gebhart/patrepeval huggingface dataset:
Alien introgression in the grasses Lolium perenne (perennial ryegrass) and Festuca pratensis (meadow fescue): the development of seven monosomic substitution lines and their molecular and cytological characterization (2011)

The isolation of the seven monosomic substitution lines provides a resource for dissecting the genetic control of important traits and for gene isolation. Parallels between the L. perenne/F. pratensis system and the Pooideae cereals such as wheat, barley, rye, oats and the model grass Brachypodium distachyon present opportunities for a comparison across the species in terms of genotype and phenotype.
A solid-state instrument for fluorescence chemical sensors using a blue light-emitting diode of high intensity (1995)

A recently introduced blue light-emitting diode with high intensity is used as radiation source for chemical sensor membranes employing fluorescence changes. An inexpensive plastic fibre coupler guides the light from the source to the membrane and the fluorescence back to the detector. Photodiodes are employed for this purpose and dye filters for wavelength discrimination. Lock-in amplification for elimination of ambient light interference is carried out with a single integrated circuit. Applications are demonstrated with sensing membranes for oxygen and carbon dioxide.
Quantitative analysis of properties and spatial relations of fuzzy image regions (1992)

Properties of objects and spatial relations between objects play an important role in rule-based approaches for high-level vision. The partial presence or absence of such properties and relationships can supply both positive and negative evidence for region labeling hypotheses. Similarly, fuzzy labeling of a region can generate new hypotheses pertaining to the properties of the region, its relation to the neighboring regions, and finally, the labels of the neighboring regions. In this paper, we present a unified methodology to characterize properties and spatial relationships of object regions in a digital image. The proposed methods can be used to arrive at more meaningful decisions about the contents of the scene.
Regulation of gene expression in melanoma: New approaches for treatment (2004)

The molecular changes associated with the transition of melanoma cells from radial growth phase (RGP) to vertical growth phase (VGP, metastatic phenotype) are not yet well defined. We have demonstrated that the progression of human melanoma is associated with loss of expression of the transcription factor AP-2. In metastatic melanoma cells, this loss resulted in overexpression of MCAM/MUC18, MMP-2, the thrombin receptor (PAR-1), and lack of c-KIT expression. The transition from RGP to VGP is also associated with overexpression of the angiogenic factor IL-8. Additionally, the transition of melanoma cells from RGP to VGP is associated with overexpression of the transcription factors CREB and ATF-1, both of which may act as survival factors for human melanoma cells. Inactivation of CREB/ATF-1 activities in metastatic melanoma cells by dominant-negative CREB or by anti-ATF-1 single chain antibody fragment (ScFv), resulted in deregulation of MMP-2 and MCAM/MUC18, increased the sensitivity of melanoma cells to apoptosis, and inhibition of their tumorigenicity and metastatic potential in vivo. In this prospect article, we summarize our data on the role of AP-2 and CREB/ATF-1 in the progression of human melanoma and report on the development of new fully human antibodies anti-MCAM/MUC18 and anti-IL-8 which could serve as new modalities for the treatment of melanoma.
Lipidated Peptidomimetics with Improved Antimicrobial Activity (2012)

We report a series of lipidated α-AApeptides that mimic the structure and function of natural antimicrobial lipopeptides. Several short lipidated α-AApeptides show broad-spectrum activity against a range of clinically related Gram-positive and Gram-negative bacteria as well as fungus. Their antimicrobial activity and selectivity are comparable or even superior to the clinical candidate pexiganan as well as previously reported linear α-AApeptides. The further development of lipidated α-AApeptides will lead to a new class of antibiotics to combat drug resistance.
Increased expression of programmed death (PD)‐1 and its ligand PD‐L1 correlates with impaired cell‐mediated immunity in high‐risk human papillomavirus‐related cervical intraepithelial neoplasia (2013)

