gebhart/patrepeval huggingface dataset:
Kinetics of retrovirus production and decay (1999)

There has been only limited success in using recombinant retroviruses to transfer genes for the purposes of human gene therapy, in part because the average number of genes delivered to the target cells (transduction efficiency) is often too low to achieve the desired therapeutic effect [Miller, AD. 1990. Blood 76:271-278; Mulligan RC. 1993. Science 260:926-932; Orkin SH, Motulsky AG. 1995. Report and recommendations of the panel to assess the NIH investment in research on gene therapy. Bethesda, MD: National Institutes of Health.]. One strategy to improve transduction efficiency is to focus on understanding and improving the processes used to produce recombinant retroviruses. In this report, we characterized the dynamics of retrovirus production and decay in batch cultures of virus producer cells using a simple mathematical model, a recombinant retrovirus encoding the Escherichia coli lacZ gene, and quantitative assays for virus activity and number. We found that the rate at which recombinant retroviruses spontaneously lose their activity (decay) is a strong function of temperature, decreasing roughly 2-fold for every 5 degrees C reduction in temperature, whereas the rate at which retroviruses are produced is only weakly affected by temperature, decreasing about 10% for every 5 degrees C reduction in temperature. In addition, we developed a simple mathematical model of virus production and decay that predicted that the virus titer in batch cultures of virus producer cells would reach a maximum steady-state at a rate that is inversely proportional to the virus decay rate and to a level that is proportional to the ratio of the virus production rate to the virus decay rate. Consistent with the model, we observed that the steady-state levels of virus titer increased more than 3-fold when the cell culture temperature was reduced from 37 to 28 degrees C. Despite their higher titers, virus stocks produced at 28 degrees C, when used in undiluted form so as to mimic human gene transfer protocols, did not transduce substantially more cells than virus stocks produced at 37 degrees C. The implications of our findings on the production of retroviruses for use in human gene therapy protocols are discussed.
Preliminary application of native Nephila edulis spider silk and fibrin implant causes granulomatous foreign body reaction in vivo in rat’s spinal cord (2022)

After spinal cord injury, gliomesenchymal scaring inhibits axonal regeneration as a physical barrier. In peripheral nerve injuries, native spider silk was shown to be an effective scaffold to facilitate axonal re-growth and nerve regeneration. This study tested a two-composite scaffold made of longitudinally oriented native spider silk containing a Haemocomplettan fibrin sheath to bridge lesions in the spinal cord and enhance axonal sprouting. In vitro cultivation of neuronal cells on spider silk and fibrin revealed no cytotoxicity of the scaffold components. When spinal cord tissue was cultured on spider silk that was reeled around a metal frame, migration of different cell types, including neurons and neural stem cells, was observed. The scaffold was implanted into spinal cord lesions of four Wistar rats to evaluate the physical stress caused on the animals and examine the bridging potential for axonal sprouting and spinal cord regeneration. However, the implantation in-vivo resulted in a granulomatous foreign body reaction. Spider silk might be responsible for the strong immune response. Thus, the immune response to native spider silk seems to be stronger in the central nervous system than it is known to be in the peripheral body complicating the application of native spider silk in spinal cord injury treatment.
High-rate operation of sulfur/mesoporous activated carbon composite electrode for all-solid-state lithium-sulfur batteries (2020)

All-solid-state lithium-sulfur batteries are promising from the perspective of high safety, low cost, and high capability. Herein, composites of sulfur and microporous carbon (MSP20, MSC30) are prepared by a melt diffusion process, and their performance as electrode materials are compared with that of composites based on nanocarbons. In addition to the type of carbon, the degree of mixing with solid electrolytes is an important factor in the formation of ionic/electronic conduction pathways. The all-solid-state cell using S-MSC30-Li3PS4 shows a high initial discharge capacity of 1488 mAh per gram of sulfur at 25 °C at a current density of 1.3 mA cm−2 and operates reversibly at a high current density of 12.7 mA cm−2 (3C) at 100 °C. The amorphization of sulfur is effective for obtaining high capacity and sulfur impregnated into the meso- and micropores of carbon is more active than sulfur that forms nanocomposites with nanocarbon.
Abstract 1658: Post-GWAS genetic and functional studies for bladder cancer: An uncommon protective synonymous coding variant within the UGT1A6 gene explains the GWAS signal and affects cellular detoxification (2012)

