gebhart/patrepeval huggingface dataset:
Fibrate induction of the adrenoleukodystrophy‐related gene (ABCD2) (2001)

X-linked adrenoleukodystrophy (X-ALD) is a neurodegenerative disease due to a defect in the ABCD1 (ALD) gene. ABCD1, and the two close homologues ABCD2 (ALDR) and ABCD3 (PMP70), are genes encoding ATP-binding cassette half-transporters of the peroxisomal membrane. As overexpression of the ABCD2 or ABCD3 gene can reverse the biochemical phenotype of X-ALD (reduced beta-oxidation of very-long-chain fatty acids), pharmacological induction of these partially redundant genes may represent a therapeutic approach to X-ALD. We previously reported that the ABCD2 and ABCD3 genes could be strongly induced by fibrates, which are hypolipidaemic drugs and peroxisome-proliferators in rodents. We provide evidence that the induction is dependent on peroxisome proliferator-activated receptor (PPARalpha) as both genes were not induced in fenofibrate-treated PPARalpha -/- knock-out mice. To further characterize the PPARalpha pathway, we cloned and analysed the promoter of the ABCD2 gene, the closest homologue of the ABCD1 gene. The proximal region (2 kb) of the rat promoter displayed a high conservation with the human and mouse cognate sequences suggesting an important role of the region in regulation of the ABCD2 gene. Classically, fibrate-induction involves interaction of PPARalpha with a response element (PPRE) characterized by a direct repeat of the AGGTCA-like motif. Putative PPRE motifs of the rat ABCD2 promoter were studied in the isolated form or in their promoter context by gel-shift assay and transfection of COS-7 cells. We failed to characterize a functional PPRE, suggesting a different mechanism for the PPARalpha-dependent regulation of the ABCD2 gene.
Effect of prostaglandin E on immune complex nephritis in NZB/W mice. (1979)

Pharmacologic quantities of prostaglandin alter the immune complex nephritis of NZB/W mice. To study the mechanism of this change, NZB/W mice received 200 micrograms. of prostaglandin E1 or E2 twice daily starting at 2, 4, or 6 months of age. Mice were sacrificed at bimonthy intervals, renal function and serologic parameters were evaluated, and renal tissue was examined by light, fluorescence, and electron microscopy. Therapy decreased the incidence of proteinuria, lessened renal pathology, and prolonged survival. Maximal beneficial effects occurred when treatment began at 2 months of age. The most striking change was a decrease in the rate of immune complexes depositing in the mesangium and their absence from peripheral loops. Accompanying this change was a reduction in glomerular hypercellularity and a decrease in renal perivascular and interstitial mononuclear infiltrates. By contrast, treatment did not alter serum levels of immunoglobulins, antinuclear antibodies, and antisingle or double-stranded DNA. These results indicate that prostaglandin E is capable of prolonging survival in NZB/W mice by decreasing the rate of immune complexes depositing in glomeruli.
Investigating Grey-Box Modeling for Predictive Analytics in Smart Manufacturing (2017)

This paper develops a two-stage grey-box modeling approach that combines manufacturing knowledge-based (white-box) models with statistical (black-box) metamodels to improve model reusability and predictability. A white-box model can use various types of existing knowledge such as physical theory, high fidelity simulation or empirical data to build the foundation of the general model. The residual between a white-box prediction and empirical data can be represented with a black-box model. The combination of the white-box and black-box models provides the parallel hybrid structure of a grey-box. For any new point prediction, the estimated residual from the black-box is combined with white-box knowledge to produce the final grey-box solution. This approach was developed for use with manufacturing processes, and applied to a powder bed fusion additive manufacturing process. It can be applied in other common modeling scenarios. Two illustrative case studies are brought into the work to test this grey-box modeling approach; first for pure mathematical rigor and second for manufacturing specifically. The results of the case studies suggest that the use of grey-box models can lower predictive errors. Moreover, the resulting black-box model that represents any residual is a usable, accurate metamodel.
Retardation of oil drop evaporation from oil-in-water emulsions (2003)

The rate of evaporation of volatile oils from oil-in-water emulsions can be strongly retarded by using a polymeric emulsion stabiliser instead of a low molar mass surfactant.
Selection of bead‐displayed, PNA‐encoded chemicals (2009)

