gebhart/patrepeval huggingface dataset:
Senescence-specific gene expression fingerprints reveal cell-type-dependent physical clustering of up-regulated chromosomal loci (2003)

Replicative senescence is the state of irreversible proliferative arrest that occurs as a concomitant of progressive telomere shortening. By using cDNA microarrays and the gabriel system of computer programs to apply domain-specific and procedural knowledge for data analysis, we investigated global changes in gene transcription occurring during replicative senescence in human fibroblasts and mammary epithelial cells (HMECs). Here we report the identification of transcriptional "fingerprints" unique to senescence, the finding that gene expression perturbations during senescence differ greatly in fibroblasts and HMECs, and the discovery that despite the disparate nature of the chromosomal loci affected by senescence in fibroblasts and HMECs, the up-regulated loci in both types of cells show physical clustering. This clustering, which contrasts with the random distribution of genes down-regulated during senescence or up-regulated during reversible proliferative arrest (i.e., quiescence), supports the view that replicative senescence is associated with alteration of chromatin structure.
Transplanted Endothelial Cells Enhance Orthotopic Bone Regeneration (2006)

The aim of this study was to determine if endothelial cells could enhance bone marrow stromal-cell-mediated bone regeneration in an osseous defect. Using poly-lactide-co-glycolide scaffolds as cell carriers, we transplanted bone marrow stromal cells alone or with endothelial cells into 8.5-mm calvarial defects created in nude rats. Histological analyses of blood vessel and bone formation were performed, and microcomputed tomography (muCT) was used to assess mineralized bone matrix. Though the magnitude of the angiogenic response between groups was the same, muCT analysis revealed earlier mineralization of bone in the co-transplantation condition. Ultimately, there was a significant increase (40%) in bone formation in the co-transplantation group (33 +/- 2%), compared with the transplantation of bone marrow stromal cells alone (23 +/- 3%). Analysis of these data demonstrates that, in an orthotopic site, transplanted endothelial cells can influence the bone-regenerative capacity of bone marrow stromal cells.
Different types of FC γ -receptors are involved in anti-Lewis Y antibody induced effector functions in vitro (2000)

Stimulation of monocytes by interaction of monoclonal antibodies (mAbs) with Fc gamma receptors (FcgammaRs) results in the activation of various monocyte effector functions. In the present investigation we show that the anti-Lewis Y (LeY) anti-tumour mAb ABL 364 and its mouse/human IgG1 chimaera induce both antibody-dependent cellular cytotoxicity (ADCC) and the release of tumour necrosis factor alpha (TNF-alpha) during mixed culture of monocytes with LeY+ SKBR5 breast cancer cells in vitro. Although anti-LeY mAb-mediated TNF-alpha release paralleled ADCC activity, cytokine release required a higher concentration of sensitizing mAb than the induction of cytolysis. The determination of the FcgammaR classes involved in the induction of the distinct effector functions showed that anti-LeY mAb-induced cytolysis was triggered by interaction between anti-LeY mAbs and FcgammaRI. In contrast, mAb-induced TNF-alpha release mainly depended on the activation of monocyte FcgammaRII. Neutralization of TNF-alpha showed no influence on monocyte ADCC activity towards SKBR5 target cells. Our data indicate an independent regulation of anti-LeY mAb induced effector functions of ADCC and TNF-alpha release which seemed to be triggered by activation of different types of FcgammaR.
Spiral QAM: A Novel Modulation Scheme Robust in the Presence of Phase Noise (2008)

In this paper, we introduce a new modulation scheme called Spiral QAM, which is optimized for phase noise, and thus robust in the presence of phase noise. Symbol mapping rules for 16 and 64 Spiral QAM are also presented. SER and BER performance of 64 Spiral QAM was compared with the conventional 64 QAM to show the superior performance of Spiral QAM in the presence of phase noise.
(3+1)-dimensional numerical simulations of femtosecond laser filaments in air: Toward a quantitative agreement with experiments (2008)

Three-dimensional numerical simulations and direct experimental measurements of the multifilamentation of femtosecond laser pulses propagating in air are quantitatively compared. Agreement is obtained in terms of the evolution of the filamentation pattern and in terms of the size and energy of the individual filaments through 12 m of propagation. These results are made possible by the combination of a massively parallel propagation code along with a nondestructive experimental diagnostic technique. Influence of the pulse duration is moreover addressed. The numerical calculations also show that single and multiple filaments exhibit almost identical spectral signature.
InP-Based Membrane Couplers for Optical Interconnects on Si (2009)

