gebhart/patrepeval huggingface dataset:
Epistasis reduces fitness costs of influenza A virus escape from stem-binding antibodies (2023)

The hemagglutinin (HA) stem region is a major target of universal influenza vaccine efforts owing to the presence of highly conserved epitopes across multiple influenza A virus (IAV) strains and subtypes. To explore the potential impact of vaccine-induced immunity targeting the HA stem, we examined the fitness effects of viral escape from stem-binding broadly neutralizing antibodies (stem-bnAbs). Recombinant viruses containing each individual antibody escape substitution showed diminished replication compared to wild-type virus, indicating that stem-bnAb escape incurred fitness costs. A second-site mutation in the HA head domain (N129D; H1 numbering) reduced the fitness effects observed in primary cell cultures and likely enabled the selection of escape mutations. Functionally, this putative permissive mutation increased HA avidity for its receptor. These results suggest a mechanism of epistasis in IAV, wherein modulating the efficiency of attachment eases evolutionary constraints imposed by the requirement for membrane fusion. Taken together, the data indicate that viral escape from stem-bnAbs is costly but highlights the potential for epistatic interactions to enable evolution within the functionally constrained HA stem domain.
Nonlinear Transistor Model Parameter Extraction Techniques (2011)

Achieve accurate and reliable parameter extraction using this complete survey of state-of-the-art techniques and methods. A team of experts from industry and academia provides you with insights into a range of key topics, including parasitics, intrinsic extraction, statistics, extraction uncertainty, nonlinear and DC parameters, self-heating and traps, noise, and package effects. Learn how similar approaches to parameter extraction can be applied to different technologies. A variety of real-world industrial examples and measurement results show you how the theories and methods presented can be used in practice. Whether you use transistor models for evaluation of device processing and you need to understand the methods behind the models you use, or you want to develop models for existing and new device types, this is your complete guide to parameter extraction.
Regulation of alkaline phosphatase promoter activity by forkhead transcription factor FKHR (2002)

Alkaline phosphatase (ALP) is a basic marker of osteoblast maturation and osteogenesis. However, the mechanisms of the ALP gene regulation in osteoblasts remain elusive. In this study, we examined the expression of forkhead transcription factor FKHR, a regulator of hepatic glucose metabolic and proapoptotic genes, in osteogenic cells and the effect of FKHR on transcription of the ALP gene. RT-PCR and immunoblot analyses revealed the expression of FKHR in osteogenic MC3T3-E1, SaOS2, and UMR 106 cells. Reporter assays demonstrated that the overexpression of FKHR stimulated ALP promoter activity through the forkhead response element in its promoter. These results suggest that ALP is a target gene regulated by FKHR and that FKHR contributes to osteoblast maturation and osteogenesis.
Effects of slightly rough surfaces on the brightness temperature of the lunar regolith (2013)

Keihm [1984] made a study on the effects of the rough lunar surface on microwave brightness temperature using geometric optics (GO), which is valid only when the microwave wavelength is much smaller than the radius of curvature of the rough surface. This approach is deficient because it has no explicit wavelength dependence. The Chang'E‐1 Lunar Orbiter carried out lunar microwave remote sensing of maria where the surface can be regarded as “slightly” rough, and this has motivated our study. We model the mare regolith as a multilayer planar layered media with a slightly rough top surface, and the temperature profile is retrieved by solving the heat conduction equation. The noncoherent method is utilized to calculate the emission of the multilayer media. To calculate the effect of the rough top surface on brightness temperatures, we use the bistatic transmission coefficients by applying the second‐order small perturbation method. Using this model, the microwave brightness temperatures of the Apollo 12 area under different roughness conditions are calculated. It is shown that a slightly rough surface will increase or decrease the microwave radiative brightness temperature of the lunar regolith and that the change is related to the roughness, incidence angle, frequency, and polarization. In the case of measurements made by the Chang'E‐1 microwave radiometer, where the incidence angle is 0°, the small‐scale roughness will increase the brightness temperature of the lunar regolith.
Promoter methylation and large intragenic rearrangements of DPYD are not implicated in severe toxicity to 5-fluorouracil-based chemotherapy in gastrointestinal cancer patients (2010)

