gebhart/patrepeval huggingface dataset:
Defensins couple dysbiosis to primary immunodeficiency in Crohn’s disease (2011)

Antimicrobial peptides, including defensins, are essential effectors in host defence and in the maintenance of immune homeostasis. Clinical studies have linked the defective expression of both α- and β-defensin to the reduced killing of certain microorganisms by the intestinal mucosa of patients suffering from ileal and colonic Crohn's disease (CD), respectively. Only recently have the events leading to defective expression of defensins in CD been further elucidated, and are discussed herein. These events may account for CD-associated alterations in the microbiome and may subsequently precipitate the development of granulomatous inflammatory lesions in genetically-predisposed patients. We also address how these discoveries may pave the way for the development of a molecular medicine aimed at restoring gut barrier function in CD.
Biodiversidad genética en bovinos criollos del Uruguay. Análisis con marcadores moleculares (2002)

"Los bovinos Criollos del Uruguay constituyenuna reserva genética de alrededor de 1000 animales,ubicada al sureste del país en unecosistema de montes serranos. Su caracterizacióngenética se ha abordado principalmente conmarcadores cromosómicos, inmunológicos,moleculares, permitiendo analizar su grado devariación y relación con razas Criollas de la regióne iberoamericanas. Los resultados preliminareshan permitido considerarla un recurso cuyadiversidad genética se ha mantenido por la presiónde la selección natural. Se ha demostrado: a)ausencia de marcadores característicos de razacebú (Bos indicus); b) presencia de translocaciónheterocigota rob 1/29; c) presencia de fenogruposdel sistema B descritos en razas iberoamericanas.Los análisis de variabilidad genética y sucomparación con reservas de la región e iberoamericanasse realizaron con los siguientes fragmentosgenómicos: a) secuencias codificantespara proteínas de la leche y suero (k-CN, b-LG, a-LA); b) secuencias codificantes para el complejode histocompatibilidad BoLa (DBR3); c) secuenciasrepetidas de dinucleótidos; microsatélites(CYP21, BM2113); d) secuencias dispersas alazar en el genoma, RAPDs. Para estos marcadores,la población se encuentra en equilibrio génico,presentando una heterocigosidad esperada deHe= 0,8.Mediante la técnica de RAPD se realiza unestudio comparativo entre bovinos Criollos,Holando Uruguayo, Hereford y bovinos de islaGran Canaria, obteniéndose una mayor similitudentre Holando y Hereford que entre éstos y elCriollo. Se demuestra un alto porcentaje degenoma compartido entre el Criollo Uruguayo y elde isla Gran Canaria (0,72). Estos resultadospermiten considerarla una reserva genética promoviendosu conservación in situ como especiedomesticada (Bos taurus) de alto valor económico.Esta conservación genética se debe realizaren aquel entorno en que han desarrollado potencialmentesus propiedades específicas (rusticidad,alta fertilidad, longevidad)"
HIV-Sheltering Platelets From Immunological Non-Responders Induce a Dysfunctional Glycolytic CD4+ T-Cell Profile (2022)

