gebhart/patrepeval huggingface dataset:
Adsorption of emerging contaminants by graphene related materials and their alginate composite hydrogels (2023)

Graphene nanosheets and nanoplatelets -alginate composite hydrogels were prepared by ionic gelation and the resulting gel beads were exploited for the removal of a mixture of eight selected emerging contaminants (ECs) in tap water, including bisphenol A, ofloxacin and diclofenac. The role of graphene related materials (GRM) on the gel bead structure, adsorption selectivity, kinetic, mechanism, and efficiency was investigated. Combined Scanning Electron Microscopy (SEM) and confocal Raman microscopy mapping showed a porous structure with pore size in the range of 100–200 µm and a homogeneous distribution of graphene nanosheets or nanoplatelets at the pores surface. The adsorption kinetic of GRM was much faster than that of granular activated carbon (GAC), the industrial sorbent benchmark, with removal capacity of ofloxacin from 2.9 to 4.3 times higher. A maximum adsorption capacity of 178 mg/g for rhodamine B was estimated by adsorption isotherm studies for reduced graphene oxide-based beads (a value comparable to that of powered activated carbon). Regeneration test performed on saturated beads by washing with EtOH, and subsequent reiterated reuses, showed no loss of adsorption performance up to the fourth reuse cycle.
Persistent increases of PKMζ in memory‐activated neurons trace LTP maintenance during spatial long‐term memory storage (2021)

PKMζ is an autonomously active PKC isoform crucial for the maintenance of synaptic long-term potentiation (LTP) and long-term memory. Unlike other kinases that are transiently stimulated by second messengers, PKMζ is persistently activated through sustained increases in protein expression of the kinase. Therefore, visualizing increases in PKMζ expression during long-term memory storage might reveal the sites of its persistent action and thus the location of memory-associated LTP maintenance in the brain. Using quantitative immunohistochemistry validated by the lack of staining in PKMζ-null mice, we examined the amount and distribution of PKMζ in subregions of the hippocampal formation of wild-type mice during LTP maintenance and spatial long-term memory storage. During LTP maintenance in hippocampal slices, PKMζ increases in the pyramidal cell body and stimulated dendritic layers of CA1 for at least 2 hr. During spatial memory storage, PKMζ increases in CA1 pyramidal cells for at least 1 month, paralleling the persistence of the memory. During the initial expression of the memory, we tagged principal cells with immediate-early gene Arc promoter-driven transcription of fluorescent proteins. The subset of memory-tagged CA1 cells selectively increases expression of PKMζ during memory storage, and the increase persists in dendritic compartments within stratum radiatum for 1 month, indicating long-term storage of information in the CA3-to-CA1 pathway. We conclude that persistent increases in PKMζ trace the molecular mechanism of LTP maintenance and thus the sites of information storage within brain circuitry during long-term memory.
Immunotherapy with peptides (2011)

Specific allergen immunotherapy is clinically effective and disease modifying. It has a duration of effect that exceeds the treatment period and prevents both the progression of allergic rhinitis to asthma and the acquisition of new allergic sensitizations. However, immunotherapy is associated with a high frequency of adverse events related to the allergenicity of vaccines. Allergenicity is conferred by the presence of intact B-cell epitopes that crosslink allergen-specific IgE on effector cells. The use of linear peptide sequences representing fragments of the native allergen is one approach to reduce allergenicity. Preclinical models of peptide immunotherapy have demonstrated efficacy in both autoimmunity and allergy. Translation of this technology into the clinic has gained momentum in recent years based on encouraging results from early clinical trials. To date, efforts have focused on two major allergens, but vaccines to a broader range of molecules are currently in clinical development. Mechanistically, peptide immunotherapy appears to work through the induction of adaptive, allergen-specific regulatory T cells that secrete the immunoregulatory cytokine IL-10. There is also evidence that peptide immunotherapy targeting allergen-specific T cells can indirectly modulate allergen-specific B-cell responses. Peptide immunotherapy may provide a safe and efficacious alternative to conventional subcutaneous and/or sublingual approaches using native allergen preparations.
Quelle implication pour la cathepsine S dans l’obésité ? (2007)