Impaired local cellular immunity contributes to the pathogenesis of persistent high-risk human papillomavirus (HR-HPV) infection and related cervical intraepithelial neoplasia (CIN), but the underlying molecular mechanisms remain unclear. Recently, the programmed death 1/programmed death 1 ligand (PD-1/PD-L1; CD279/CD274) pathway was demonstrated to play a critical role in attenuating T-cell responses and promoting T-cell tolerance during chronic viral infections. In this study, we examined the expression of PD-1 and PD-L1 on cervical T cells and dendritic cells (DCs), respectively, from 40 women who were HR-HPV-negative (-) or HR-HPV-positive (+) with CIN grades 0, I and II-III. We also measured interferon-γ, interleukin-12 (IL-12) and IL-10 in cervical exudates. The most common HPV type was HPV 16, followed by HPV 18, 33, 51 and 58. PD-1 and PD-L1 expression on cervical T cells and DCs, respectively, was associated with HR-HPV positivity and increased in parallel with increasing CIN grade. The opposite pattern was observed for CD80 and CD86 expression on DCs, which decreased in HR-HPV+ patients in parallel with increasing CIN grade. Similarly, reduced levels of the T helper type 1 cytokines interferon-γ and IL-12 and increased levels of the T helper type 2 cytokine IL-10 in cervical exudates correlated with HR-HPV positivity and CIN grade. Our results suggest that up-regulation of the inhibitory PD-1/PD-L1 pathway may negatively regulate cervical cell-mediated immunity to HPV and contribute to the progression of HR-HPV-related CIN. These results may aid in the development of PD-1/PD-L1 pathway-based strategies for immunotherapy of HR-HPV-related CIN.
Seeding of intravascular stents with genetically engineered endothelial cells. (1989)

The use of intravascular stents may be limited by both local thrombosis and restenosis due to intimal proliferation. In an effort to provide solutions to these problems, we seeded stents with genetically engineered endothelial cells in vitro. Using retroviral-mediated gene transfer, we inserted the gene for either bacterial beta-galactosidase or human tissue-type plasminogen activator (t-PA) into cultured sheep endothelial cells. The endothelial cells were seeded onto stainless steel stents and grown until the stents were covered. Expression of intracellular beta-galactosidase and high level secretion of t-PA were demonstrated both before and after the transduced cells were seeded onto the stents. Eight stents were expanded by in vitro balloon inflation, with observation of the seeded endothelial layer both prior to and after expansion. Most of the endothelial cells remained on the stents after balloon inflation. We conclude that intravascular stents can be coated with a layer of genetically engineered endothelial cells that can be either specifically labeled or made to secrete high levels of a therapeutic protein. Much of the layer of genetically engineered cells remains after the expansion of the stent in vitro. In vivo implantation of stents coated with genetically engineered endothelial cells may allow 1) introduction of genetically engineered endothelial cells directly into the vascular wall and 2) improvement of stent function through localized delivery of anticoagulant, thrombolytic, or antiproliferative molecules.
Gold nanoparticles in theranostic oncology: current state-of-the-art (2012)

GNPs present versatile scaffolds for efficient delivery of cancer chemotherapeutics. Tuneable chemistry of the GNPs contributes to their ever increasing use in oncology research. The promises of a functional cancer therapy using GNPs have been extensively demonstrated, although the materials are still in their infancy stage and not surfaced to meet clinical standards.
Synthesis and Characterization of a Doxorubicin−Gd(III) Contrast Agent Conjugate:  A New Approach toward Prodrug−Procontrast Complexes (2006)

We have prepared the first MRI prodrug-procontrast complex by conjugating doxorubicin to a Gd(III) chelate using an acid-labile linker. The relaxometric properties of the adduct and pH activation are reported.
The Breast Cancer-Associated Glycoforms of MUC1, MUC1-Tn and sialyl-Tn, Are Expressed in COSMC Wild-Type Cells and Bind the C-Type Lectin MGL (2015)