Immunological non-responders (InRs) are HIV-infected individuals in whom the administration of combination antiretroviral therapy (cART), although successful in suppressing viral replication, cannot properly reconstitute patient circulating CD4<sup>+</sup> T-cell number to immunocompetent levels. The causes for this immunological failure remain elusive, and no therapeutic strategy is available to restore a proper CD4<sup>+</sup> T-cell immune response in these individuals. We have recently demonstrated that platelets harboring infectious HIV are a hallmark of InR, and we now report on a causal connection between HIV-containing platelets and T-cell dysfunctions. We show here that <i>in vivo</i>, platelet-T-cell conjugates are more frequent among CD4<sup>+</sup> T cells in InRs displaying HIV-containing platelets (<350 CD4<sup>+</sup> T cells/μl blood for >1 year) as compared with healthy donors or immunological responders (IRs; >350 CD4<sup>+</sup> T cells/μl). This contact between platelet containing HIV and T cell in the conjugates is not infectious for CD4<sup>+</sup> T cells, as coculture of platelets from InRs containing HIV with healthy donor CD4<sup>+</sup> T cells fails to propagate infection to CD4<sup>+</sup> T cells. In contrast, when macrophages are the target of platelets containing HIV from InRs, macrophages become infected. Differential transcriptomic analyses comparing InR and IR CD4<sup>+</sup> T cells reveal an upregulation of genes involved in both aerobic and anaerobic glycolysis in CD4<sup>+</sup> T cells from InR vs. IR individuals. Accordingly, InR platelets containing HIV induce a dysfunctional increase in glycolysis-mediated energy production in CD4<sup>+</sup> T cells as compared with T cells cocultured with IR platelets devoid of virus. In contrast, macrophage metabolism is not affected by platelet contact. Altogether, this brief report demonstrates a direct causal link between presence of HIV in platelets and T-cell dysfunctions typical of InR, contributing to devise a platelet-targeted therapy for improving immune reconstitution in these individuals.
Cardioprotective Actions of Specific Thromboxane Receptor Antagonist in Acute Myocardial Ischemia (1987)

Summary: Thromboxane A2 (TxA2) has been implicated as a potential mediator of myocardial damage during acute ischemia. A potent and specific TxA2 receptor antagonist, SQ-29,548 (2 mg/kg bolus + 2 mg/kg/h) was tested in a cat acute coronary ligation model of myocardial ischemia over a 5-h observation period. Those cats given the TxA2 receptor antagonist had a significant reduction in elevated S-T segment from 0.32 to 0.17 mV (p < 0.01) in contrast to cats given only vehicle which showed a progressive increase in S-T segment elevation over the 5-h course of the experiment. Furthermore, the rise in plasma creatine kinase (CK) activity during myocardial ischemia was significantly attenuated after SQ-29,548 administration (p < 0.05). This was confirmed by direct myocardial biopsies which demonstrated a reduction in the loss of myocardial CK and nitrogenous compounds from the ischemic region. Because heart rate (HR), mean arterial blood pressure (MABP), and the pressure rate index (PRI) were unaffected by SQ-29,548 administration, its mechanism of protection probably does not occur through reduction of myocardial oxygen demand. Furthermore, specificity of SQ-29,548 for thromboxane/endoperoxide receptors was demonstrated in the isolated cat coronary arteries. These data suggest that SQ-29,548 reduces the damage associated with myocardial ischemia through direct TxA2 receptor antagonism. The data are also consistent with an important role of TxA2 in the pathophysiology of myocardial ischemia.
Automated volumetric lung segmentation of thoracic CT images using fully convolutional neural network (2018)

Deep Learning models such as Convolutional Neural Networks (CNNs) have achieved state-of-the-art performance in 2D medical image analysis. In clinical practice; however, most analyzed and acquired medical data are formed of 3D volumes. In this paper, we present a fast and efficient 3D lung segmentation method based on V-net: a purely volumetric fully CNN. Our model is trained on chest CT images through volume to volume learning, which palliates overfitting problem on limited number of annotated training data. Adopting a pre-processing step and training an objective function based on Dice coefficient addresses the imbalance between the number of lung voxels against that of background. We have leveraged Vnet model by using batch normalization for training which enables us to use higher learning rate and accelerates the training of the model. To address the inadequacy of training data and obtain better robustness, we augment the data applying random linear and non-linear transformations. Experimental results on two challenging medical image data show that our proposed method achieved competitive result with a much faster speed.
The Bystander Response in C3H 10T½ Cells: The Influence of Cell-to-Cell Contact (2004)