La cathepsine S (CTSS) est une protéase à cystéine dont l’implication physiopathologique est établie dans l’athérosclérose et la présentation d’antigène. Par une approche transcriptomique, nous avons montré que la CTSS est exprimée dans le tissu adipeux humain et augmente avec la corpulence. Cette revue décrit les études menées par la suite montrant que la CTSS circulante varie avec les changements de masse grasse chez l’obèse et suggérant un nouveau rôle de cette protéase dans le développement normal et pathologique du tissu adipeux.
Virus Particle Core Defects Caused by Mutations in the Human Immunodeficiency Virus Capsid N-Terminal Domain (2005)

The N-terminal domains (NTDs) of the human immunodeficiency virus type 1 (HIV-1) capsid (CA) protein have been modeled to form hexamer rings in the mature cores of virions. In vitro, hexamer ring units organize into either tubes or spheres, in a pH-dependent fashion. To probe factors which might govern hexamer assembly preferences in vivo, we examined the effects of mutations at CA histidine residue 84 (H84), modeled at the outer edges of NTD hexamers, as well as a nearby histidine (H87) in the cyclophilin A (CypA) binding loop. Although mutations at H87 yielded infectious virions, mutations at H84 produced assembly-competent but poorly infectious virions. The H84 mutant viruses incorporated wild-type levels of CypA and viral RNAs and showed nearly normal signals in virus entry assays. However, mutant CA proteins assembled aberrant virus cores, and mutant core fractions retained abnormally high levels of CA but reduced reverse transcriptase activities. Our results suggest that HIV-1 CA residue 84 contributes to a structure which helps control either NTD hexamer assembly or the organization of hexamers into higher-order structures.
Shoot-tip culture for massive production of radish foundation seeds (2023)

Shoot-tip culture was used to produce clonal plants of radish stock seeds.Using 6-benzyladenine (BA), the largest number of RA2 line multi-shoots were formed with an average of 14.67 shoots on 1.33 µM BA in early seedlings and 11.33 shoots on 1.78 µM BA in juvenile seedlings.The largest number of RA4 line multi-shoots were formed with an average of 11.67 shoots on 2.22 µM BA in early seedlings and 13.67 shoots on 1.33 µM BA in juvenile seedlings.There was little difference in the significance level by BA concentration in both lines.Using Thidiazuron (TDZ), the number of RA2 line multi-shoots increased with increasing TDZ concentration, forming the largest number of multi-shoots in 0.45 µM TDZ (7.0 and 3.0 multi-shoots for early and juvenile seedlings, respectively), but few multi-shoots were formed from TDZ 2.25 and 4.5 µM.RA4 line produced almost no multi-shoots in early seedlings, and 3.7 multi-shoots were produced in 0.23 and 0.45 µM TDZ in juvenile seedlings, but not at higher concentrations.Analysis of the tissue culture seedlings grown by cultivating the generated multi-shoots with Radish Foundation seeds using SSR marker revealed a weak pattern of mutation in the generated tissue culture seedlings, but there was no mutant.In addition, in terms of root roots, both RA2 and RA4 lines generally had the best rooting, number of roots, and degree of root development in 4.9 µM indol-3-butyric acid (IBA).
Sorghum Brown Midrib19 (Bmr19) Gene Links Lignin Biosynthesis to Folate Metabolism (2021)

Genetic analysis of brown midrib sorghum (<i>Sorghum bicolor</i>) mutant lines assembled in our program has previously shown that the mutations fall into four allelic groups, <i>bmr2</i>, <i>bmr6</i>, <i>bmr12</i> or <i>bmr19</i>. Causal genes for allelic groups <i>bmr2</i>, <i>bmr6</i> and <i>bmr12</i>, have since been identified. In this report, we provide evidence for the nature of the <i>bmr19</i> mutation. This was accomplished by introgressing each of the four <i>bmr</i> alleles into nine different genetic backgrounds. Polymorphisms from four resequenced bulks of sorghum introgression lines containing either mutation, relative to those of a resequenced bulk of the nine normal midrib recurrent parent lines, were used to locate their respective causal mutations. The analysis confirmed the previously reported causal mutations for <i>bmr2</i> and <i>bmr6</i> but failed in the case of <i>bmr12</i>-bulk due to a mixture of mutant alleles at the locus among members of that mutant bulk. In the <i>bmr19</i>-bulk, a common G → A mutation was found among all members in <i>Sobic.001G535500</i>. This gene encodes a putative folylpolyglutamate synthase with high homology to maize <i>Bm4.</i> The brown midrib phenotype co-segregated with this point mutation in two separate F<sub>2</sub> populations. Furthermore, an additional variant allele at this locus obtained from a TILLING population also showed a brown midrib phenotype, confirming this locus as <i>Bmr19</i>.
Trust Analysis of Link State Network Routing (2008)