Abstract Background: A recent genome-wide association study (GWAS) of bladder cancer identified a single nucleotide polymorphism (SNP), rs11892031, within the UGT1A gene cluster on chromosome 2q37.1, as a novel risk factor. UGT1A locus encodes nine UGT proteins that belong to phase II cellular detoxification system. UGTs are functionally important for detoxification of aromatic amines, which are known risk factors for bladder cancer found in industrial chemicals and tobacco smoke. UGTs are composed of shared exons 2-5 and individual alternative first exons that define enzymatic activity and substrate specificity. Materials and results: We sequenced all nine highly similar alternative first exons of UGT genes in more than 2,000 individuals and identified 27 non-synonymous and 19 synonymous known coding variants, but no novel variants. Imputation based on the GWAS dataset, a combined reference panel of HapMap 3 and 1000 Genomes Projects, and a subset of GWAS samples genotyped for all the identified coding variants, generated data for 1,170 SNPs within the whole UGT region. Of these markers, the strongest association was detected for an uncommon (MAF&amp;lt;0.03) protective genetic variant rs17863783 (OR=0.55, 95%CI=0.44-0.69, p=3.3x10-7 in 4,035 cases and 5, 284 controls; D’=0.96, r2=0.23 with rs11892031). No residual association in this region was detected after adjustment for rs17863783. Rs17863783 is a synonymous coding variant Val209Val within the functional UGT1A6.1 splicing form, strongly expressed in the liver, kidney and bladder. We found the protective T allele of rs17863783 to be associated with increased mRNA expression of UGT1A6.1 in in-vitro exontrap assays and in human liver tissue samples. We suggest rs17863783 may protect from bladder cancer by increasing the removal of carcinogens from bladder epithelium by the UGT1A6.1 protein. Conclusions: Our study shows an example of genetic and functional role of an uncommon protective genetic variant in a complex human disease such as bladder cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1658. doi:1538-7445.AM2012-1658
Nanoparticles for targeting the infarcted heart (2011)

We report a nanoparticulate system capable of targeting the heart after myocardial infarction (MI). Targeting is based on overexpression of angiotensin II type 1 (AT1) receptor in the infarcted heart. Liposomes 142 nm in diameter were conjugated with a ligand specific to AT1. The nanoparticles were able to specifically target cardiac cells in vitro, and in the infarcted heart after intravenous injection in vivo. This system may be useful for delivering therapeutic agents specifically to the infarcted heart.
Type I interferon signaling is required for the APOBEC3/Rfv3-dependent neutralizing antibody response but not innate retrovirus restriction (2017)

APOBEC3 can restrict retroviruses in a type I IFN-independent manner in vivo. By contrast, the ability of APOBEC3 to promote NAb responses is type I IFN-dependent. These findings reveal novel insights on the interplay between type I IFNs and APOBEC3 in vivo that may have implications for augmenting antiretroviral NAb responses.
Making stretchy dielectric, conductive, and semiconductor polymers (2021)

The increasing demand for devices that are deformable, wearable, or implantable has been driving the development of functional materials that are additionally compliant and repeatedly stretchable. I will introduce our recent efforts in developing elastomeric dielectrics, semiconductors, and conductors. The formation of interpenetrating networks and other microstructural control techniques are used to (1) enhance the electromehcanical responses of dielectric elastomers, (2) protect the conductive percolation network of silver nanowires and carbon nanotubes at large-strain deformations, and (3) to impart elastic deformability to semiconductor materials that are otherwise not stretchy. Explorations of devices incorporating these materials will also be presented.
Regional distribution of iron and iron‐regulatory proteins in the brain in aging and Alzheimer's disease (1992)