Although radiation-induced heritable damage in mammalian cells was thought to result from the direct interaction of radiation with DNA, it is now accepted that biological effects may occur in cells that were not themselves traversed by ionizing radiation but are close to those that were. However, little is known about the mechanism underlying such a bystander effect, although cell-to-cell communication is thought to be of importance. Previous work using the Columbia microbeam demonstrated a significant bystander effect for clonogenic survival and oncogenic transformation in C3H 10T(1/2) cells. The present study was undertaken to assess the importance of the degree of cell-to-cell contact at the time of irradiation on the magnitude of this bystander effect by varying the cell density. When 10% of cells were exposed to a range of 2-12 alpha particles, a significantly greater number of cells (P < 0.0001) were inactivated when cells were irradiated at high density (>90% in contact with neighbors) than at low density (<10% in contact). In addition, the oncogenic transformation frequency was significantly higher in high-density cultures (P < 0.0004). These results suggest that when a cell is hit by radiation, the transmission of the bystander signal through cell-to-cell contact is an important mediator of the effect, implicating the involvement of intracellular communication through gap junctions.
Mechanistic Aspects of Ethylbenzene Dehydrogenation with CO<sub>2</sub> over K<sub>2</sub>O/B<sub>2</sub>O<sub>3</sub> -TiO<sub>2</sub> - ZrO<sub>2</sub> Bi-Functional Catalysts (2007)

TiO 2 -ZrO 2 bi-functional catalysts were prepared by co-precipitation method using aqueous NH 3 solution as a hydrolyzing agent. Either K 2 O promoter or B 2 O 3 promoter has been deposited 60% TiO 2 - ZrO 2 by wet-impregnation techniques. The catalytic activity of both K 2 O promoted and B 2 O 3 promoted TiO 2 -ZrO 2 acid base bi-functional catalysts has been studied for the oxidative dehydrogenation of ethylbenzene in the presence of CO 2 . The higher conversion of ethylbenzene and higher selectivity of styrene has been obtained on the K 2 O promoted TiO 2 -ZrO 2 catalysts. On the other hand, B 2 O 3 promoted TiO 2 - ZrO 2 catalysts exhibited lower catalytic activity than those of K 2 O promoted TiO 2 - ZrO 2 catalysts. In the mechanistic point of view both K 2 O promoted TiO 2 -ZrO 2 catalysts and B 2 O 3 promoted TiO 2 - ZrO 2 catalysts following the different pathways. This synergistic promotional effects of K 2 O and CO 2 enhanced the selectivity of styrene (98 - 99%) by sustaining the higher conversions of ethylbenzene (60 -65%).
Mold populations and dust mite allergen concentrations in house dust samples from across Puerto Rico (2015)

Lifetime childhood asthma prevalence (LCAP) percentages in Puerto Rico Health Regions (HR) are substantially higher in northeastern vs. southwestern HR. Higher average relative humidity in the northeast might promote mold and mite exposures and possibly asthma prevalence. To test this hypothesis, mold contamination, Environmental Relative Moldiness Index (ERMI) values were measured in floor dust (n = 26) and dust mite allergen concentrations in bed dust (n = 14). For this analysis, the eight HR were divided into those with LCAP > 30% (n = 3) and < 30% (n = 5). The average ERMI value was significantly greater (Wilcoxon Rank Sum, p < 0.001) in high than in low LCAP HR (14.5 vs. 9.3). The dust mite antigens Der p 1, Der f 1, and Blo t 5 were detected in 90% of bed samples, but the concentrations were not significantly different in high vs. low LCAP HR. Mold exposures might partially explain the differences in LCAP HR in Puerto Rico.
“Turning” in the interpretation of verse (1981)

In the performance of poetry oral interpreters are obliged to indicate the ends of lines or where the poet “turns” from one verse to the next. These turnings are significant clues to meanings of both nontraditional verse, such as e.e. cummings” “in Just‐,” as well as imagistic and traditional poetry. Run‐on lines produce especially interesting tensions. In addition to pausing there are many ways in which oral interpreters may indicate turnings of a poem.
Wannier-Stark localization in a 1.55 mu m InGaAs/InAlAs superlattice waveguide modulator structure (1991)

