gebhart/patrepeval huggingface dataset:
The Nucleotide Excision Repair Pathway Protects Borrelia burgdorferi from Nitrosative Stress in Ixodes scapularis Ticks (2016)

The Lyme disease spirochete Borrelia burgdorferi encounters a wide range of environmental conditions as it cycles between ticks of the genus Ixodes and its various mammalian hosts. Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are potent antimicrobial molecules generated during the innate immune response to infection, however, it is unclear whether ROS and RNS pose a significant challenge to B. burgdorferi in vivo. In this study, we screened a library of B. burgdorferi strains with mutations in DNA repair genes for increased susceptibility to ROS or RNS in vitro. Strains with mutations in the methyl-directed mismatch repair gene mutS1 are hypersensitive to killing by ROS, while strains lacking the nucleotide excision repair (NER) gene uvrB show increased susceptibility to both ROS and RNS. Therefore, mutS1-deficient and uvrB-deficient strains were compared for their ability to complete their infectious cycle in Swiss Webster mice and I. scapularis ticks to help identify sites of oxidative and nitrosative stresses encountered by B. burgdorferi in vivo. Both mutS1 and uvrB were dispensable for infection of mice, while uvrB promoted the survival of spirochetes in I. scapularis ticks. The decreased survival of uvrB-deficient B. burgdorferi was associated with the generation of RNS in I. scapularis midguts and salivary glands during feeding. Collectively, these data suggest that B. burgdorferi must withstand cytotoxic levels of RNS produced during infection of I. scapularis ticks.
Porous polyelectrolyte materials with controlled luminescence properties based on aromatic‐aromatic interactions with rhodamine B (2021)

A series of porous materials made of sodium alginate have been synthesized by freeze‐drying including rhodamine B as pigment complexed or not with the aromatic polymer poly(sodium 4‐styrenesulfonate). By means of aromatic‐aromatic interactions between the aromatic polymer and the dye, the luminescent properties of the final materials can be controlled. This is mainly produced by avoiding the dye self‐aggregation in the solid state in a higher extent as the excess of the aromatic polyelectrolyte over the dye increases. The solid materials present a structure made of microsheets and microfibers of alginate, density ranging between 17 and 26 mg/cm 3 , porosity higher than 97%, and Young's modulus ranging between 8 and 24 kPa. This work highlights the role or aromatic polyelectrolytes to control properties of both the polymer and its aromatic counterions in the solid state, making use of aromatic‐aromatic interactions.
100G and beyond (2012)

This paper provides an overview of the latest generation of commercial high capacity transmission systems. It also shows how the approaches used there will be extended to build even higher capacity systems in the future.
NAMPT Is the Cellular Target of STF-31-Like Small-Molecule Probes (2014)

The small-molecule probes STF-31 and its analogue compound 146 were discovered while searching for compounds that kill VHL-deficient renal cell carcinoma cell lines selectively and have been reported to act via direct inhibition of the glucose transporter GLUT1. We profiled the sensitivity of 679 cancer cell lines to STF-31 and found that the pattern of response is tightly correlated with sensitivity to three different inhibitors of nicotinamide phosphoribosyltransferase (NAMPT). We also performed whole-exome next-generation sequencing of compound 146-resistant HCT116 clones and identified a recurrent NAMPT-H191R mutation. Ectopic expression of NAMPT-H191R conferred resistance to both STF-31 and compound 146 in cell lines. We further demonstrated that both STF-31 and compound 146 inhibit the enzymatic activity of NAMPT in a biochemical assay in vitro. Together, our cancer-cell profiling and genomic approaches identify NAMPT inhibition as a critical mechanism by which STF-31-like compounds inhibit cancer cells.
The Leukocyte Function-Associated Antigen-1 (LFA-1)-Binding Site on ICAM-3 Comprises Residues on Both Faces of the First Immunoglobulin Domain (1998)