Our results indicate that DPYD promoter methylation and large intragenic rearrangements do not contribute significantly to the development of 5-FU severe toxicity in gastrointestinal cancer patients, supporting the need for additional studies on the mechanisms underlying genetic susceptibility to severe 5-FU toxicity.
A manual for the CHAOS runtime library (1995)

Procedures are presented that are designed to help users efficiently program irregular problems (e.g. unstructured mesh sweeps, sparse matrix codes, adaptive mesh partial differential equations solvers) on distributed memory machines. These procedures are also designed for use in compilers for distributed memory multiprocessors. The portable CHAOS procedures are designed to support dynamic data distributions and to automatically generate send and receive messsage by capturing communications patterns at runtime.
Atypical Fibroxanthoma in the Setting of Chronic Lymphocytic Leukemia and Other Non-Hodgkin Lymphomas (2011)

AFX did not demonstrate aggressive features such as recurrence or metastasis in patients with concomitant CLL or other NHL. More studies are needed to definitively characterize the behavior of AFX in this patient population.
Power controlled system revenue maximization in large-scale heterogeneous cellular networks (2014)

In the heterogeneous cellular network, each mobile station perceives different channel gains to different base stations. Therefore, it is important to associate a mobile station with the right base station with transmit power control so as to achieve substantial improvement in spectrum-efficiency and energy-efficiency. Despite its importance, the problem that maximizes the overall system revenue with minimum total transmit power consumption through joint BS association and power control has remained largely unsolved for the large-scale heterogeneous cellular network, mainly due to its non-convex and combinatorial nature. To solve this problem, this paper first proposes a single-stage formulation that captures two interactive objectives, i.e., the maximization of overall system revenue and the minimization of total transmit power consumption. The single-stage optimization problem is then efficiently solved by the proposed POSEM algorithm based on the theory of coalition formation game and the idea of simulated annealing. Finally, our analysis shows that the proposed algorithm is guaranteed to converge to the global optimal solution fast.
On the Development of a Force-Feedback Mouse and Its Integration Into a Graphical User Interface (1994)

Abstract A novel computer input-output device utilizing force feedback has been developed. Elements of electromechanical and controller design are discussed. Issues relating to hardware/software integration with a workstation and the X Windows graphical user-interface are presented. Results from experiments demonstrating the ability of the system to simulate linear sliders, mechanical limit stops such as the edges of the display or of a window, and mechanical push-buttons are given. Based on these results, several design guidelines and possible uses for force feedback in general purpose graphical user-interfaces are proposed.
Significant evidence for a heritable contribution to cancer predisposition: a review of cancer familiality by site (2012)

Both environmentally and genetically-based familial clustering have clinical significance, and these results support increased surveillance for cancer of the same sites among close relatives of affected individuals for many more cancers than are typically considered.
Challenges in securing the domain name system (2006)

Two main security threats exist for DNS in the context of query/response transactions. Attackers can spoof authoritative name servers responding to DNS queries and alter DNS responses in transit through man-in-the-middle attacks, and alter the DNS responses stored in caching name servers. The IETF has defined the digital signature-based DNSSEC for protecting DNS query/response transactions through a series of requests for comments.
Parthenolide induces proliferation inhibition and apoptosis of pancreatic cancer cells in vitro (2010)

The parthenolide can inhibit the cell growth, migration, and induce the apoptosis in human pancreatic cancer. These findings may provide a novel approach for pancreatic cancer treatment.
Modulation of cisplatin sensitivity and growth rate of an ovarian carcinoma cell line by bombesin and tumor necrosis factor-alpha. (1992)