Abstract: Network routing security has received more attention recently. But there are no good design guidelines on how to construct secure network routing domains. There are also no proper evaluation methods to validate the many proposed secure routing frameworks. We analyze network routing security issues via a new approach: trust relations among network routers. Based on the presented trust models for link state routing, we analyze network routing survivability issues. Then we outline the research directions to build secure network routing.
Carbohydrate Scaffolds for the Production of Bioactive Compounds (2005)

Recent efforts in the use of carbohydrates as scaffolds for the production of bioactive compounds are reported. Orthogonally protected and solid phase supported monosaccharides for the production of libraries, exploiting the combinatorial approach by derivatisation of each hydroxyl group with different pharmacophores, are described. Example of peptidomimetics synthesised on a carbohydrate skeleton orienting proper amino acid residues, are also reported. In order to increase the conformational rigidity of the sugar templates, a variety of original bicyclic or policyclic polyfunctionalised structures have been synthesised from carbohydrates. Same of them have spiro or condensed bicyclic structures, others include one or more sugars in a macrocyclic framework or in cyclopeptides in order to induce bioactive peptide loops. Keywords: carbohydrate, solid phase, libraries of compounds, sugar amino acid, bicyclic compounds
Terminally differentiated CD8 effector T cells have NK-like features and are potent mediators of HIV-specific ADCC (2017)

Abstract Chronic viral infection and persistent antigenic stimulation is associated with a rise of late-stage differentiated CD8 T cells including a unique subset of CD8 T cells expressing FCg receptor IIIa (CD16). Expansion of CD16+ CD8 T cells is observed in other chronic diseases like HCV, but not HIV-1 infection. CD16 mediates antibody dependent cellular cytotoxicity (ADCC), most notably on NK cells, and is associated with protection from HIV-1 acquisition. Using cryopreserved PBMC from healthy and HIV-1 chronically infected donors from Uganda, we compared phenotypic, transcriptional, and functional changes in CD16+ CD8 T cells. We found that chronic, untreated HIV-1 infection is associated with elevated numbers of CD45RA+CD57+ terminal effector CD16+ CD8 T cells compared to healthy individuals, and display a distinct transcriptional profile in between conventional CD8 T cells and NK cells, characterized by high IKZF2 and KLRF1, and low expression of IL7R. This transcriptional profile translates into a NKp80+ IL-7Rα-surface phenotype and high expression of the Helios transcription factor. Additionally, CD16+ CD8 T cells are capable of mediating ADCC at levels similar to that of NK cells. These CD16+ CD8 T cells are highly activated and correlate positively with expansion of the CD8 T cell compartment and plasma levels of soluble factors of antiviral immunity and inflammation, such as IP-10, TNF, IL-6, and TNFRII. These data indicate that terminally differentiated, effector CD8 T cells acquire innate, NK cell-like characteristics during chronic HIV-1 infection, and suggest that HIV-specific ADCC is part of the repertoire of functions CD8 T cells use to combat the ability of HIV-1 to escape the TCR-specific, anti-viral effects of CD8 T cells.
XRAI: Better Attributions Through Regions (2019)

Saliency methods can aid understanding of deep neural networks. Recent years have witnessed many improvements to saliency methods, as well as new ways for evaluating them. In this paper, we 1) present a novel region-based attribution method, XRAI, that builds upon integrated gradients (Sundararajan et al. 2017), 2) introduce evaluation methods for empirically assessing the quality of image-based saliency maps (Performance Information Curves (PICs)), and 3) contribute an axiom-based sanity check for attribution methods. Through empirical experiments and example results, we show that XRAI produces better results than other saliency methods for common models and the ImageNet dataset.
Orientation analysis of collagen fibers in healing tendon by using second-harmonic-generation microscopy (2017)