The authors present an optical waveguide modulator structure based on Wannier-Stark localization in a InGaAs-InAlAs superlattice. Optical waveguide transmission below the superlattice bandgap displays expected F/sup -1/ oscillatory behavior leading to various modulation schemes. An 11 dB extinction ratio was obtained by applying a 0.7 V drive voltage to a 100 mu m long waveguide device operating at 1.55 mu m under a transverse-electric (TE)-polarization mode. On-state attenuation was 5 dB. Lower open-state attenuation (3 dB) can be obtained simultaneously with a higher extinction ratio (13 dB) but in that case a larger drive voltage (1.6 V) is needed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Fish biorobotics: kinematics and hydrodynamics of self-propulsion (2007)

As a result of years of research on the comparative biomechanics and physiology of moving through water, biologists and engineers have made considerable progress in understanding how animals moving underwater use their muscles to power movement, in describing body and appendage motion during propulsion, and in conducting experimental and computational analyses of fluid movement and attendant forces. But it is clear that substantial future progress in understanding aquatic propulsion will require new lines of attack. Recent years have seen the advent of one such new avenue that promises to greatly broaden the scope of intellectual opportunity available to researchers: the use of biorobotic models. In this paper we discuss, using aquatic propulsion in fishes as our focal example, how using robotic models can lead to new insights in the study of aquatic propulsion. We use two examples: (1) pectoral fin function, and (2) hydrodynamic interactions between dorsal and caudal fins. Pectoral fin function is characterized by considerable deformation of individual fin rays, as well as spanwise (along the length) and chordwise (across the fin) deformation and area change. The pectoral fin can generate thrust on both the outstroke and instroke. A robotic model of the pectoral fin replicates this result, and demonstrates the effect of altering stroke kinematics on the pattern of force production. The soft dorsal fin of fishes sheds a distinct vortex wake that dramatically alters incoming flow to the tail: the dorsal fin and caudal fin act as dual flapping foils in series. This design can be replicated with a dual-foil flapping robotic device that demonstrates this phenomenon and allows examination of regions of the flapping performance space not available to fishes. We show how the robotic flapping foil device can also be used to better understand the significance of flexible propulsive surfaces for locomotor performance. Finally we emphasize the utility of self-propelled robotic devices as a means of understanding how locomotor forces are generated, and review different conceptual designs for robotic models of aquatic propulsion.
Proteomic Approach to Evaluate Mechanisms That Contribute to Food Allergenicity: Comparative 2D-DIGE Analysis of Radioallergosorbent Test Positive and Negative Patients (2011)

Proteomic profiles of RAST(+) subjects with severe food allergies and RAST(-) subjects were compared using 2D-DIGE analysis to obtain candidate biomarkers specific to food allergies. Our analysis highlighted 52 proteins that were differentially expressed between the RAST(+) and RAST(-) groups of which 37 were successfully identified that include chondroitin sulfates, zinc finger proteins, C-type lectins, retinoic acid binding proteins, heat shock proteins, myosin, cytokines, mast cell expressed proteins, and MAP kinases. Biological network analysis tool Metacore revealed that most of these regulated proteins play a role in immune tolerance, hypersensitivity and modulate cytokine patterns inducing a Th2 response that typically results in IgE-mediated allergic response which has a direct or indirect biological link to food allergy. Identifying unique biomarkers associated with certain allergic phenotypes and potentially cross-reactive proteins through bioinformatics analyses will provide enormous insight into the mechanisms that underlie allergic response in patients with food allergies.
A search for amino acids and nucleobases in the Martian meteorite Roberts Massif 04262 using liquid chromatography‐mass spectrometry (2013)

