tall. PoP applications require large bandwidth and thinner packages challenging package developers to address warpage control for high yield processes. The design optimization of this package was established through rigorous finite element analysis of materials selection and structural modifications. The simulation methodology was validated by measuring the warpage as a function of temperature for the experimental prototypes. The details for the simulation and verification processes for the wide I/O process will be discussed. The variation between finite element analysis predictions and the experimental builds was ~10%, which allowed us to complete package design optimization with our simulation tools. The prototype build includes a standard and a low CTE substrate.
ChemInform Abstract: Organolanthanoid‐Catalyzed Intramolecular Hydroamination/Cyclization of Amines Tethered to 1,2‐Disubstituted Alkenes. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
Experimental demonstration of 1600 km SSMF transmission of a generalized direct detection optical virtual SSB-OFDM system (2008)

We experimentally demonstrate a generalized VSSB-OFDM format that judiciously determines the frequency gap between an inserted RF tone and the signal. The proposed scheme for 10 Gbps exhibits ~3 dB penalty after 1600 km SSMF transmission, and has an 8 dB improvement over the regular VSSB-OFDM.
Interaction of Human Mesenchymal Stem Cells With Disc Cells (2006)

Addition of MSCs to AF cells resulted in an up-regulation of the proteoglycans synthesis. This study provides the rationale for further investigation of the potential of MSC therapy in treating intervertebral disc degeneration.
EFFECT OF A BINARY BLEND COMPOSED OF POLOXAMER AND PVP ON AQUEOUS SOLUBILITY OF GRISEOFULVIN (2014)

Objective: The aim of this study was to improve the aqueous solubility of a poorly water soluble drug griseofulvin. Methods: To accomplish this goal a technique of solid dispersion with polyvinyl pyrolidone (k30) and poloxamer 407 was used. Solubility of griseofulvin alone and the solid dispersion were performed in 10 ml purified water and measured spectrophotometricaly atλ max 295 nm to detect the coefficient of improvement. Results: Solubility of griseofulvin alone was found to be 0.812 mg and the solubility of solid dispersion ranged from1.64 to 9.56 mg. After generating polynomial models correlating the variables using a D-Optimal mixture design, an optimal formulation with desired response was proposed by the statistical package. For validation, a new solid dispersion formulation based on the optimized composition was prepared and tested for solubility of griseofulvin. The optimized solid dispersion formulation enhances the solubility of griseofulvin by about 12 folds. Increase the amount of poloxamer in the optimized formulation increases the griseofulvin solubility to about 6 folds more than the optimized form. Conclusion: solid dispersion technique in conjunction with statistical design was shown to be very efficient for the optimization and improvement of aqueous solubility of poorly soluble drugs.
Robust strict positive realness: characterization and construction (2003)

Let P be a convex set of real polynomials. Consideration is given to the question of when there exists a real polynomial b(s), or, more generally, a real transfer function b(s), such that p(s)/b(s) is strictly positive real for all p(s) in P. Necessary and sufficient conditions are found for the transfer function case, and when the degree of the polynomials in P is restricted, such conditions are also found for the polynomial b(s) case. Closely related results are also obtained for a z-transform version of the problem. The results have application in adaptive systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Comparison of Primary Rat Hepatocyte Attachment to Collagen and Plasma‐Polymerised Allylamine on Glass (2006)

Abstract Summary: Cellular attachment to substrata is a crucial stage in cell culture and tissue engineering. Many cells including hepatocytes attach poorly to synthetic substrata and favour attachment to ECM proteins. Currently, cellular attachment to synthetic materials is often optimised by applying ECM protein coatings such as collagen. In this work, ppAAm was examined as an alternative coating method to collagen type‐I gel to promote attachment of primary rat hepatocytes to glass. XPS analysis was used to quantify the composition of the nitrogen containing ppAAm surfaces where the nitrogen is present in the form of amine, imine and possibly amide functionalities. Phase contrast microscopy and total cellular protein measurements indicated that hepatocyte attachment to glass was significantly improved by coating with ppAAm, collagen type‐I gel or collagen type‐I gel on ppAAm. In addition, cytochrome P450 activity and albumin secretion of hepatocytes cultured on ppAAm were similar to the levels observed in hepatocytes plated on collagen type‐I gel or collagen type‐I gel on ppAAm. In conclusion, the ppAAm coating was shown to improve the attachment of hepatocytes to glass while maintaining similar functionality to cells cultured on collagen type‐I gel. Phase contrast images of primary rat hepatocytes plated on collagen type‐I gel (top) and plasma polymerised allylamine (bottom) after 24 h in culture. magnified image Phase contrast images of primary rat hepatocytes plated on collagen type‐I gel (top) and plasma polymerised allylamine (bottom) after 24 h in culture.