The lack of efficient identification and isolation methods for specific molecular binders has fundamentally limited drug discovery. Here, we have developed a method to select peptide nucleic acid (PNA) encoded molecules with specific functional properties from combinatorially generated libraries. This method consists of three essential stages: (1) creation of a Lab-on-Bead library, a one-bead, one-sequence library that, in turn, displays a library of candidate molecules, (2) fluorescence microscopy-aided identification of single target-bound beads and the extraction--wet or dry--of these beads and their attached candidate molecules by a micropipette manipulator, and (3) identification of the target-binding candidate molecules via amplification and sequencing. This novel integration of techniques harnesses the sensitivity of DNA detection methods and the multiplexed and miniaturized nature of molecule screening to efficiently select and identify target-binding molecules from large nucleic acid encoded chemical libraries. Beyond its potential to accelerate assays currently used for the discovery of new drug candidates, its simple bead-based design allows for easy screening over a variety of prepared surfaces that can extend this technique's application to the discovery of diagnostic reagents and disease markers.
EFFECT OF SOLUBLE POLYLACTIC ACID IN COMBINATION WITH GAMMA RADIATION ON GROUND BEEF INOCULATED WITH E. COLI O157:H71 (1999)

Ground beef was inoculated with E. coli O157:H7 and treated with gamma radiation with and without the incorporation of a 2% soluble polylactic acid solution (SPLA) and stored at 4C for up to 7 days. Frozen samples received an average maximum dose of 125 krads, at an average dose rate of 17.1 krads/h. The pH, water activity and moisture (%) were determined. A complete randomized block design with three replications was used to determine the effects of gamma radiation, SPLA, and gamma radiation in combination with SPLA. SPLA gave a maximum log reduction of E. coli O157:H7 populations of 0.70 log10 CFU/mL after 48 h at 4C. Gamma radiation reduced E. coli O157:H7 by 4.55 log10 CFU/mL. When SPLA and gamma radiation were combined, the cellular death of E. coli O157:H7 was not significantly increased by the presence of SPLA.
Residual Li Reactive Coating with Co3O4for Superior Electrochemical Properties of LiNi0.91Co0.06Mn0.03O2Cathode Material (2018)

The necessity of developing Ni-rich layered oxides cathode materials with more than 90% of Ni content is rapidly increasing for satisfying the demand of achieving the high capacity of Li-ion batteries. However, including more Ni contents results in increased formation of undesirable Li residues at the surface as well as deteriorating several types of degradation behaviors during cycling, which are the critical factors of design rules for the cathode material. In this study, the facile synthesis of an electrochemically active material, LiCoO2, is realized at the surface of LiNi0.91Co0.06Mn0.03O2 via the conventional dry coating method utilizing the Li-reactive capability of Co3O4. First-principles calculations are performed to investigate the possible formation of LiCoO2 from the phase diagram. The formation of the electrochemically active coating material considerably reduces the Li residues, increases the capacity, and exhibits a better cycle life with enhanced rate capability. The presence of LiCoO2 phase is verified from transmission electron microscopy (TEM) images, energy-dispersive X-ray spectroscopy (EDS) elemental mapping, and electron energy loss spectroscopy (EELS) spectra. Superior performance of Co3O4 is further demonstrated by comparing the results with those from conventional coating materials of Al2O3, TiO2, V2O3, and ZnO, whose electrochemical performance is worse in all of aspects.
Lasing and waveguiding in smectic A liquid crystal optical fibers (2013)

We demonstrate a new class of soft matter optical fibers, which are self-assembled in a form of smectic-A liquid crystal microtubes grown in an aqueous surfactant dispersion of a smectic-A liquid crystal. The diameter of the fibers is highly uniform and the fibers are highly birefringent. They are characterized by a line topological defect in the core of the fiber with an optical axis pointing from the defect core towards the surface. We demonstrate guiding of light along the fiber and Whispering Gallery Mode (WGM) lasing in a plane perpendicular to the fiber. The light guiding as well as the lasing threshold are significantly dependent on the polarization of the excitation beam. The observed threshold for WGM lasing is very low (≈ 75μJ/cm(2)) when the pump beam polarization is perpendicular to the direction of the laser dye alignment and is similar to the lasing threshold in nematic droplets. The smectic-A fibers are soft and flexible and can be manipulated with laser tweezers demonstrating a promising approach for realization of soft photonic circuits.
Design and Synthesis of Thermal Contracting Polymer with Unique Eight-Membered Carbocycle Unit (2018)