A twofold change in the cisplatin (DDP) sensitivity of 2008 human ovarian carcinoma cells is sufficient to reduce tumor response in vivo. The DDP sensitivity of these cells can be enhanced by activation of the epidermal growth factor and protein kinase C signal transduction pathways. We report here that two endogenous growth factors, bombesin and tumor necrosis factor alpha (TNF alpha), enhanced DDP sensitivity by factors of 1.7 +/- 0.1 (SD)-fold and 1.8 +/- 0.1 (SD)-fold, respectively. Both agents also produced sensitization in an 11-fold DDP-resistant 2008 subline. Neither bombesin nor TNF alpha changed the accumulation of DDP, glutathione content, or glutathione-S-transferase activity in 2008 cells. However, a 2-h exposure to both bombesin and TNF alpha was sufficient to increase 2008 cloning efficiency by up to 2.6 +/- 0.1 (SD)-fold and 2.2 +/- 0.1 (SD)-fold, and it increased average colony size by 1.35 +/- 0.1 (SD)-fold and 1.55 +/- 0.1 (SD)-fold, respectively. Bombesin increased intracellular free calcium, and this was blocked by the bombesin receptor-specific antagonist SC196, demonstrating that 2008 cells have functional bombesin receptors. These results indicate that bombesin and TNF alpha can enhance sensitivity to DDP in both DDP sensitive and resistant variants of a human ovarian carcinoma and that both agents serve as growth factors for this tumor.
EXPRESSION AND CELLULAR COLOCALISATION OF FRACTALKINE IN ACUTE RENAL ALLOGRAFT REJECTION (1999)

963 The CX3C chemokine Fractalkine is a unique transmembrane molecule for which initial studies have indicated endothelial cell restricted expression and cytokine-inducibility. Fractalkine mediates the capture, integrin-independent adhesion and activation of NK cells, CD8+ T-cells and monocytes. Trafficking of these cells to interstitial sites is central to cellular immune processes in acute renal allograft rejection (AAR). The aim of this study was to identify the expression and cellular colocalisation of Fractalkine in AAR. Using in situ hybridisation with a radiolabelled Fractalkine riboprobe (generated from a RT-PCR synthesised cDNA product ligated into a pGEM-7Zf(+) vector between SP6 and T7 promoter regions) and indirect immunohistochemistry (IHC) with a polyclonal goat anti-human Fractalkine antibody (R & D) we studied snap frozen, cryostat sectioned renal biopsy material from 15 patients with AAR. Fractalkine was expressed at mRNA and protein level by endothelium at interstitial sites local to inflammatory cell infiltrates. Serial section IHC identified presence of NK cells (CD56 +ve), monocytes/macrophages (CD68 +ve) and CD8+ T-cells within these infiltrates. In moderate and severe AAR there was heavy expression of Fractalkine mRNA by tubular epithelial cells, however there was low level protein expression at these sites. There was no expression of Fractalkine mRNA or protein by infiltrating leukocytes. There was sparse and occasional endothelial cell expression in normal kidney. Semi-quantitative RT-PCR showed IL-1β and TNF-α inducible upregulation of Fractalkine mRNA expression (maximal at 6 hours) by cultured human vein endothelial cells and proximal tubular epithelial cells. Expression was heaviest by endothelial cells. In conclusion: (i) Fractalkine is expressed by interstitial endothelium in AAR, (ii) colocalisation to infiltrating leukocyte subsets indicates a central role for this chemokine in directing their recruitment in AAR and (iii) expression patterns by proximal tubular epithelial cells suggests post-transcriptional regulation of protein synthesis. Fractalkine may represent a novel therapeutic target in AAR.
Single-electron transistors featuring silicon nitride tunnel barriers prepared by atomic layer deposition (2016)

Single electron transistors (SET) featuring metal (Ni) electrodes and silicon nitride dielectric barriers prepared by atomic layer deposition are fabricated and tested. Electrical characterization of the devices reveals electrostatic energy parameters consistent with the parameters of the designed tunnel junctions. In addition, an analysis of temperature dependence of conductance confirms the formation of metal-insulator-metal (MIM) junctions with negligible in-series contribution of any surface native metal oxide. However, the fabricated devices exhibit a very high level of electrical noise, far exceeding the commonly observed shot noise. Experimental investigation reveals the random telegraph signal (RTS) nature of the observed excess noise. The RTS noise in electronic devices is commonly associated with charging of external traps that are electrostatically coupled to the SET island. In the devices under study, however, the defects that result in the observed RTS noise are demonstrated to reside within the tunnel junctions. Our results also indicate the critical importance of interface states and surface preparation for achieving good performance of the SETs fabricated using ALD to form the tunnel barrier.
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications (2008)