Aberrant glycosylation occurs in the majority of human cancers and changes in mucin-type O-glycosylation are key events that play a role in the induction of invasion and metastases. These changes generate novel cancer-specific glyco-antigens that can interact with cells of the immune system through carbohydrate binding lectins. Two glyco-epitopes that are found expressed by many carcinomas are Tn (GalNAc-Ser/Thr) and STn (NeuAcα2,6GalNAc-Ser/Thr). These glycans can be carried on many mucin-type glycoproteins including MUC1. We show that the majority of breast cancers carry Tn within the same cell and in close proximity to extended glycan T (Galβ1,3GalNAc) the addition of Gal to the GalNAc being catalysed by the T synthase. The presence of active T synthase suggests that loss of the private chaperone for T synthase, COSMC, does not explain the expression of Tn and STn in breast cancer cells. We show that MUC1 carrying both Tn or STn can bind to the C-type lectin MGL and using atomic force microscopy show that they bind to MGL with a similar dead adhesion force. Tumour associated STn is associated with poor prognosis and resistance to chemotherapy in breast carcinomas, inhibition of DC maturation, DC apoptosis and inhibition of NK activity. As engagement of MGL in the absence of TLR triggering may lead to anergy, the binding of MUC1-STn to MGL may be in part responsible for some of the characteristics of STn expressing tumours.
Immune modulation with interleukin‐4 and interleukin‐10 prevents crescent formation and glomerular injury in experimental glomerulonephritis (1997)

Crescentic glomerulonephritis (GN) demonstrates immunopathological features of a T helper (Th)1-directed delayed-type hypersensitivity (DTH) response. The capacity of Th2 cytokines to attenuate crescentic glomerular injury in this disease was examined by administering interleukin (IL)-4 and IL-10, singly and in combination. GN was induced by i.v. administration of sheep anti-mouse glomerular basement membrane (GBM) globulin to mice sensitized to sheep globulin 10 days earlier. Treatment (2.5 microg, i.p.) with IL-4, IL-10, or both IL-4 and IL-10 (IL-4 + 10), was started 1 h before sensitization and continued daily until the end of the study (10 days after administration of anti-GBM globulin). Control mice treated with PBS developed GN with glomerular accumulation of T cells and macrophages, crescents in 42.5 +/- 4.5 % of glomeruli (normal 0 %), proteinuria (8.3 +/- 0.9 mg/24 h, normal 0.74 +/- 0.08 mg/24 h, p <0.001) and renal impairment (creatinine clearance [cr/cl]: 93 +/- 12 microl/min, normal 193 +/- 10 microl/min, p < 0.001). Treatment with either IL-4, IL-10, or IL-4 + 10 prevented crescent formation (crescentic glomeruli: 0.8 +/- 0.5, 1.2 +/- 0.9, and 1.4 +/- 1.0 %, respectively, all p < 0.01 compared to control) and attenuated proteinuria (3.6 +/- 1.0, 2.2 +/- 0.5, and 2.9 +/- 0.5 mg/24 h, respectively, all p < 0.01 compared to control). IL-4 + 10 prevented development of renal impairment (cr/cl: 183 +/- 22 microl/min); IL-10 given alone limited the decline in renal function (cr/cl: 150 +/- 20 microl/min), but IL-4 alone did not provide any significant protection (cr/cl: 121 +/- 17 microl/min). All treatments markedly diminished glomerular T cell and macrophage accumulation, reduced interferon-gamma production by splenic T cells, prevented cutaneous DTH to the disease-initiating antigen and reduced antigen-specific immunoglobulin of the IgG2a and IgG3 isotypes. These data demonstrate that crescentic GN and renal impairment can be prevented by administration of Th2 cytokines and that this effect is associated with attenuation of the Th1 response to the disease-initiating antigen.
Whiskers (2018)

Haptic cues are a valuable feedback mechanism for smart glasses. Prior work has shown how they can support navigation, deliver notifications and cue targets. However, a focus on actuation technologies such as mechanical tactors or fans has restricted the scope of research to a small number of cues presented at fixed locations. To move beyond this limitation, we explore perception of in-air ultrasonic haptic cues on the face. We present two studies examining the fundamental properties of localization, duration and movement perception on three facial sites suitable for use with glasses: the cheek, the center of the forehead, and above the eyebrow. The center of the forehead led to optimal performance with a localization error of 3.77mm and accurate duration (80%) and movement perception (87%). We apply these findings in a study delivering eight different ultrasonic notifications and report mean recognition rates of up to 92.4% (peak: 98.6%). We close with design recommendations for ultrasonic haptic cues on the face.
Second-harmonic distortion in vertical-cavity surface-emitting lasers with lateral loss effects (1999)