It is well established that iron, which is of considerable importance for normal neurological function, is highly regulated in all organ systems. However, until recently, iron regulation in the nervous system has received little attention. This study quantitatively compares the levels of the major iron-regulatory proteins, transferrin and ferritin, and iron itself in three cerebral cortical regions of the human brain from material collected at autopsy. Three groups were studied: 1) normal adult (under 65 yr of age), 2) aged (greater than 65), and 3) Alzheimer's disease. Normally, transferrin is more abundant in white matter than in gray matter. Ferritin is approximately 10x more abundant than transferrin throughout the brain regions examined and is evenly distributed, as is iron, in the gray and white matter. In Alzheimer's disease transferrin is consistently decreased particularly in the white matter of the various cerebral cortical regions examined whereas the iron and ferritin changes are inconsistent. The observations in this study are consistent with our general hypothesis that iron homeostasis is disrupted in the aging brain and the alterations in iron-regulatory proteins are exacerbated in Alzheimer's disease. The decrease in transferrin levels could indicate a decreased mobility and subsequent utilization of iron in the brain. Such a decrease in iron availability could play a significant role in neuronal degeneration and increased peroxidative damage known to occur in Alzheimer's disease.
Functional subregions of the human entorhinal cortex (2015)

The entorhinal cortex (EC) is the primary site of interactions between the neocortex and hippocampus. Studies in rodents and nonhuman primates suggest that EC can be divided into subregions that connect differentially with perirhinal cortex (PRC) vs parahippocampal cortex (PHC) and with hippocampal subfields along the proximo-distal axis. Here, we used high-resolution functional magnetic resonance imaging at 7 Tesla to identify functional subdivisions of the human EC. In two independent datasets, PRC showed preferential intrinsic functional connectivity with anterior-lateral EC and PHC with posterior-medial EC. These EC subregions, in turn, exhibited differential connectivity with proximal and distal subiculum. In contrast, connectivity of PRC and PHC with subiculum followed not only a proximal-distal but also an anterior-posterior gradient. Our data provide the first evidence that the human EC can be divided into functional subdivisions whose functional connectivity closely parallels the known anatomical connectivity patterns of the rodent and nonhuman primate EC.
<i>H</i><sub><i><b>∞</b></i></sub>‐output regulation of linear heterogeneous multiagent systems over switching graphs (2018)

Summary In this paper, we analyze H ∞ ‐output regulation of linear heterogeneous multiagent systems. The agents are subject to modeled and unmodeled disturbances and communicate over a switching graph. We derive a sufficient condition that guarantees H ∞ output regulation for the mentioned setup. This sufficient condition places requirements on both the single‐agent systems and the switching graph. The requirement on the single‐agent systems is an H ∞ ‐criterion that should be satisfied by a proper design of the controller. Meanwhile, the switching graph needs to be maximally connected. Moreover, we derive an upper bound for the overall ‐gain of the output synchronization error with respect to the unmodeled disturbances over a fixed communication graph. We illustrate our technical developments by a simulation example.
Functional differentiation of B lymphocytes in congenital agammaglobulinemia. I. Generation of hemolytic plaque-forming cells. (1977)

Despite the absence of B lymphocytes, peripheral blood lymphocytes (PBL) from four of five patients with congenital agammaglobulinemia (cAgamma) generated a specific hemolytic plaque-forming cell (HcPFC) response in vitro to sheep red blood cells and ovalbumin. The kinetics, antigenic, and cellular requirements were similar to normals, but significantly less HcPFC were found in patient cultures. Normal but not patient HcPFC-precursor cells were inactivated by treatment with anti-mu antisera whereas generated HcPFC in both controls and patients were sensitive to treatment with anti-mu. Pokeweed mitogen (PWM) and dextran sulfate (DXS) enhanced the HcPFC-response of normal PBL; cAgamma-cells were unresponsive to DxS and, in the presence of PWM, the development of HcPFC was inhibited. These findings indicate the presence of B lymphocyte precursors in the majority of patients with cAgamma investigated.
Matting with a depth map (2010)

Depth maps are becoming a readily available commodity of the stereo pipeline. We propose to make use of this new free information to improve a key step of postproduction that is matting. We extend the work of Levin et al on closed form matting to introduce two new depth-aware techniques. First we explore how depth can be used as an extra channel in the matting process. Then we see how depth can be used as a diffusion guide for matting. Our results show that both techniques can reduce the amount of time needed to pull a matte.
Thermodynamic and Kinetic Relationships between Lewis Acid−Lewis Base Complexes Relevant to the P<sub>2</sub>Pt(OTf)<sub>2</sub>-Catalyzed Diels−Alder Reaction (2002)