Accurately reconstructing the large-scale gene order in an ancestral genome is a critical step to better understand genome evolution. In this paper, we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral genomic orders with duplications. The method starts from the order of genes in modern genomes and predicts predecessor and successor relationships in the ancestor. Then a greedy algorithm is used to reconstruct the ancestral orders by connecting genes into contiguous regions based on predicted adjacencies. Computer simulation was used to validate the algorithm. We also applied the method to reconstruct the ancestral chromosome X of placental mammals and the ancestral genomes of the ciliate Paramecium tetraurelia.
PCP-A1, a Defensin-like Brassica Pollen Coat Protein That Binds the S Locus Glycoprotein, Is the Product of Gametophytic Gene Expression (1998)

Self-incompatibility (SI) in Brassica species is controlled by a single polymorphic locus (S) with multiple specificities. Two stigmatically expressed genes that have been cloned from this region encode the S locus glycoprotein (SLG) and S receptor kinase (SRK). Both appear to be essential for the operation of SI. It is believed that rejection of incompatible pollen grains is effected by recognition events between an as yet unidentified S locus-encoded pollen coating-borne protein and the SLG/SRK. We previously identified a small pollen coat protein PCP7 (renamed here PCP-A1, for pollen coat protein, class A, 1) that binds with high affinity to SLGs irrespective of S genotype. Here, we report the cloning of PCP-A1 from Brassica oleracea and demonstrate that it is unlinked to the S locus. In situ localization of PCP-A1 transcripts revealed that they accumulate specifically in pollen at the late binucleate/trinucleate stage of development rather than in the tapetum, which previously was taken to be the principal source of the pollen coat. PCP-A1 is characterized by the presence of a structurally important motif consisting of eight cysteine residues shared by the plant defensins. Based on the presence of this motif and other data, homology modeling has been used to produce a putative structure for PCP-A1. Protein-protein interaction analyses demonstrate that SLG exists in monomeric and dimeric forms, both of which bind PCP-A1. Evidence is also presented for the existence of putative membrane-associated PCP-A1 binding proteins in stigmatic tissue.
Exploring A New Method for Food Likability Rating Based on DT-CWT Theory (2018)

In this paper, we mainly investigate subjects' food likability based on audio-related features as a contribution to EAT ? the ICMI 2018 Eating Analysis and Tracking challenge. Specifically, we conduct 4-level Double Tree Complex Wavelet Transform decomposition of an audio signal, and obtain five sub-audio signals with frequencies ranging from low to high. For each sub-audio signal, not only 'traditional' functional-based features but also deep learning-based features via pretrained CNNs based on SliCQ-nonstationary Gabor transform and a cochleagram map, are calculated. Besides, the original audio signals based Bag-of-Audio-Words features extracted by the openXBOW toolkit are used to enhance the model as well. Finally, the early fusion of all these three kinds of features can lead to promising results, yielding the highest UAR of 79.2 % by means of a leave-one-speaker-out cross-validation, which holds a 12.7 % absolute gain compared with the baseline of 66.5 % UAR.
Caractérisation des canaux calciques dans les polynucléaires neutrophiles : rôle dans la phagocytose et la production des radicaux libres oxygénés (2013)