ICAM-3 (CD50), a member of the Ig superfamily, is a major ligand for the leukocyte integrin LFA-1 (CD11a/CD18). This interaction represents one of several Ig superfamily/integrin ligand-receptor pairs that have been described to date. ICAM-3 is highly expressed on resting leukocytes and on APCs. In addition to an adhesive function, ICAM-3 can act as a signal-transducing molecule on T cells, providing a costimulatory signal for cell proliferation. Eighteen point mutations in ICAM-3 were generated, and residues important for binding of functional blocking Abs were identified. Mutation of seven of the residues reduced or abrogated adhesion to LFA-1, including three residues that are located on strand A of the ABED face of domain 1. In contrast, extensive mutagenesis analysis of ICAM-1 has shown that only residues on the GFC face interact with LFA-1. Our results provide evidence for a more extensive binding interface between ICAM-3 and LFA-1 than has previously been described. ICAM-3 appears to be unique among the ICAMs in utilizing residues on both faces of domain 1 for interaction with its ligand LFA-1.
Controlled Formation of Polymer Nanocapsules with High Diffusion‐Barrier Properties and Prediction of Encapsulation Efficiency (2014)

Polymer nanocapsules with high diffusion-barrier performance were designed following simple thermodynamic considerations. Hindered diffusion of the enclosed material leads to high encapsulation efficiencies (EEs), which was demonstrated based on the encapsulation of highly volatile compounds of different chemical natures. Low interactions between core and shell materials are key factors to achieve phase separation and a high diffusion barrier of the resulting polymeric shell. These interactions can be characterized and quantified using the Hansen solubility parameters. A systematic study of our copolymer system revealed a linear relationship between the Hansen parameter for hydrogen bonding (δh ) and encapsulation efficiencies which enables the prediction of encapsulated amounts for any material. Furthermore EEs of poorly encapsulated materials can be increased by mixing them with a mediator compound to give lower overall δh values.
Chemosensitivity of human melanoma metastases in mouse subrenal capsule assay???can it predict tumour response to combined cytostatic plus interferon therapy in metastatic melanoma? (1996)

We have analysed the chemosensitivity of 121 human melanoma metastases in the 6-day mouse subrenal capsule assay (SRCA). A total of 13 different chemotherapy regimens were analysed in four successive series. By the original criteria of the assay, 75% of tumours were sensitive to at least one regimen. The most effective combinations, giving sensitivity rates > 40%, were of dacarbazine, vincristine, and BCNU (DOB) with or without metronidazole, followed by cisplatin plus etoposide (Plat-VP16) combined with interferon. On the basis of the SRCA screening we developed a four-drug chemotherapy regimen combined with interferon for metastatic melanoma. Retrospectively analysed the assay correctly identified 77% of clinical responders and 54% of clinical non-responders. The overall predictive accuracy was 65%. Despite the limitations of the assay, it can be used for screening new drugs or combinations.
Uplink interference protection and scheduling for energy efficient OFDMA networks (2012)

One of the key challenges for future orthogonal frequency division multiple access-based networks is inter-cell interference coordination. With full frequency reuse and small inter-site distances, coping with co-channel interference (CCI) in such networks has become increasingly important. In this article, an uplink interference protection (ULIP) technique to combat CCI is introduced and investigated. The level of uplink interference originating from neighbouring cells (affecting co-channel mobile stations (MSs) in the cell of interest) can be effectively controlled by reducing the transmit power of the interfering MSs. This is done based on the target signal-to-noise-plus-interference ratio (SINR) and tolerable interference of the vulnerable link. Bands are prioritised in order to differentiate those (vulnerable/victim) MSs that are to be protected from interference and those (aggressor/interfering MSs) that are required to sacrifice transmission power to facilitate the protection. Furthermore, MSs are scheduled such that those users with poorer transmission conditions receive the highest interference protection, thus balancing the areal SINR distribution and creating a fairer allocation of the available resources. In addition to interference protection, the individual power reductions also serve to decrease the total system uplink power, resulting in a greener system. It is shown through analytic derivation that the introduction of ULIP guarantees an increase in energy efficiency for all MSs, with the added benefit that gains in overall system throughput are also achievable. Extensive system level simulations validate these findings.
Boundary Lubrication Mechanisms for High-Performance Friction Modifiers (2018)