The Pt(II) Lewis acids P2Pt(OTf)2 (2; P2 = dppe (a), R-BINAP (b)), which catalyze the Diels−Alder reaction of acryloyl-N-oxazolidinone (4) with cyclopentadiene (HCp), were generated in situ by activation of P2Pt(S-BINOL) precursors 1 with 2 equiv of triflic acid (HOTf). Catalysts 2 and catalytically relevant Lewis acid−Lewis base complexes [P2Pt(L2)]2+[OTf]-2 (L2 = 2 H2O (3), dienophile 4 (6), Diels−Alder adduct 5 (8)) were characterized by 1H and 31P NMR spectroscopy at 195 K. 2a was also characterized by X-ray crystallography. The thermodynamic relationships between 2, 3, 6, 8, and a BF4- analogue of 2 were determined through competitive binding experiments monitored by 31P NMR at 195 K, to assess the effects of competitive inhibition of counterions, additives, and product on substrate coordination to the catalyst. These experiments demonstrated that the Lewis bases bind to [P2Pt]2+ with relative strengths BF4- ≪ OTf- < 4 < 5 ≪ H2O. The rates of two ligand exchange processes (dienophile/dienophile (k1) and dienophile/OTf- (k2)) were measured at 270 K by simulation of exchange-broadened 31P NMR spectra of 2/6 equilibrium mixtures, revealing that ligand substitution occurs more rapidly in the dppe system than the R-BINAP system (180 times faster for k2). Finally, the reaction of HCp with 6 to give 8 was monitored by 31P and 1H NMR at 195 K; attack of HCp on Pt-coordinated 4 occurred much faster than ligand exchange, indicating that ligand exchange is the turnover-limiting step of the catalytic cycle.
Selective dry etching of III-nitrides in inductively coupled plasmas (2001)

A parametric cmpariosn of etch rate and etch selectivity has been performed for GaN, InN and AIN etched in chlorine- and boron halides-based Inductively Coupled Plasma (ICP) discharges. Chlorine-based chemistries produced controllable etch rates (50~150 nm/min) and maximum etch selectivities ~6 for InN over GaN and ~10 for InN over AlN. Maximum etch selectivities of ~100 for InN over GaN and InN over AlN were obtained in boron halides-based discharges and smooth etched surface morphologies were also achieved.
(Invited) Durable Nanoparticle for Fuel Cell Electrocatalyst (2016)

Demand on the practical synthetic approach to the high performance electrocatalyst is rapidly increasing for the fuel cell commercialization. However, sluggish kinetics hindered high performance. Therefore methods to improve the activity of catalysts that facilitate reaction kinetic have been and continue to be a popular area of research. Since electrocatalytic reactions occur on the catalyst surface, nanoparticles (NPs) with high surface area are promising candidates to overcome problems. However, their low stability at harsh operating condition impedes nanoparticle utilization. Here we present a synthesis of highly durable and active nanoparticle based electrocatalyst for fuel cell electrocatalyst. One example is ordered intermetallic face-centered tetragonal (fct)-PtFe NPs encapsulated by thin-layer carbon shell. Only few nanometers of carbon shells which is in situ formed from dopamine coating could effectively prevent the coalescence of NPs. This carbon shell also protects the NPs from detachment and agglomeration as well as dissolution throughout the harsh fuel cell operating conditions. The other is carbon encapsulated metal phosphide NPs for robust hydrogen evolution reaction. Anti-oxidative carbon shell prevent surface oxidation of NPs, leading exceptionally long-term durability. We believe that thin-layer carbon shell encapsulation of NPs can open a new possibility for the development of highly active and durable electrocatalyst in near future.
Technique for 25 nm x-ray nanolithography (2001)

