gebhart/patrepeval huggingface dataset:
β1,4 N-Acetylgalactosaminyltransferase (GM2/GD2/GA2 synthase) forms homodimers in the endoplasmic reticulum: a strategy to test for dimerization of Golgi membrane proteins (1997)

Many Golgi membrane-bound glycosyltransferases exist as intermolecular disulfide bonded species, some of which have been demonstrated to be homodimers. Evidence for homodimer formation has come primarily from radiation inactivation experiments. We utilized an alternative strategy to test for homodimer formation of the cloned beta 1,4 N-acetylgalactosaminyltransferase (GalNAcT) responsible for synthesis of the glycosphingolipids GM2, GD2, and GA2. We stably transfected CHO cells with myc epitopetagged GalNAcT, which localizes primarily to the Golgi, and a hemagglutinin (HA) epitope-tagged GalNAcT fusion protein in which the cytoplasmic domain of GalNAcT was replaced by an ER retention signal. We then sought evidence for dimer formation between the two forms of GalNAcT. Immunoprecipitation with anti-myc or anti-HA co-immunoprecipitated the HA-tagged form or the myc-tagged form, respectively, providing evidence for the physical association of the two forms of GalNAcT. As a result of this association, GalNAcT/myc increased in the ER as demonstrated by Western blots and immunofluorescence. The rapid formation of dimers provided further evidence for dimer formation occurring in the ER. In summary, these results demonstrate that GalNAcT forms homodimers as a result of intermolecular disulfide bond formation in the ER. Furthermore, this ER motif strategy is potentially useful for demonstrating homodimer formation of other Golgi enzymes.
Safe Starting Regions for Iterative Methods (1977)

A search procedure based on interval computation is given for finding safe starting regions in n dimensions for iterative methods for solving systems of nonlinear equations. The procedure can search an arbitrary n-dimensional rectangle for a safe starting region for a quadratically convergent iterative method. The procedure is more powerful than continuation methods.
Engineering adoptive T cell therapy to co-opt Fas ligand-mediated death signaling in ovarian cancer enhances therapeutic efficacy (2021)

Abstract Background In the U.S., more than 50% of ovarian cancer patients die within 5 years of diagnosis, highlighting the need for innovations such as engineered T cell therapies. Mesothelin (Msln) is an attractive immunotherapy target for this cancer, as it is overexpressed by the tumor and contributes to malignant and invasive phenotypes, making antigen loss disadvantageous to the tumor. We previously showed that adoptively transferred T cells engineered to be Msln-specific (TCR 1045 ) preferentially accumulate within established ovarian tumors, delay tumor growth and significantly prolong survival in the ID8 VEGF mouse model. However, T cell persistence and anti-tumor activity were not sustained, and we and others have previously detected FasL in the tumor vasculature and the tumor microenvironment (TME) of human and murine ovarian cancers, which can induce apoptosis in infiltrating lymphocytes expressing Fas receptor (Fas). Methods To concurrently overcome this mechanism for potential immune evasion and enhance T cell responses, we generated an immunomodulatory fusion protein (IFP) containing the Fas extracellular binding domain fused to a 4-1BB co-stimulatory domain, rather than the natural death domain. T cells engineered to express TCR 1045 alone or in combination with the IFP were transferred into ID8 VEGF -tumor bearing mice and evaluated for persistence, proliferation, anti-tumor cytokine production, and therapeutic efficacy. Results Relative to T cells modified only to express TCR 1045 , T cells engineered to express both TCR 1045 and a Fas IFP preferentially persisted in the TME of tumor-bearing mice due to improved T cell proliferation and survival. Moreover, adoptive immunotherapy with IFP + T cells significantly prolonged survival in tumor-bearing mice, relative to TCR 1045 T cells lacking the IFP. Conclusions Fas/FasL signaling can mediate T cell death in the ovarian cancer microenvironment, as well as induce activation-induced cell death, an apoptotic mechanism responsible for regulating T cell expansion. Upregulation of FasL by tumor cells and tumor vasculature represents a mechanism for protecting growing tumors from attack by tumor-infiltrating lymphocytes. As many solid tumors overexpress FasL, an IFP that converts the Fas-mediated death signal into pro-survival and proliferative signals may provide an opportunity to enhance engineered adoptive T cell therapy against many malignancies.
Observation of magnetic fields due to persistent currents in a ring made of a Y1Ba2Cu3O7-δcoated conductor (2000)