It is uncommon for a solid substance to expand upon cooling and contract upon heating. In this work, we synthesized a carbocycle monomer that contains 1,2:5,6-dibenzocyclooctadiene (DBCOD) unit and the corresponding polymers with different amounts of DBCOD in the polymer main chain. The films produced from this DBCOD-based polymer showed reversible thermal contraction behavior with the negative thermal expansion (NTE) coefficient of −625 ppm/K (100–200 °C). Differential scanning calorimetry (DSC), variable-temperature nuclear magnetic resonance (VT-NMR), and density-functional theory (DFT) calculations indicated that the population of the chair conformer of DBCODs increased with the rise of temperature due to the conversion from twist-boat to chair conformer. This led to giant thermal contraction. Furthermore, the value of the NTE coefficient could be adjusted by the amount of DBCODs and their surrounding physical environment. This is the first demonstration of a linear polymer that exhibits reversible thermal contraction. The new monomer can be covalently incorporated into a variety of polymeric materials to construct negative thermal expansion or zero expansion materials for the specific applications.
Magnetic Order and Symmetry in the 2D Semiconductor CrSBr (2021)

The advent of two-dimensional (2D) magnets offers unprecedented control over electrons and spins. A key factor in determining exchange coupling and magnetic order is symmetry. Here, we apply second harmonic generation (SHG) to probe a 2D magnetic semiconductor CrSBr. We find that monolayers are ferromagnetically ordered below 146 K, an observation enabled by the discovery of a large magnetic dipole SHG effect in the centrosymmetric structure. In multilayers, the ferromagnetic monolayers are coupled antiferromagnetically, and in contrast to other 2D magnets, the Néel temperature of CrSBr increases with decreasing layer number. We identify magnetic dipole and magnetic toroidal moments as order parameters of the ferromagnetic monolayer and antiferromagnetic bilayer, respectively. These findings establish CrSBr as an exciting 2D magnetic semiconductor and extend the SHG probe of magnetic symmetry to the monolayer limit, opening the door to exploring the applications of magnetic-electronic coupling and the magnetic toroidal moment.
Controversy about uterine effects and safety of SERMs: the saga continues (2002)

From the perspective of endometrial safety, there has been great controversy about what special management, if any, tamoxifen-treated patients should undergo. Periodic blind endometrial sampling or transvaginal ultrasound has been advocated by some. Because of the problems associated with either of these techniques alone, we recommended an approach that used transvaginal ultrasound and then proceeded to sonohysterography when the endometrial echo on transvaginal ultrasound was not reliably thin and distinct. The American College of Obstetricians and Gynecologists (ACOG), in its committee opinion, stated that patients receiving tamoxifen therapy should only have an annual pelvic exam with pap smear if they remain asymptomatic. Newer data suggest, however, that there are high- and low-risk groups that can be identified by pretreatment screening. Before tamoxifen therapy, 17% of patients have polyps. These patients have 17 times the incidence of atypical hyperplasia than those whose uterus was negative before tamoxifen therapy. Such findings call into question the validity of the only study of raloxifene where uterine safety was the primary endpoint. In that study, any woman with baseline endometrial findings other than pristinely negative (i.e., low risk) was excluded. However, other raloxifene studies without pretreatment screening show relative risk (RR) = 0.8 (95% CI = 0.2, 2.7) for endometrial carcinoma. This compares with the women over 50 years of age in the Breast Cancer Prevention Trial (National Surgical Adjuvant Breast and Bowel Project P-1) with tamoxifen when the RR = 4.01 (95% CI= 1.70, 10.90). The existence of potentially high- and low-risk groups should be taken into account in any future clinical trials looking at the endometrial safety of selective estrogen receptor modulators (SERMs).
Using confined carbonate crystals for the fabrication of nanosized metal oxide@carbon with superior lithium storage capacity (2016)

A new method is proposed for the fabrication of high-performance nanosized MnO@C, CoO/Co<sub>3</sub>O<sub>4</sub>@C, and Fe<sub>3</sub>O<sub>4</sub>/γ-Fe<sub>2</sub>O<sub>3</sub>@C in a self-generated soft oxidizing atmosphere.
Solid‐State Electrochromic Devices via Ionic Self‐Assembled Multilayers (ISAM) of a Polyviologen (2007)