We present the design, fabrication, and characterization of a membrane coupler processed on an indium phosphide membrane layer on a silicon-on-insulator wafer, that is used for applications in optical interconnects on silicon. Measured coupler efficiency is 50%. The photonic device fabrication is compatible with wafer scale processing steps, guaranteeing compatibility towards future generation electronic integrated circuit processing.
Wilhelm Keim (1934–2018) (2018)

Wilhelm "Willi" Keim, professor emeritus at the RWTH Aachen University, passed away on September 30, 2018. Keim was best known for his role in developing the Shell higher olefins process (SHOP), and also made pioneering contributions to the areas of liquid-liquid biphasic catalysis, and green and sustainable chemistry.
Anisotropic multimode joint Rayleigh- and Love-wave inversion (2021)

Obtaining anisotropic near surface elastic properties is of interest for engineering, environmental, and geophysical exploration purposes. State of the art depth imaging workflows are anisotropic. While surface-wave inversion has been used for building near surface velocity models for depth imaging, by itself and jointly with first arrival analysis, it is being carried out assuming the subsurface is isotropic. There is a need to incorporate anisotropy in surface-wave inversion and to pursue joint estimation of VS and transversely isotropic parameters. In this study, we demonstrate multimode joint estimation of VS and transversely isotropic parameters, which can provide near surface anisotropy for different applications.
Novel Method for Probing the Specificity Binding Profile of Ligands: Applications to HIV Protease (2008)

A detailed understanding of factors influencing the binding specificity of a ligand to a set of desirable targets and undesirable decoys is a key step in the design of potent and selective therapeutics. We have developed a general method for optimizing binding specificity in ligand-receptor complexes based on the theory of electrostatic charge optimization. This methodology can be used to tune the binding of a ligand to a panel of potential targets and decoys, along the continuum from narrow binding to only one partner to broad binding to the entire panel. Using HIV-1 protease as a model system, we probe specificity in three distinct ways. First, we probe interactions that could make the promiscuous protease inhibitor pepstatin more selective toward HIV-1 protease. Next, we study clinically approved HIV-1 protease inhibitors and probe ways to broaden the binding profiles toward both wild-type HIV-1 protease and drug-resistant mutants. Finally, we study a conformational ensemble of wild-type HIV-1 protease to 'design in' broad specificity to known drugs before resistance mutations arise. The results from this conformational ensemble were similar to those from the drug-resistant ensemble, suggesting the use of a conformational wild-type ensemble as a tool to develop escape-mutant-resistant inhibitors.
Frequency Stabilization of a Semiconductor Laser under Direct Frequency Shift Keying Using the Saturated Absorption Signal (1994)

The oscillating frequency of a semiconductor laser was stabilized at the Rb-D 2 absorption line under direct frequency shift keying (FSK). The control system equipped with a peak-hold circuit provided the frequency stability of 10 -9 &gt;σ(2, τ)&gt;10 -12 at the averaging time 0.05 s&lt;τ&lt;40 s when the Doppler-limited absorption line was used as a frequency reference. This stability was better than that obtained by the traditional control system without the peak-hold circuit under direct FSK. Using the saturated absorption signal, the frequency stability was improved more than one order of magnitude in comparison with that obtained using the Doppler-limited absorption signal.
Type III secretion and in planta recognition of the Xanthomonas avirulence proteins AvrBs1 and AvrBsT (2001)

summary The hrp gene cluster of the plant pathogen Xanthomonas campestris pv. vesicatoria (Xcv) encodes a type III secretion system required for the delivery of virulence and avirulence proteins into the plant. Some of these effector proteins, e.g. AvrBs1 and AvrBsT, are recognized by pepper plants carrying corresponding resistance genes, triggering the hypersensitive reaction (HR). In this study, epitope tagged AvrBs1 and AvrBsT proteins were detected in culture supernatants only in the presence of a functional type III apparatus and not in a hrcV mutant, showing that both proteins are secreted by Xcv in an hrp-dependent manner. Expression of both avirulence genes is constitutive and independent of the hrp gene regulators, hrpG and hrpX. Transient expression of avrBs1 and avrBsT in resistant host plants using Agrobacterium tumefaciens-mediated gene transfer resulted in the induction of a specific HR. This indicates that recognition occurs intracellularly, and suggests that during the Xcv infection, AvrBs1 and AvrBsT are translocated from Xcv into the plant cell. We describe a conserved protein motif which is present in the N-terminal region of all known Xcv avirulence proteins and discuss its potential role in translocation into plant cells.
Supplementary Table 1 from Identification of Hypermethylated Genes Associated with Cisplatin Resistance in Human Cancers (2023)