A ring comprising a coated conductor was fabricated. First, the two ends of a biaxially textured Ni tape were connected by means of the atomic diffusion bonding technique. Then buffer layers and a YBCO film were deposited on the ring. All the films were well textured as confirmed by XRD pole figures. The B-H loops, where B and H are the magnetic field at the centre of the ring and the applied field, respectively, were measured as a function of temperature. The persistent current density (Jc) flowing circularly was estimated from the remanent field of B. In the range of temperatures from 72 to 20 K, Jc changed from 0 to 2×105 A cm-2.
Design techniques for reducing the cogging torque in surface-mounted PM motors (2002)

Several techniques may be adopted in motor design of surface-mounted permanent magnet motors in order to reduce the cogging torque. This paper describes the various techniques, (both classical and innovative techniques), giving for each of them a theoretical justification. To this aim, a simple original model of the cogging torque mechanism and a Fourier analysis are introduced. As a result, it is highlighted that some techniques are not always utilizable, and some of the well known ones may be even depreciatory when not used correctly. In addition, effects on back EMF are discussed.
Experimental and Theoretical Atomic-Resolved EELS Studies on Nitrogen Doped Single-Walled Carbon Nanotubes (2014)

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Trans esterification studies on castor oil as a first step towards its use in bio diesel production. (2008)

Castor (Ricinus communis L.) is a fast growing plant of marginal and moderately saline land widely spread throughout tropical regions. It is cultivated at arid coastal sandy belt and inland waste land of Pakistan for obtaining oil from its seeds, which being of medicinal importance is an economical commodity. Facing a great shortage of mineral diesel, scientists are nowadays actively working for converting oil obtained from wild/less commercially important plants into bio diesel for economic purposes. Non-edible oil yielding plants including castor bean, which cannot compete with edible oil yielding plants of commercial importance, are considered good candidates for such research work. The work presented herein deals with the transesterification of oil extracted from castor bean as a step towards possibility of converting it into bio diesel.
Path-Sensitive Inference of Function Precedence Protocols (2007)

Function precedence protocols define ordering relations among function calls in a program. In some instances, precedence protocols are well-understood (e.g., a call to pthread_mutex_init must always be present on all program paths before a call to pthread_mutex_lock). Oftentimes, however, these protocols are neither well- documented, nor easily derived. As a result, protocol violations can lead to subtle errors that are difficult to identify and correct. In this paper, we present CHRONICLER, a tool that applies scalable inter-procedural path-sensitive static analysis to automatically infer accurate function precedence protocols. Chronicler computes precedence relations based on a program's control-flow structure, integrates these relations into a repository, and analyzes them using sequence mining techniques to generate a collection of feasible precedence protocols. Deviations from these protocols found in the program are tagged as violations, and represent potential sources of bugs. We demonstrate CHRONICLER's effectiveness by deriving protocols for a collection of benchmarks ranging in size from 66 K to 2 M lines of code. Our results not only confirm the existence of bugs in these programs due to precedence protocol violations, but also highlight the importance of path sensitivity on accuracy and scalability.
Minimizing the Disaster Risk in Optical Telecom Networks (2012)

Regional failures caused by disasters precipitate huge amount of loss and jeopardize many connections. A risk model for disasters, considering differentiated services, is introduced and a disaster-aware provisioning scheme is proposed to reduce the risk.
Mouse Genetics (1999)

Gene characterization holds great promise for understanding molecular mechanisms of disease. Although glaucoma gene identification is very valuable and allows assessment of an individual's genetic risk, it is not by itself sufficient to answer detailed questions about pathogenesis. Despite the recent identification of a number of glaucoma genes, there are still many questions regarding the ways in which mutations in these genes cause disease. The mouse system, including the ability to alter specific genes, provides a powerful experimental system for hypothesis testing and molecular dissection of pathogenesis subsequent to gene identification. The ability to control both genetic and environmental factors will allow the use of mice to identify modifier genes that alter complex glaucoma phenotypes and that are especially difficult to identify in human families. By providing a bridge between gene identification and tests of gene function, mouse studies will be an important complement to those in humans and other species. This article summarizes the recent use of mice and the future potential of applying approaches of mouse genetics to intraocular pressure and glaucoma research.
1397-P: A Pregnancy Lifestyle Intervention Improves Metabolic Profile of Women and Infants by Reducing Gestational Weight Gain (GWG): The GLOW Randomized Controlled Trial (2019)