We recently reported a new molecular heterocyclic friction modifier (FM) that exhibits excellent friction and wear reduction in the boundary lubrication regime. This paper explores the mechanisms by which friction reduction occurs with heterocyclic alkyl-cyclen FM molecules. We find that these chelating molecules adsorb onto (oxidized) steel surfaces far more tenaciously than conventional FMs such as simple alkylamines. Molecular dynamics simulations argue that the surface coverage of our heterocyclic FM molecules remains close to 100% even at 200 °C. This thermal stability allows the FMs to firmly anchor to the surface, allowing the hydrocarbon chains of the molecules to interact and trap base oil lubricant molecules. This results in thicker boundary film thickness compared with conventional FMs, as shown by optical interferometry measurements.
A variable step size evolutionary affine projection algorithm (2011)

It is well known that the affine projection algorithm (APA) offers a good tradeoff between convergence rate/tracking and computational complexity. Recently, the evolutionary APA (E-APA) with a variable projection order has been proposed. In this paper, we propose a variable step size (VSS) version of the E-APA, called VSS-E-APA. It is shown that the VSS-E-APA is robust to near-end signal variations. Also, it has both a fast convergence speed and a small steady-state error and a much reduced numerical complexity than the VSS-APA.
Wide Field-of-View, Large-Area Long-wave Infrared Silicon Metalenses (2023)

Long-wave infrared (LWIR, 8-12 $μm$ wavelengths) is a spectral band of vital importance to thermal imaging. Conventional LWIR optics made from single-crystalline Ge and chalcogenide glasses are bulky and fragile. The challenge is exacerbated for wide field-of-view (FOV) optics, which traditionally mandates multiple cascaded elements that severely add to complexity and cost. Here we designed and experimentally realized a LWIR metalens platform based on bulk Si wafers featuring 140$^\circ$ FOV. The metalenses, which have diameters exceeding 4 cm, were fabricated using a scalable wafer-level process involving photolithography and deep reactive ion etching. Using a metalens-integrated focal plane array, we further demonstrated wide-angle thermal imaging.
Figure S2 from A Comparative Study of Neuroendocrine Heterogeneity in Small Cell Lung Cancer and Neuroblastoma (2023)

&lt;p&gt;Known NBL prognostic factors consistently associate with outcome across different NBL studies but not NE scores.&lt;/p&gt;
Microsatellite Instability and Epigenetic Inactivation of MLH1 and Outcome of Patients With Endometrial Carcinomas of the Endometrioid Type (2007)

MSI is not associated with survival in patients with endometrioid endometrial cancer.
Electric Conduction of Electroluminescent Metal Chelate Thin Films (1999)

Abstract Electric conduction in vacuum-deposited films of electroluminescent metal-chelates, tris-(8-hydroxyquinoline) aluminum (Alq3) and zinc bis-(2-(o-hydroxypheyl)-benzoxazolate)) (ZnPBO), were studied by current (I)-voltage (V) measurement. The I-V characteristics demonstrated that the films exhibited trap-controlled conduction. For the Alq3 film, conductivity σ was estimated to be 3.0 × 10−15 Scm−1 from the characteristic in ohmic current region. From the I-V characteristic in space charge limited current region, further, carrier mobility μ of the Alq3 film was estimated to be 5.0 × 10−7 cm2V−1s−1; this value is in good agreement with electron mobility evaluated by the time-of-fight technique. For ZnPBO, the values of σ and μ were estimated to be 2.0 × 10−14 Scm−1 and 7.0 × 10−6 cm2V−1s−1, respectively.
Pectin and polyacrylamide composite hydrogels: Effect of pectin on structural and dynamic mechanical properties (2004)

Abstract Composite hydrogels of pectin and polyacrylamide were synthesized and evaluated by scanning electron microscopy, atomic force microscopy, light microscopy, and dynamic mechanical analysis. The crosslinking polymerization of acrylamide in pectin solution resulted in a composite having a macroporous pectin domain with an interstitial polyacrylamide domain. This composite had improved mechanical properties compared to those of either polymer alone, and it absorbed and retained more water than crosslinked polyacrylamide alone. Furthermore, crosslinking polymerization of acrylamide in an existing pectinate scaffold resulted in a double‐network architecture, where filamentous polyacrylamide networks penetrated through pores of the pectin scaffold. It was found that pectins dictated the features of microstructure in the composites through regulating the coordination of phase separation of the two components and water partition between the two phases. Results from this study highlight potential new uses of pectins in protecting the physical structure of environmentally sensitive polymers from mechanical damage related to freezing, lyophilization, and other conditions experienced during their use in biomedical and industrial products. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 92: 1893–1901, 2004
Incrementalite et adaptativite en optimisation combinatoire (1997)