The influence of lateral loss effects on the second-harmonic distortion (SHD) of vertical-cavity surface-emitting lasers is investigated theoretically. Two parameters, differential confinement factor and differential cavity loss, are defined for the consideration of self-focusing and diffraction loss. It is found that SHD increases at low modulation frequencies due to the presence of differential cavity loss, especially for lasers with small core radius.
Clonal analysis of the glycosylation of immunoglobulin G secreted by murine hybridomas (1989)

A panel of 10 hybridomas was assembled to assess the influence of various genetic and biological factors upon glycosylation of secreted monoclonal IgG. After exhaustive Pronase digestion of IgG, glycopeptides were characterized chromatographically by apparent size, charge, and concanavalin A (Con A)-Sepharose and Lens culinaris (LcH)-agarose affinity. Six glycosylation phenotypes were found to be common among all clones studied. Despite this phenotypic heterogeneity in glycosylation of IgG, considerable similarity exists between different clones. In particular, virtually all IgG glycopeptides bear a core fucose residue. Second, the majority of the glycosylation repertoire is comprised of two phenotypes, characterized by glycopeptides which differ in affinity for Con A-Sepharose. Of these, the predominantly expressed phenotype is the same for all clones. The carbohydrate structure derived from this phenotype, elucidated by 500-MHz 1H NMR spectroscopy, is (Formula: see text). Significant variability between different hybridomas exists in the relative expression of the two major phenotypes. Other differences between clones may reflect the expression of an additional site which is glycosylated differently. However, there is no apparent correlation of phenotype with either the hybridoma's parentage or the serologically defined polypeptide structure of the IgG which it secretes. In addition to clonal variability, other sources of variability in phenotypic expression were identified. A generational variability is apparent upon continuous culturing of the same hybridoma. Also, differences in culture medium pH or proliferative state of the cells may have a modest influence upon the glycosylation phenotype.
EfficientNet: Rethinking Model Scaling for Convolutional Neural Networks (2019)

Convolutional Neural Networks (ConvNets) are commonly developed at a fixed resource budget, and then scaled up for better accuracy if more resources are available. In this paper, we systematically study model scaling and identify that carefully balancing network depth, width, and resolution can lead to better performance. Based on this observation, we propose a new scaling method that uniformly scales all dimensions of depth/width/resolution using a simple yet highly effective compound coefficient. We demonstrate the effectiveness of this method on scaling up MobileNets and ResNet. To go even further, we use neural architecture search to design a new baseline network and scale it up to obtain a family of models, called EfficientNets, which achieve much better accuracy and efficiency than previous ConvNets. In particular, our EfficientNet-B7 achieves state-of-the-art 84.3% top-1 accuracy on ImageNet, while being 8.4x smaller and 6.1x faster on inference than the best existing ConvNet. Our EfficientNets also transfer well and achieve state-of-the-art accuracy on CIFAR-100 (91.7%), Flowers (98.8%), and 3 other transfer learning datasets, with an order of magnitude fewer parameters. Source code is at https://github.com/tensorflow/tpu/tree/master/models/official/efficientnet.
Effects of micro- and nano-structures on the self-cleaning behaviour of lotus leaves (2006)

When rain falls on lotus leaves water beads up with a high contact angle. The water drops promptly roll off the leaves, collecting dirt along the way. This self-cleaning ability or lotus effect has, in recent years, stimulated much research effort worldwide for a variety of applications ranging from self-cleaning window glasses, paints, and fabrics to low friction surfaces. What are the mechanisms giving rise to the lotus effect? Although chemical composition and surface structure are believed important, a systematic experimental investigation of their effects is still lacking. By altering the surface structure of the leaves while keeping their chemical composition approximately the same, we report in this study the influence of micro- and nano-scale structures on the wetting behaviour of lotus leaves. The findings of this work may help design self-cleaning surfaces and improve our understanding of wetting mechanisms.
Physiological regulation of a decontrolled lac operon (1977)