Among pregnant women with overweight or obesity, intensive interventions have reduced GWG but had only small effects on metabolic profile. In the Gestational weight gain and Optimal Wellness (GLOW) randomized controlled trial, we randomized pregnant women with overweight or obesity to a lifestyle intervention (n=199) or standard care (n=195) to evaluate the intervention’s efficacy in reducing GWG and improving metabolic biomarkers during pregnancy and in cord blood. Women in the intervention, vs. those in standard care, had significantly lower weekly rate of GWG from 10 to 32 weeks’ gestation (mean [SD], mean condition difference [95% CI]: 0.31 [0.18] vs. 0.42 [0.16], -0.11 [-0.15 to -0.08] kg/week) and lower total GWG (10.2 [5.6] vs. 12.4 [5.3], -2.2 [-3.3 to -1.1] kg). The intervention significantly reduced women’s fasting insulin, HOMA-IR and leptin from 10 to 32 weeks’ gestation and cord blood C-peptide, and yielded a borderline significant reduction of cord blood leptin (Table). The intervention’s effect on each biomarker was partially mediated by GWG, with the proportion of mediation effects ranging from 50 to 90% (all p-values &amp;lt;.02). Reducing GWG via lifestyle intervention resulted in improved metabolic profile of women and their infants. Disclosure A. Ferrara: None. M.M. Hedderson: None. S.D. Brown: None. A. Tsai: None. J. Feng: None. Y. Zhu: None. M.N. Galarce: None. S.M. Marcovina: None. C. Quesenberry: None. Funding National Institutes of Health (NICHDR01HD073572, NIDDKP30DK092924)
The Critical Choice of PEDOT:PSS Additives for Long Term Stability of Roll‐to‐Roll Processed OPVs (2015)

The impact of additives mixed with poly(3,4‐ethylenedioxythiophene):polysty­renesulfonate (PEDOT:PSS) on the stability of organic photovoltaic modules is investigated for fully ambient roll‐to‐roll (R2R) processed indium tin oxide free modules. Four different PEDOT:PSS inks from two different suppliers are used. The modules are manufactured directly on barrier foil without a UV filter to accelerate degradation and enable completion of the study in a reasonable time span. The modules are subjected to stability testing following well‐established protocols developed by the international summit on organic photovoltaic stability (ISOS). For the harsh indoor test (ISOS‐L‐3) only a slight difference in stability is observed between the different modules. During both ISOS‐L‐3 and ISOS‐D‐3 one new failure mode is observed as a result of tiny air inclusions in the barrier foil and a R2R method is developed to detect and quantify these. During outdoor operation (ISOS‐O‐1) the use of ethylene glycol (EG) as an additive is found to drastically increase the operational stability of the modules as compared to dimethylsulfoxide (DMSO) and a new failure mode specific to modules with DMSO as the additive is identified. The data are extended in an ongoing experiment where DMSO is used as additive for long‐term outdoor testing in a solar park.
Erratum: Spin-Scattering and Magnetic Ordering in EuB6 (1971)

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Misuse study of latch attachment: a series of frontal sled tests. (2007)

This study was initiated to quantify the effects of the misuse in LATCH lower webbing. In the short period since the implementation of the LATCH system several cases of potential misuses have been reported. A series of sled tests in frontal impact mode were conducted with various misuse conditions (loose attachment of LATCH lower webbing, misrouting of LATCH lower webbing and child seat back inclination) for both forward and rearward facing child safety seats (FFCSS and RFCSS). Results from these tests are compared and discussed with that of the standard test with no misuse and showed that as the slack in the lower LATCH webbing increased, ATD injury measures exceeded the limits. The FFCSS tests in the reclined condition yielded lower injury values for all except the chest G's when compared to the standard upright test. In the misrouting tests the ATD kinematics depended on the routing pivot point, the lower the pivot point the better the ATD kinematics. Similar findings were also observed in the RFCSS tests. The use of top tether with the FFCSS substantially improved the performance of the Hybrid III 3 year old ATD in spite of misuse conditions and the injury values were lower than the corresponding tests with no top tether. The effective reduction was 37% in the HIC values, 6% in the chest G's, 30% in the head excursion, 22 % in the knee excursion and finally 37 % reduction in the Nij values.
Through-Space Charge Modulation Overriding Substituent Effect: Rise of the Redox Potential at 3.35 V in a Lithium-Phenolate Stereoelectronic Isomer (2020)