Abstract The investigation into whether Mars contains signatures of past or present life is of great interest to science and society. Amino acids and nucleobases are compounds that are essential for all known life on Earth and are excellent target molecules in the search for potential Martian biomarkers or prebiotic chemistry. Martian meteorites represent the only samples from Mars that can be studied directly in the laboratory on Earth. Here, we analyzed the amino acid and nucleobase content of the shergottite Roberts Massif (RBT) 04262 using liquid chromatography‐mass spectrometry. We did not detect any nucleobases above our detection limit in formic acid extracts; however, we did measure a suite of protein and nonprotein amino acids in hot‐water extracts with high relative abundances of β‐alanine and γ‐amino‐ n ‐butyric acid. The presence of only low (to absent) levels of several proteinogenic amino acids and a lack of nucleobases suggest that this meteorite fragment is fairly uncontaminated with respect to these common biological compounds. The distribution of straight‐chained amine‐terminal n ‐ω‐amino acids in RBT 04262 resembled those previously measured in thermally altered carbonaceous meteorites (Burton et al. 2012; Chan et al. 2012). A carbon isotope ratio of −24‰ ± 6‰ for β‐alanine in RBT 04262 is in the range of reduced organic carbon previously measured in Martian meteorites (Steele et al. 2012). The presence of n ‐ω‐amino acids may be due to a high temperature Fischer‐Tropsch‐type synthesis during igneous processing on Mars or impact ejection of the meteorites from Mars, but more experimental data are needed to support these hypotheses.
Gradual Photochemical-Induced Conversion of Liquid Polydimethylsiloxane Layers to Carbon Containing Silica Coatings by VUV Irradiation at 172 nm (2009)

Thin liquid layers of polydimethylsiloxane (PDMS) were irradiated by VUV light under nitrogen atmosphere using a Xe(2)- excimer lamp. The irradiated layers were analyzed with infrared reflection absorption spectroscopy (IRRAS) and X-ray photoelectron spectroscopy (XPS), showing a gradual photochemical-induced conversion of the liquid PDMS to solid SiO(2)-like coatings. IRRAS measurements revealed a smooth frequency shift of the maximal absorption band from 1111 to 1231 cm(-1) with increasing irradiation energy density caused by a gradual shift from the asymmetric Si-O stretching vibration of PDMS to the longitudinal optical (LO) mode of SiO(2). The shift was found to be dependent on the applied irradiation energy density and the O/Si ratio in the film analyzed by XPS measurements. The atomic ratio of O/Si increases from 1:1 to about 2.5:1. At the same time, the atomic ratio of C/Si decreases from 2:1 down to 1:6.5. Images taken by high resolution field emission scanning electron microscopy (FESEM) and scanning force microscopy (SFM) show a smooth surface without cracks or pores. The controllable coating properties in combination with the possibility for local irradiation using masks are promising high potential for the coating technology.
Properties of Phenytoin Binding Sites in the Rat Brain: Regional Distribution and Postnatal Development (1988)

Specific [3H]phenytoin binding in rat cortical membranes is associated with a micromolar affinity site through which diazepam can exert an enhancing effect. In contrast to diazepam, ( + )bicuculline, isoguvacine and pentobarbital inhibited Phenytoin binding, while GABA and (-)baclofen had no effect. Decreased Phenytoin binding and a loss of the diazepam effect were observed in phospholipase A2-treated membranes. Binding in the absence and presence of diazepam demonstrated differential postnatal development. Furthermore, the degree to which binding was enhanced by diazepam varied from one brain region to another. The regional variations of Phenytoin binding, both in the presence and absence of diazepam, did not correlate positively with the regional distribution of either the central benzodiazepine receptors or the peripheral type binding sites in the brain.
Security of Blind Signatures Revisited. (2011)

Abstract. We revisit the definition of unforgeability of blind signatures as proposed by Pointcheval and Stern (Journal of Cryptology 2000). Surprisingly, we show that this established definition falls short in two ways of what one would intuitively expect from a secure blind signature scheme: It is not excluded that an adversary submits the same message m twice for signing, and then produces a signature for m ′ = m. The reason is that the forger only succeeds if all messages are distinct. Moreover, it is not excluded that an adversary performs k signing queries and produces signatures on k + 1 messages as long as each of these signatures does not pass verification with probability 1. Finally, we proposed a new definition, honest-user unforgeability, that covers these attacks. We give a simple and efficient transformation that transforms any unforgeable blind signature scheme (with deterministic verification) into an honest-user unforgeable one.