Dans cette these, nous nous interessons a accroitre l'efficacite de methodes permettant de resoudre un probleme d'optimisation combinatoire pour une serie d'instances. Nous developpons des versions adaptatives aux methodes conventionnelles, i. E. Qui utilisent des informations provenant d'une precedente resolution. Dans le cas particulier ou la nouvelle instance ne se distingue de la precedente que par le nombre de variables, on parle de methodes incrementales. Une etude menee sur differents problemes polynomiaux a confirme l'interet des algorithmes incrementaux. L'utilisation de fonctions d'evaluation incrementales dans les methodes de separation-evaluation permet un gain important car les evaluations sont realisees a maintes reprises et pour des instances tres voisines. Nous proposons trois methodes qui different sur la position de l'instance de reference dans l'arbre de recherche. Elles sont validees sur le probleme np-difficile du placement de taches sur un systeme distribue. Nous avons mis en evidence les capacites adaptatives des reseaux de neurones : nous avons defini comment perturber un reseau pour que celui-ci quitte un etat stable et converge vers un nouvel etat representatif d'une solution a une nouvelle instance, voisine de la precedente. Cette methode presente un interet pratique evident car elle est independante du probleme et de la transformation appliquee a l'instance. Les differentes versions du modele de hopfield presentent un manque de selectivite qui se traduit experimentalement par des neurones qui conservent des activations loin a la fois de 0 et de 1. Comme le mecanisme d'activation competitive est particulierement apte a realiser cette separation, nous avons generalise les regles permettant son instauration pour definir une nouvelle extension du modele de hopfield. L'etude sur l'adaptativite est menee avec ce modele dont la validite a ete confirmee sur le probleme du recouvrement d'ensembles.
The Future SEM Sees 3 Dimensions... Bringing Deconvolution Techniques to the Electron Microscope. (2013)

Extended abstract of a paper presented at Microscopy and Microanalysis 2013 in Indianapolis, Indiana, USA, August 4 – August 8, 2013.
Dynamics of dichoptic masking in the primary visual cortex (2014)

The inputs from the two eyes interact in a nonlinear fashion. This interaction can be either excitatory or inhibitory: Excitatory interaction (combination) occurs first in the primary visual cortex but little is known about the site of the inhibitory interaction (suppression). To investigate the latter, experimental paradigms typically present distinct inputs to the eyes (dichoptic presentation, one target and one mask are respectively presented to different eyes at the same time). Here we used magnetoencephalography (MEG) source imaging to establish the site of the cortical neural signature of interocular suppression in visual cortex.

We presented different noise stimuli to each eye: The target-noise was presented for contrasts ranging between 0 and 32 %. The mask-contrast was presented to the other eye at fixed contrast (32%). We flickered the two noise stimuli (4 and 6 Hz) to elicit a frequency-tagged steady-state visual evoked response (SSVER) that was readily detectable in MEG traces [1]. Four participants passively observed the visual presentation while keeping their gaze fixed on the center of the screen. The Brainstorm application was used to analyze the MEG data [3]. MEG source time series were extracted from cortical regions of interest (ROIs) defined from the visual retinotopic maps of each participant obtained from previous fMRI acquisitions.

Using the power of the cortical responses to the frequency-tagged stimuli, we constructed contrast response functions for all the ROIs (Figure 1 A). To investigate dynamics of propagation of the response along visual cortical areas, the instantaneous phase of the signal was identified in each ROI. As expected [2], when the target was presented alone, the power of the responses was found to increase monotonically with contrast (Figure 1 B, solid line). When a mask was added to the other eye, the contrast response was attenuated (Figure 1 B, dotted line). Interestingly, the mask presented at a fixed contrast was also found to be gradually suppressed with increasing target contrast (Figure 1 C). These effects were revealed for responses as early as the primary visual cortex. In the time-domain, we detected a progressive phase shift between the cortical responses along the ventral and dorsal streams.