Raising the operating potential of the organic positive electrode materials is a crucial challenge if they are to compare with lithium-ion inorganic counterparts. Although many efforts have been directed on tuning through substituent electronic effect, the chemistries than can operate above 3 V vs Li+/Li0, and thus be air stable in the Li-reservoir form (alike the conventional inorganic Li-ion positive electrode materials) remain finger-counted. Herein, we report on a new n-type organic Li-ion positive electrode material—the tetralithium 2,5-dihydroxy-1,4-benzenediacetate—with a remarkably high redox potential of 3.35 V vs Li+/Li0 attained notably in the solid phase. The origin of the high-energy content in this quinone derivative is found in a stereoelectronic chameleonic effect with an intramolecular conformation change and charge modulation leading to a redox potential increase of 650 mV in the solid state as compared to the same chemistry tested in solution (2.70 V vs Li+/Li0). The conformational dependent electroactivity rationale is supported by electrochemical and crystallography analysis, comparative infrared spectroscopy, and DFT calculation. We identify and make a linear correlation between the enolate vibrational modes and the redox potential, with general applicability for possibly other phenolate redox chemistries. Owing to these effects, this lithiated quinone is stable in ambient air and can be processed and handled alike the conventional inorganic Li-ion positive electrode materials. Whereas intrinsic to high voltage operation stability issues remain to be solved for practical implementation, our fundamental in nature and proof-of-concept study highlights the strong amplitude of through-space charge modulation effects in designing new organic Li-ion positive electrode chemistries with practical operating potential.
Enhanced Piezo‐Photoelectric Catalysis with Oriented Carrier Migration in Asymmetric Au−ZnO Nanorod Array (2020)

Current photocatalytic semiconductors often have low catalytic performance due to limited light utilization and fast charge carrier recombination. Formation of Schottky junction between semiconductors and plasmonic metals can broaden the light absorption and facilitate the photon-generated carriers separation. To further amplify the catalytic performance, herein, an asymmetric gold-zinc oxide (Asy-Au-ZnO) nanorod array is rationally designed, which realizes the synergy of piezocatalysis and photocatalysis, as well as spatially oriented electron-hole pairs separation, generating a significantly enhanced catalytic performance. In addition to conventional properties from noble metal/semiconductor Schottky junction, the rationally designed heterostructure has several additional advantages: 1) The piezoelectric ZnO under light and mechanical stress can directly generate charge carriers; 2) the Schottky barrier can be reduced by ZnO piezopotential to enhance the injection efficiency of hot electrons from Au nanoparticles to ZnO; 3) the unique asymmetric nanorod array structure can achieve a spatially directed separation and migration of the photon-generated carriers. When ultrasound and all-spectrum light irradiation are exerted simultaneously, the Asy-Au-ZnO reaches the highest catalytic efficiency of 95% in 75 min for dye degradation. It paves a new pathway for designing unique asymmetric nanostructures with the synergy of photocatalysis and piezocatalysis.
Generic model of superexchange effects in magnetoelastic oxides (2013)

Room temperature magnetic properties of tetragonally distorted SrTi1−xMxO3 epitaxial films occur when M = Fe or Co is in a magnetoelastic 4+ valence state. However, these ions can limit the saturation magnetization by magnetic superexchange through M–O–M bonding when the concentration (x) is high enough to create a population of antiferromagnetic (AFM) spin pairs. For moderate concentrations, a random distribution of isolated spin sites is interspersed with AFM-coupled sites below the Neel temperature. Analysis of this model involves the following assumptions: (1) the fraction of unpaired sites with 6 equivalent near neighbors is F = (1 − x)6, leaving (1 − F) as the fraction of paired sites, (2) the variation of saturation magnetization with temperature for the unpaired paramagnetic sites is treated by the orbit-lattice strain model reported previously, and the canted contributions of the antiferromagnetic pairs by a reverse Brillouin function. The model is applied to SrTiO3 compounds containing substitutions of low-spin Co4+ ions that reveal how the exchange-coupled group can become part of the magnetoelastic alignment system as T approaches the effective Neel temperature (TN) of the paired spins. Evidence of this effect in the form of magnetic moment peaks at TN is found in thermomagnetic data from zero-field cooled films in a partially magnetized state.
Bmp6 Expression in Murine Liver Non Parenchymal Cells: A Mechanism to Control their High Iron Exporter Activity and Protect Hepatocytes from Iron Overload? (2015)