The expression of the lac operon was studied under a variety of growth conditions in induced and in constitutive cells of Escherichia coli that carried different catabolite-insensitive lac promoters. Use of such "decontrolled" lac operons permitted a study of the expression of an operon that was presumably subject only to passive control. Since the use of toluenized cells was demonstrated not to be completely reliable, all enzyme assays were performed on sonic supernatant fluids. The cells contained different catabolite-insensitive promoters, which included the L1 and UV5 lac promoters, as well as others isolated in this study. There were three major observations. First, small but real carbon source effects were seen. Second, there was only a small change in beta-galactosidase specific activity with changes in the growth rate. This result implies a limited transcription and/or translation capacity within the cell. Third, at rapid growth rates, most promoters exhibited a decreased expression. The UV5 promoter, which was the "strongest" promoter, was an exception. A mechanism to explain this promoter-dependent control is discussed.
Elevation of vascular endothelial growth factor in Indonesian advanced stage nasopharyngeal carcinoma. (2009)

Studies on the role of vascular endothelial growth factor (VEGF) as the most potent angiogenic factor in disease progression of nasopharyngeal carcinoma (NPC) remain limited, partly be due to the geographical distribution of the disease. However, it has never been reported from Indonesian population despite its common incidence. Therefore, we aimed to study the possible prognostic value of VEGF in Indonesian advanced stage NPC. A clinical examination, CT scan, and the tumor tissue and plasma collection were performed before a combined therapy, and a local control rate was reassessed every 3 months to determine progression-free survival (PFS). Plasma VEGF-A was measured in 40 patients by ELISA, and VEGF and vWF expressions were examined in 30 patients by immunohistochemistry. Survival curves were plotted based on plasma VEGF-A level, VEGF, and microvessel density (MVD) count indicated by vWF expressions vs PFS. The median follow up was 16 months. Patients with high VEGF-A level (≥ 834pg/ml) presented shorter survival rate, as compared to those of low level (< 834pg/ml) (41.2% vs 82.6%; p=0.009, log rank 6.81). Patients with overexpressed VEGF (≥ 25%) showed shorter survival than those with low expression (<25%) (45.5% vs 79.6%; p=0.05, log rank 3.84). Patients with higher MVD count (≥ 25%) also had shorter survival than those with lower MVD count (53.4% vs 80%; p=0.101, log rank=2.70). In conclusion, an elevated plasma VEGF level predicts shorter survival for Indonesian advanced stage NPC in this study. However, more samples may be required to draw a better conclusion on a possible role of VEGF as a prognostic factor in the disease progression of NPC. This data is also substantial for the development of anti-VEGF as a possible targeted therapy for NPC.
Detection and location of moving objects using deterministic relaxation algorithms (1996)

Two important problems in motion analysis are addressed in this paper: change detection and moving object location. For the first problem, the inter-frame difference is modelized by a mixture of Laplacian distributions, a Gibbs random field is used for describing the label field, and HCF (highest confidence first) algorithm is used for solving the resulting optimization problem. The solution of the second problem is based on the observation of two successive frames alone. Using the results of change detection an adaptive statistical model for the couple of image intensities is identified. Then the labeling problem is solved using HCF algorithm. Results on real image sequences illustrate the efficiency of the proposed method.
TheAspergillus nidulansGATA transcription factor geneareBencodes at least three proteins and features three classes of mutation (2001)

In Aspergillus nidulans, the principal transcription factor regulating nitrogen metabolism, AREA, belongs to the GATA family of DNA-binding proteins. In seeking additional GATA factors, we have cloned areB, which was originally identified via a genetic screen for suppressors of areA loss-of-function mutations. Based on our analysis, areB is predicted to encode at least three distinct protein products. These arise from the use of two promoters, differential splicing and translation initiating at AUG and non-AUG start codons. All the putative products include a GATA domain and a putative Leu zipper. These regions show strong sequence similarity to regulatory proteins from Saccharomyces cerevisiae (Dal80p and Gzf3p), Penicillium chrysogenum (NREB) and Neurospora crassa (ASD4). We have characterized three classes of mutation in areB; the first are loss-of-function mutations that terminate the polypeptides within or before the GATA domain. The second class truncates the GATA factor either within or upstream of the putative Leu zipper but retains the GATA domain. The third class fuses novel gene sequences to areB with the potential to produce putative chimeric polypeptides. These novel gene fusions transform the putative negative-acting transcription factor into an activator that can partially replace areA.