Abstract A PV was synthesized by polymerization of N , N ′‐bis( δ ‐aminopropyl)‐4,4′‐bipyridinium bromide hydrobromide (APD) and isophthaloyl chloride (ISP). The PV was completely soluble in water as well as in organic solvents. The spectroelectrochemical and EC properties of the resulting ionic self‐assembled multilayers of PV/poly‐(2‐acrylamido‐2‐methylpropanesulfonic acid) (PAMPs) were examined by cyclic voltammetry, FT‐IR spectroscopy, UV‐vis spectroscopy, optical switching and current density measurements. Solid state devices made of PV films sandwiched with PANI as a counter electrode have switching times of 100–250 ms. 40 Bilayer films of PV/PAMPs show high contrast (ΔT = 61%) in 0.1 M NaClO 4 liquid electrolyte solution and CE as high as 57 cm 2 · C −1 , one of the highest reported so far for any bipyridinium salt system. magnified image
Lipid droplet consumption is functionally coupled to vacuole homeostasis independent of lipophagy (2018)

Lipid droplets (LDs) store neutral lipids and are integrated into a cellular metabolic network that relies on functional coupling with various organelles. Factors mediating efficient coupling and mechanisms regulating them remain unknown. Here, we conducted a global screen in <i>S. cerevisiae</i> to identify genes required for the functional coupling of LDs and other organelles during LD consumption. We show that LD utilization during growth resumption is coupled to vacuole homeostasis. ESCRT-, V-ATPase- and vacuole protein sorting-mutants negatively affect LD consumption, independent of lipophagy. Loss of ESCRT function leads to the accumulation of LD-derived diacylglycerol (DAG), preventing its conversion into phosphatidic acid (PA) and membrane lipids. In addition, channeling of DAG from LD-proximal sites to the vacuole is blocked. We demonstrate that utilization of LDs requires intact vacuolar signaling via TORC1 and its downstream effector Sit4p. These data suggest that vacuolar status is coupled to LD catabolism via TORC1-mediated regulation of DAG-PA interconversion and explain how cells coordinate organelle dynamics throughout cell growth.
PMM.40 Peripartum cardiomyopathy (PPCM) – A rare presentation with abnormal liver function mimicking HELLP syndrome (2014)

Objectives To report the rare case of a woman who was induced at term for deranged liver function, was later was recognised as secondary to cardiac dysfunction and a literature review of this rare condition. Methods We reviewed the case notes and investigations of the above woman and collected the demographic details, predisposing risk factors, antenatal/ intrapartum and postnatal care. Results A 34 yr old woman in her second pregnancy, was induced at term as her liver enzymes were raised, and she had an emergency caesarean section for fetal distress. Postpartum the liver function was further deteriorating with borderline low platelets. Clinical examination revealed a cardiac murmur and echocardiogram showed right heart failure, with ejection fraction less than 30%. Cardiologists diagnosed peripartum cardiomyopathy and the woman was transferred to cardiac centre for further management. Women with PPCM usually present with dyspnea, dizziness, chest pain, cough, neck vein distension, fatigue, and peripheral oedema. They can also manifest as arrhythmias, embolic events due to the dilated, dysfunctional left ventricle, acute myocardial infarction due to decreased perfusion to the coronary arteries, jugular venous distention, S3 and S4 gallop, and hepatomegaly. Diagnosis of PPCM requires the exclusion of other causes of heart failure: myocardial infarction, sepsis, severe preeclampsia, pulmonary embolism, valvular diseases. Conclusions PPCM occurs in previously healthy women in the third trimester of pregnancy and up to 5 months postpartum. The incidence is low (0.1% of pregnancies) but morbidity and mortality rates are high (5%–32%) with highly variable outcomes. Early multi-disciplinary involvement including senior Obstetricians, anaesthetists, intensivists, cardiologists and neonatologists helps in improving the outcomes.
Recognizing novel 3-D objects under new illumination and viewing position using a small number of example views or even a single view (2002)