The image-forming limit of x-ray lithography is said to be ∼70 nm using existing devices and technologies. This article presents methods to extend the limit to 25 nm or even below. Preparatory to the study, a light source was designed to improve x-ray beam toward shorter wavelength. In addition, a simulation code has been developed to evaluate the methods. The first method is to use a mask with a larger period and pattern than deigned images. The mask forms the designed images with an enlarged period. Two-dimensional, 25 nm width images can be formed using a 100 nm period pattern mask at 8 μm gap. The second method is to use a mask with interference slits. Since the image pattern is sharply focused, ⩽25 nm images can be formed at 8–12 μm gaps. Multiple exposures are applied to both methods in order to fill in the clearances of the images. Simulation results are shown in both methods for typical patterns.
A cross-sectional study evaluating tick-borne encephalitis vaccine uptake and timeliness among adults in Switzerland (2021)

The goal of this study was to evaluate timeliness of Tick-borne Encephalitis vaccination uptake among adults in Switzerland. In this cross-sectional survey, we collected vaccination records from randomly selected adults 18-79 throughout Switzerland. Of 4,626 participants, data from individuals receiving at least 1 TBE vaccination (n = 1875) were evaluated. We determined year and age of first vaccination and vaccine compliance, evaluating dose timeliness. Participants were considered "on time" if they received doses according to the recommended schedule ± a 15% tolerance period. 45% of participants received their first TBE vaccination between 2006 and 2009, which corresponds to a 2006 change in the official recommendation for TBE vaccination in Switzerland. 25% were first vaccinated aged 50+ (mean age 37). More than 95% of individuals receiving the first dose also received the second; ~85% of those receiving the second dose received the third. For individuals completing the primary series, 30% received 3 doses of Encepur, 58% received 3 doses of FSME-Immun, and 12% received a combination. According to "conventional" schedules, 88% and 79% of individuals received their second and third doses "on time", respectively. 20% of individuals receiving Encepur received their third dose "too early". Of individuals completing primary vaccination, 19% were overdue for a booster. Among the 31% of subjects receiving a booster, mean time to first booster was 7.1 years. We estimate that a quarter of adults in Switzerland were first vaccinated for TBE aged 50+. Approximately 80% of participants receiving at least one vaccine dose completed the primary series. We further estimate that 66% of individuals completing the TBE vaccination primary series did so with a single vaccine type and adhered to the recommended schedule.
Optical flow sensor for continuous invasive measurement of blood flow velocity (2019)

Continuous monitoring of intrapulse measurement of blood flow in humans is currently not achievable with clinically available instruments. In this paper, we demonstrate a method of measuring the instantaneous variations in flow during pulsatile blood flow with an optical flow sensor comprising a fiber Bragg grating sensor and illumination from a 565 nm Light-Emitting-Diode. The LED illumination heats the blood and fluctuations in temperature, due to variations in flow, are detected by the fiber sensor. A set of experiments at different flow rates (20 to 900 mL/min) are performed in a simulated cardiac circulation setup with pulsatile flow. Data are compared with an in-line time of flight ultrasound flow sensor. Our results show that the optical and ultrasonic signals correlate with Pearson coefficients ranging from -0.83 to -0.98, dependent on the pulsatile frequency. Average flow determined by ultrasound and the optical fiber sensor showed a parabolic relationship with R<sup>2</sup> = 0.99. An abrupt step change in flow induced by occlusion and release of the circuit tubing demonstrated that the optical fiber and ultrasound sensor had similar response. The method described is capable of intrapulse blood flow measurement under pulsatile flow conditions, with potential applications in medicine where continuous blood flow sensing is desired.
Machine Generation of Arabic Diacritical Marks. (2006)

The absence of the vowelization marks from the modern Arabic text represents a major obstacle in machine translation and other text understanding applications. In this paper we present a formulation of the problem of automatic generation of the Arabic diacritic marks from unvoweled text using a Hidden Markov Model (HMM) approach. The model considers the word sequence of unvoweled Arabic text as an observation sequence, and the possible diacritized expressions of the words as hidden states. The optimal sequence of diacritized words (or states) is then obtained efficiently using a dynamic programming algorithm. We present the basic algorithm and its evaluation, and discuss its limitations as well as various ramifications for improving its performance. 1.
Hierarchically structured layered-double-hydroxide@zeolitic-imidazolate-framework derivatives for high-performance electrochemical energy storage (2016)

Using CoAl-based layered-double-hydroxide@zeolitic-imidazolate-framework-67 as the precursor, resulting oxidation, carbonization and sulfurization derivative-based supercapacitors exhibit significantly enhanced energy storage capability.