Tendon rupture is a trauma that is difficult to fully recover from. Therefore, non-destructive and non-invasive evaluation method for the tendon healing is strongly required. In this study, we performed the orientation analysis of collagen fiber in healing tendon by two-dimensional Fourier transform (2D-FT) of SHG image. The extracted 2D-FT power spectra imply the correlation with the degree of the tendon healing. These results indicate that SHG microscopy has a unique potential as a non-destructive and non-invasive indicator of tendon healing.
Time-Resolved Laser-Induced Breakdown Spectroscopy of Iron Ore (1990)

Laser-induced plasmas are highly transient phenomena, lasting for several microseconds. The lines of a plasma spectrum do not appear simultaneously, and, furthermore, they exist for a range of lifetimes. Time-resolved laser-induced breakdown spectroscopy (TRELIBS) has been shown to be effective in increasing the line-to-background ratios of spectra. The results of time-resolved spectroscopy of the excimer laser-induced plasmas of iron ore are presented. The period of the plasma lifetime which is optimum for spectrochemical analysis of ore was determined.
A Theoretical-Study of the Scattering of Ultrasound from Blood (1981)

A theoretical treatment of the scattering of ultrasound from blood is given, assuming that the blood behaves essentially as a continuum. The scattering then arises from fluctuations in the mass density and compressibility of the blood, which is caused by a fluctuation in the red cell concentration. An expression for the received signal in ultrasonic blood velocity measurements is given. The stochastic properties of the signal are discussed with reference the information content about the velocity field in the blood. Since the signal is Gaussian, all available information is contained in the power spectrum, which is a blurred approximation to the velocity distribution in the region of observation.
A phase IV, two-armed, randomized, cross-over study comparing compliance with once-a-month administration of vitamin D3 to compliance with daily administration of a fixed-dose combination of vitamin D3 and calcium during two 6-month periods (2015)

In this study, a once-monthly administration of vitamin D3 was preferred over a once-daily administration of a fixed-dose combination of vitamin D3 and calcium, with a better compliance but without any significant difference in the increase in vitamin D levels.
[Evaluation of 2 years' experience with assisted circulation by diastolic counterpulsation]. (1975)

The authors report their two years' experience of circulatory assistance by diastolic counter-pulsation with an intra-aortic balloon. This technique was used in 23 patients: 9 cases of cardiogenic shock due to acute myocardial infarction, 9 septal ruptures, 1 rupture of the papillary muscle of the mitral valve, 1 acute ventricular aneurysm, 2 high risk coronary arteriographies and 1 case of early post-infarction recurrent ischemia. It confirms the gravity of cardiogenic shock as, in spite of the frequent improvement in hemodynamic parameters under counter-pulsation, there was only one survivor. The efficacy is greater in cases of septal rupture, where the author obtained 3 survivors out of 6 operated cases. The security of the method and its innocuity permit one to carry out high risk coronary arteriography and extend the indications for circulatory assistance, to certain cases of unstable angina or early recurrent anginal following acute infarction.
Computed Ultrasound Tomography in Echo mode (CUTE) of speed of sound for diagnosis and for aberration correction in pulse-echo sonography (2014)

Sound speed as a diagnostic marker for various diseases of human tissue has been of interest for a while. Up to now, mostly transmission ultrasound computed tomography (UCT) was able to detect spatially resolved sound speed, and its promise as a diagnostic tool has been demonstrated. However, UCT is limited to acoustically transparent samples such as the breast. We present a novel technique where spatially resolved detection of sound speed can be achieved using conventional pulse-echo equipment in reflection mode. For this purpose, pulse-echo images are acquired under various transmit beam directions and a two-dimensional map of the sound speed is reconstructed from the changing phase of local echoes using a direct reconstruction method. Phantom results demonstrate that a high spatial resolution (1 mm) and contrast (0.5 % of average sound speed) can be achieved suitable for diagnostic purposes. In comparison to previous reflection-mode based methods, CUTE works also in a situation with only diffuse echoes, and its direct reconstruction algorithm enables real-time application. This makes it suitable as an addition to conventional clinical ultrasound where it has the potential to benefit diagnosis in a multimodal approach. In addition, knowledge of the spatial distribution of sound speed allows full aberration correction and thus improved spatial resolution and contrast of conventional B-mode ultrasound.
Smartphone-readable RPA-LFA for the high-sensitivity detection of Leishmania kDNA using nanophosphor reporters (2023)