A method is presented for class-based recognition using a small number of example views taken under several different viewing conditions. The main emphasis is on using a small number of examples. Previous work assumed that the set of examples is sufficient to span the entire space of possible objects, and that in generalizing to a new viewing conditions a sufficient number of previous examples under the new conditions will be available to the recognition system. Here we have considerably relaxed these assumptions and consequently obtained good class-based generalization from a small number of examples, even a single example view, for both viewing position and illumination changes. In addition, previous class-based approaches only focused on viewing position changes and did not deal with illumination changes. Here we used a class-based approach that can generalize for both illumination and viewing position changes. The method was applied to face and car model images. New views under viewing position and illumination changes were synthesized from a small number of examples.
An Accented Cinema: Exilic and Diasporic Filmmaking (2002)

Hamid Naficy. An Accented Cinema: Exilic and Diasporic Filmmaking. Princeton: Princeton University Press 2001 374 pgs
Quantitative Analysis of Cheese Microstructure using SEM Imagery (2007)

Abstract. Structural properties of cheese highly influence its chemical, mechanical and nutritive proper-ties. The analysis and quantification of relevant features in food imagery is the basis of modern food, and in particular cheese, microscopy. Processing Scanning Electron Microscopy (SEM) images is a powerful tool to estimate microstructural cheese features. In this paper, we present an ad-hoc method to analyse SEM cheese imagery and to quanti-tatively characterise a number of features of cheese microstructure, using simple and efficient image processing techniques. An experimental analysis is presented on a number of traditional Sicilian cheese varieties.
Cycling to Cancer with Cyclin D1 (2002)

Genetic aberrations in the regulatory circuits that govern transit through the G(1) phase of the cell cycle occur frequently in human cancer and overexpression of the G(1) phase cyclin, cyclin D1, is one of the most commonly observed alterations. Cyclin D1 accumulates and activates its cognate CDK (CDK4/6) in response to mitogenic growth factors in early to mid G(1) phase. The resulting cyclin D1-dependent kinase initiates the phosphorylation-dependent inactivation of the retinoblastoma tumor suppressor protein. Mitogen-dependent activation of the cyclin D1 kinase occurs through increased transcription, protein accumulation, cyclin/CDK assembly, reduced cyclin proteolysis, and decreased nuclear export. Perturbations at any step, which result in reduced growth factor requirements for cyclin D1/CDK activation, will provide cells with a distinct growth advantage over their normal counterparts and thus likely represents an early event in neoplasia.
Preclinical evaluation of a low-frequency transcranial MRI-guided focused ultrasound system in a primate model (2016)

This study investigated thermal ablation and skull-induced heating with a 230 kHz transcranial MRI-guided focused ultrasound (TcMRgFUS) system in nonhuman primates. We evaluated real-time acoustic feedback and aimed to understand whether cavitation contributed to the heating and the lesion formation. In four macaques, we sonicated thalamic targets at acoustic powers of 34-560 W (896-7590 J). Tissue effects evaluated with MRI and histology were compared to MRI-based temperature and thermal dose measurements, acoustic emissions recorded during the experiments, and acoustic and thermal simulations. Peak temperatures ranged from 46 to 57 °C, and lesions were produced in 5/8 sonicated targets. A linear relationship was observed between the applied acoustic energy and both the focal and brain surface heating. Thermal dose thresholds were 15-50 cumulative equivalent minutes at 43 °C, similar to prior studies at higher frequencies. Histology was also consistent with earlier studies of thermal effects in the brain. The system successfully controlled the power level and maintained a low level of cavitation activity. Increased acoustic emissions observed in 3/4 animals occurred when the focal temperature rise exceeded approximately 16 °C. Thresholds for thermally-significant subharmonic and wideband emissions were 129 and 140 W, respectively, corresponding to estimated pressure amplitudes of 2.1 and 2.2 MPa. Simulated focal heating was consistent with the measurements for sonications without thermally-significant acoustic emissions; otherwise it was consistently lower than the measurements. Overall, these results suggest that the lesions were produced by thermal mechanisms. The detected acoustic emissions, however, and their association with heating suggest that cavitation might have contributed to the focal heating. Compared to earlier work with a 670 kHz TcMRgFUS system, the brain surface heating was substantially reduced and the focal heating was higher with this 230 kHz system, suggesting that a reduced frequency can increase the treatment envelope for TcMRgFUS and potentially reduce the risk of skull heating.