Bmp6 is the main activator of hepcidin, the liver hormone that negatively regulates plasma iron influx by degrading the sole iron exporter ferroportin in enterocytes and macrophages. Bmp6 expression is modulated by iron but the molecular mechanisms are unknown. Although hepcidin is expressed almost exclusively by hepatocytes (HCs), Bmp6 is produced also by non-parenchymal cells (NPCs), mainly sinusoidal endothelial cells (LSECs). To investigate the regulation of Bmp6 in HCs and NPCs, liver cells were isolated from adult wild type mice whose diet was modified in iron content in acute or chronic manner and in disease models of iron deficiency (Tmprss6 KO mouse) and overload (Hjv KO mouse). With manipulation of dietary iron in wild-type mice, Bmp6 and Tfr1 expression in both HCs and NPCs was inversely related, as expected. When hepcidin expression is abnormal in murine models of iron overload (Hjv KO mice) and deficiency (Tmprss6 KO mice), Bmp6 expression in NPCs was not related to Tfr1. Despite the low Bmp6 in NPCs from Tmprss6 KO mice, Tfr1 mRNA was also low. Conversely, despite body iron overload and high expression of Bmp6 in NPCs from Hjv KO mice, Tfr1 mRNA and protein were increased. However, in the same cells ferritin L was only slightly increased, but the iron content was not, suggesting that Bmp6 in these cells reflects the high intracellular iron import and export. We propose that NPCs, sensing the iron flux, not only increase hepcidin through Bmp6 with a paracrine mechanism to control systemic iron homeostasis but, controlling hepcidin, they regulate their own ferroportin, inducing iron retention or release and further modulating Bmp6 production in an autocrine manner. This mechanism, that contributes to protect HC from iron loading or deficiency, is lost in disease models of hepcidin production.
Streptococcus pneumoniae biofilm formation and dispersion during colonization and disease (2015)

Streptococcus pneumoniae (the pneumococcus) is a common colonizer of the human nasopharynx. Despite a low rate of invasive disease, the high prevalence of colonization results in millions of infections and over one million deaths per year, mostly in individuals under the age of 5 and the elderly. Colonizing pneumococci form well-organized biofilm communities in the nasopharyngeal environment, but the specific role of biofilms and their interaction with the host during colonization and disease is not yet clear. Pneumococci in biofilms are highly resistant to antimicrobial agents and this phenotype can be recapitulated when pneumococci are grown on respiratory epithelial cells under conditions found in the nasopharyngeal environment. Pneumococcal biofilms display lower levels of virulence in vivo and provide an optimal environment for increased genetic exchange both in vitro and in vivo, with increased natural transformation seen during co-colonization with multiple strains. Biofilms have also been detected on mucosal surfaces during pneumonia and middle ear infection, although the role of these biofilms in the disease process is debated. Recent studies have shown that changes in the nasopharyngeal environment caused by concomitant virus infection, changes in the microflora, inflammation, or other host assaults trigger active release of pneumococci from biofilms. These dispersed bacteria have distinct phenotypic properties and transcriptional profiles different from both biofilm and broth-grown, planktonic bacteria, resulting in a significantly increased virulence in vivo. In this review we discuss the properties of pneumococcal biofilms, the role of biofilm formation during pneumococcal colonization, including their propensity for increased ability to exchange genetic material, as well as mechanisms involved in transition from asymptomatic biofilm colonization to dissemination and disease of otherwise sterile sites. Greater understanding of pneumococcal biofilm formation and dispersion will elucidate novel avenues to interfere with the spread of antibiotic resistance and vaccine escape, as well as novel strategies to target the mechanisms involved in induction of pneumococcal disease.