Figure 1

A. Localization of V1 on the activity map B. Normalized power of SSVER response as a function of contrast for target only (solid line), target and mask (dotted line); C. Normalized power in a 32% contrast mask as the contrast in the target is increasing. ...
Adding Active Power Regulation to Wind Farms with Variable Speed Induction Generators (2007)

Larger wind power integration in the power system requires generated power regulation in wind farms. In this work, an active power control system for wind farms equipped with variable speed wind turbines is proposed, aiming at minimizing the active power variations due to wind speed variations. The proposed control scheme achieves the active power regulation goal without significative reduction in total power production of the wind farm, and takes advantage of the non-uniform wind distribution along the farm. Employing suitable tools for wind power forecast, such performance can still be improved. With this methodology, the wind power generation drawbacks are reduced, allowing a better integration of the wind energy into the power system.
Supplementary Figure Legends from Complete Regression of Metastatic Renal Cell Carcinoma by Multiple Injections of Engineered Mesenchymal Stem Cells Expressing Dodecameric TRAIL and HSV-TK (2023)

&lt;p&gt;PDF file - 125K&lt;/p&gt;
Retrieval of individualized head-related transfer functions for hearing aid applications (2017)

The capability of modern hearing aids to provide hearing-impaired humans with enhanced signals, which ultimately leads to an increased speech intelligibility, may benefit from fitting the device for each subject individually. This ideally also involves the exploitation of Head-Related Impulse Responses (HRIRs). However, HRIRs vary from person to person and thus require tedious measurements for each individual. In this work, we investigate two approaches which aim at speeding up the HRIR acquisition procedure. These are continuous measurements and interpolation, where Dynamic Time Warping (DTW) as well as linear interpolation of the magnitude and phase responses are considered. In contrast to related publications, the continuous HRIR measurements are not performed in anechoic environments here. The quality of the obtained HRIRs is assessed by means of the system mismatch and the proposed error of relative transfer functions. Both measures reveal that continuous HRIR measurements are on average much more capable than the investigated interpolation approaches, and they furthermore provide a more uniform performance for different source directions.
Polystyrene Network−Network Interdiffusion (2002)

Neutron reflectivity was used to study the interdiffusion of thin film bilayers of cross-linked deuterated and protonated polystyrene. The films were spun-cast and cross-linked by γ radiation. Interfacial broadening was studied as a function of annealing time for different cross-link densities. The samples were annealed in a vacuum at 150 °C, and neutron reflectivity measurements were performed in air at room temperature. The interface was observed to broaden rapidly at short annealing times and then plateau to an equilibrium value. The interfacial broadening was modeled using a solution to the Fokker−Planck equation with a parabolic external potential to obtain the equilibrium interfacial width and effective diffusion coeffcient as a function of the average network mesh size, N̄c. The interfacial width was found to scale as N̄c0.47±0.1. The effective diffusion coefficient was found to be independent of N̄c.
Tracing the Stemness of Porcine Skin-Derived Progenitors (pSKP) Back to Specific Marker Gene Expression (2009)

Multipotent skin-derived progenitors (SKP) can produce both neural and mesodermal progeny in vitro, sharing the characteristics of embryonic neural crest stem cells. However, the molecular basis for the property of multiple lineage potential and neural crest origin of SKPs is still elusive. Here we report the cooperative expression of pluripotency related genes (POU5F1, SOX2, NANOG, STAT3) and neural crest marker genes (p75NTR, TWIST1, PAX3, SNAI2, SOX9, SOX10) in GFP-transgenic porcine skin-derived progenitors (pSKP). The proportion of cells positive for POU5F1, nestin, fibronectin, and vimentin were 12.3%, 15.1%, 67.9% and 53.7%, showing the heterogeneity of pSKP spheres. Moreover, pSKP cells can generate both neural (neurons and glia) and mesodermal cell types (smooth muscle cells and adipocytes) in vitro, indicating the multiple lineage potency. Four transcription factors (POU5F1, SNAI2, SOX9, and PAX3) were identified that were sensitive to mitogen (FBS) and/or growth factors (EGF and bFGF). We infer that POU5F1, SNAI2, SOX9, and PAX3 may be the key players for maintaining the neural crest derived multipotency of SKP cells in vitro. This study has provided new insight into the molecular mechanism of stemness for somatic-derived stem cells at the level of transcriptional regulation.