Neutrophils represent 50-70% of human blood leukocytes; their role is to protect the body against pathogens. Calcium is a second messenger which plays an important role in chemotaxis, phagocytosis, degranulation and the production of reactive oxygen species (ROS) in order to eliminate microbes. In neutrophils, the mechanism of store-operated calcium entry (SOCE) is essential for calcium homeostasis. However, neutrophil SOCE is not well understood because of the lack of specific pharmacological tools. It is necessary to first identify and characterize new molecules using a model of Jurkat T cells in which SOCE was the best characterized. 2-APB is the most widely used molecule in SOCE characterization due to its dual activity with a potentiation at lower concentrations [1-10 μM] and an inhibition at higher concentrations [> 20 μM]. However, this molecule lacks specificity because it acts on other cellular targets such as inositol (1,4,5)-trisphosphate receptors (InsP3Rs). The first step is to select from a library of 8 commercial 2-APB analogues (Methoxy-APB, Dimethoxy-APB, Cyclic-APB, Benzothienyl-APB, Thienyl-APB and MDEB) those that are more specific and also more efficient molecules than 2-APB. Two interesting molecules were identified, MDEB as the only SOCE potentiating product currently known and the Benzothienyl-APB, which is a strong inhibitor. Like 2-APB, all these analogues inhibit InsP3Rs except MDEB, which seems to be more specific. The effect of MDEB on the calcium current, ICRAC, was also studied using the patch-clamp technique. MDEB increases ~4 times the ICRAC amplitude in comparison with control. Otherwise, MDEB slows down the fast Ca2 +-dependent inactivation of ICRAC. Functionally, MDEB at increasing concentrations inhibits IL-2 synthesis in stimulated Jurkat T cells despite its potentiating activity on SOCE. The inhibition is due to MDEB induced apoptosis in stimulated Jurkat T cells. MDEB and Benzothienyl-APB were then used as tools to study SOCE in a neutrophil-like cell model, the differentiated PLB-985 cells. SOCE was induced either by treatment of cells with thapsigargin (Tg) or physiologically with the chemotactic peptides fMLF and WKYMVm, ligands of formyl peptide receptors FPR and FPRL1 respectively. In addition, Tg-induced SOCE was modulated by 2-APB, potentiated by MDEB and inhibited by Benzothienyl-APB. The consequences of these analogues on neutrophil functions were also studied. Phagocytosis of yeasts by PLB-985 cells and intraphagosomal ROS production were inhibited by MDEB and Benzothienyl-APB. Furthermore, extracellular ROS were also inhibited by Benzothienyl-APB. However, because of the high interference of MDEB with our techniques, its activities could not be studied. In conclusion, MDEB and Benzothienyl-APB are new analogues of 2-APB potentiating and inhibiting SOCE, which allow us in the future a better understanding of leukocyte SOCE and its cellular roles.
ChemInform Abstract: α‐Metalated Tertiary Enol Carbamates. New Acyl Anion Equivalents. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
N-Benzyl-1-(dimethylamino)-2-methyl-1-oxopropan-2-aminium bromide (2006)

The title compound, C 13 H 21 N 2 O + ·Br − , was crystallized from a CH 2 Cl 2 solution of N 2 , N 2 -dibenzyl- N , N ,2-trimethylalaninamide and BBr 3 . The geometry of the cation is unexceptional. Intermolecular N—H...O and N—H...Br hydrogen bonds link two cations and two anions into a hydrogen-bonded cluster. The crystal packing is further stabilized by van der Waals forces.
Thin-Film Composite Pressure Retarded Osmosis Membranes for Sustainable Power Generation from Salinity Gradients (2011)

Pressure retarded osmosis has the potential to produce renewable energy from natural salinity gradients. This work presents the fabrication of thin-film composite membranes customized for high performance in pressure retarded osmosis. We also present the development of a theoretical model to predict the water flux in pressure retarded osmosis, from which we can predict the power density that can be achieved by a membrane. The model is the first to incorporate external concentration polarization, a performance limiting phenomenon that becomes significant for high-performance membranes. The fabricated membranes consist of a selective polyamide layer formed by interfacial polymerization on top of a polysulfone support layer made by phase separation. The highly porous support layer (structural parameter S = 349 μm), which minimizes internal concentration polarization, allows the transport properties of the active layer to be customized to enhance PRO performance. It is shown that a hand-cast membrane that balances permeability and selectivity (A = 5.81 L m(-2) h(-1) bar(-1), B = 0.88 L m(-2) h(-1)) is projected to achieve the highest potential peak power density of 10.0 W/m(2) for a river water feed solution and seawater draw solution. The outstanding performance of this membrane is attributed to the high water permeability of the active layer, coupled with a moderate salt permeability and the ability of the support layer to suppress the undesirable accumulation of leaked salt in the porous support. Membranes with greater selectivity (i.e., lower salt permeability, B = 0.16 L m(-2) h(-1)) suffered from a lower water permeability (A = 1.74 L m(-2) h(-1) bar(-1)) and would yield a lower peak power density of 6.1 W/m(2), while membranes with a higher permeability and lower selectivity (A = 7.55 L m(-2) h(-1) bar(-1), B = 5.45 L m(-2) h(-1)) performed poorly due to severe reverse salt permeation, resulting in a similar projected peak power density of 6.1 W/m(2).