Early diagnosis of infectious diseases improves outcomes by enabling earlier delivery of effective treatment, and helps prevent further transmission by undiagnosed persons. We demonstrated a proof-of-concept assay combining isothermal amplification and lateral flow assay (LFA) for early diagnosis of cutaneous leishmaniasis, a vector-borne infectious disease that affects ca. 700,000 to 1.2 million people annually. Conventional molecular diagnostic techniques based on polymerase chain reaction (PCR) require complex apparatus for temperature cycling. Recombinase polymerase amplification (RPA) is an isothermal DNA amplification method that has shown promise for use in low-resource settings. Combined with lateral flow assay as the readout, RPA-LFA can be used as a point-of-care diagnostic tool with high sensitivity and specificity, but reagent costs can be problematic. In this work, we developed a highly-sensitive smartphone-based RPA-LFA for the detection of Leishmania panamensis DNA using blue-emitting [(Sr0.625Ba0.375)1.96Eu0.01Dy0.03]MgSi2O7 (SBMSO) persistent luminescent nanophosphors as LFA reporters. The greater detectability of nanophosphors allows the use of a reduced volume of RPA reagents, potentially reducing the cost of RPA-LFA. The limit of detection (LOD) of RPA with gold nanoparticle-based LFA readout is estimated at 1 parasite per reaction, but LOD can be 100-fold better, 0.01 parasites per reaction, for LFA based on SBMSO. This approach may be useful for sensitive and cost-effective point-of-care diagnosis and contribute to improved clinical and economic outcomes, especially in resource-limited settings.
Effect of laryngoplasty on respiratory noise reduction in horses with laryngeal hemiplegia (2004)

Laryngoplasty reduces upper airway noise in horses with laryngeal hemiplegia, but is not as effective as bilateral ventriculocordectomy in this regard, although respiratory noise reduction occurs more rapidly than with bilateral ventriculocordectomy. Residual noise during exercise cannot be used as a predictor of improvement in upper airway function in individual horses following laryngoplasty. The degree of arytenoid abduction obtained following surgery does not affect upper airway flow mechanics. Interestingly, we found that the greater the arytenoid abduction, the louder the respiratory noise.
The mass uptake of cholesterol ester from low density lipoproteins by cultured smooth muscle and adventitial cells of human aortas. (1980)

Cultured human smooth muscle and adventitial cells were incubated with human serum and low density lipoprotein (LDL) to study the uptake and accumulation of cholesterol ester from exogenous LDL. The cellular total cholesterol varied with the amount of LDL cholesterol in the medium. The cholesterol ester content increased 4-fold after 2 hours of incubation. A 6-fold rise occurred by 24 hours and continued to 72 hours. The cholesterol ester of the adventitial cells was markedly depleted by incubation with abetalipoproteinemic serum or with a lipid-depleted plasma fraction. By the use of 14C-labeled LDL free cholesterol in the incubation medium, we calculated that some 70-80% of the total accumulated cholesterol ester after 24 hours of incubation was derived from LDL cholesterol ester, and only 20-30% was synthesized by the cells. These studies demonstrated conclusively that human cells greatly increase their cholesterol ester mass after incubation with LDL.
A Novel Thermochemical Metal Halide Treatment for High-Performance Sb2Se3 Photocathodes (2020)

The fabrication of cost-effective photostable materials with optoelectronic properties suitable for commercial photoelectrochemical (PEC) water splitting represents a complex task. Herein, we present a simple route to produce Sb<sub>2</sub>Se<sub>3</sub> that meets most of the requirements for high-performance photocathodes. Annealing of Sb<sub>2</sub>Se<sub>3</sub> layers in a selenium-containing atmosphere persists as a necessary step for improving device parameters; however, it could complicate industrial processability. To develop a safe and scalable alternative to the selenium physical post-processing, we propose a novel SbCl<sub>3</sub>/glycerol-based thermochemical treatment for controlling anisotropy, a severe problem for Sb<sub>2</sub>Se<sub>3</sub>. Our procedure makes it possible to selectively etch antimony-rich oxyselenide presented in Sb<sub>2</sub>Se<sub>3</sub>, to obtain high-quality compact thin films with a favorable morphology, stoichiometric composition, and crystallographic orientation. The treated Sb<sub>2</sub>Se<sub>3</sub> photoelectrode demonstrates a record photocurrent density of about 31 mA cm<sup>-2</sup> at -248 mV against the calomel electrode and can thus offer a breakthrough option for industrial solar fuel fabrication.