Supplementary Table 1 from Identification of Hypermethylated Genes Associated with Cisplatin Resistance in Human Cancers
Adenosine triphosphate: adenosine monophosphate phosphotransferase isozymes in rat liver and hepatomas. (1970)

Summary Adenylate kinase (ATP:AMP phosphotransferase, EC 2.7.4.3) activity was measured in rat liver and in a series of Morris hepatomas. The adenylate kinase activity was 128 units/g tissue in a group of highly differentiated hepatomas, 65 units/g in well-differentiated hepatomas, and 16 units/g in a group of poorly differentiated hepatomas. Rat liver adenylate kinase activity was 148 units/g. It increased to 287 units/g upon fasting and decreased to 92 units/g upon refeeding of a glucose diet. However, adenylate kinase activity in highly, well-, and poorly-differentiated hepatomas did not respond significantly to dietary alterations in the host animals. Four electrophoretically distinct forms of adenylate kinase were found in supernatants from rat liver and hepatomas. The four isozymes have isoelectric points at pH9s 5.9 (I), 7.0 (II), 7.6 (III), and 8.2 (IV) and were found in all tumors examined. The activities of Isozymes I, III, and IV were reasonably constant in liver and hepatomas, but the activity of Isozyme III decreased from 121 units/g in normal liver to 14 units/g in the poorly differentiated Novikoff hepatoma. Isozyme III was the major adenylate kinase isozyme in rat liver. It increased to 220 units/g in the liver of fasted rats and decreased to 80 units/g in the liver of refed rats. Isozyme III is the predominant form of adenylate kinase which, in liver, is susceptible to dietary regulation, and the form which, in the tumors, decreases with decreasing differentiation.
Over 14% Efficiency Folding-Flexible ITO-free Organic Solar Cells Enabled by Eco-friendly Acid-Processed Electrodes (2020)

Environment-friendly manufacturing and mechanical robustness are imperative for commercialization of flexible OSCs as green-energy source, especially in portable and wearable self-powered flexible electronics. Although, the commonly adopted PEDOT:PSS electrodes that are treated with severely corrosive and harmful acid lack foldability. Herein, efficient folding-flexible OSCs with highly conductive and foldable PEDOT:PSS electrodes processed with eco-friendly cost-effective acid and polyhydroxy compound are demonstrated. The acid treatment endows PEDOT:PSS electrodes with high conductivity. Meanwhile, polyhydroxy compound doping contributes to excellent bending flexibility and foldability due to the better film adhesion between PEDOT:PSS and PET substrate. Accordingly, folding-flexible OSCs with high efficiency of 14.17% were achieved. After 1,000 bending or folding cycles, the device retained over 90% or 80% of its initial efficiency, respectively. These results represent one of the best performances for ITO-free flexible OSC reported so far and demonstrate a novel approach toward commercialized efficient and foldable green-processed OSCs.
CpG island methylator phenotype and its association with malignancy in sporadic duodenal adenomas (2014)

CpG island methylator phenotype (CIMP) has been found in multiple precancerous and cancerous lesions, including colorectal adenomas, colorectal cancers, and duodenal adenocarcinomas. There are no reports in the literature of a relationship between CIMP status and clinicopathologic features of sporadic duodenal adenomas. This study sought to elucidate the role of methylation in duodenal adenomas and correlate it with KRAS and BRAF mutations. CIMP+ (with more than 2 markers methylated) was seen in 33.3% of duodenal adenomas; 61% of these CIMP+ adenomas were CIMP-high (with more than 3 markers methylated). Furthermore, CIMP+ status significantly correlated with older age of patients, larger size and villous type of tumor, coexistent dysplasia and periampullary location. MLH1 methylation was seen in 11.1% of duodenal adenomas and was significantly associated with CIMP+ tumors, while p16 methylation was an infrequent event. KRAS mutations were frequent and seen in 26.3% of adenomas; however, no BRAF mutations were detected. Furthermore, CIMP-high status was associated with larger size and villous type of tumor and race (non-white). These results suggest that CIMP+ duodenal adenomas may have a higher risk for developing malignancy and may require more aggressive management and surveillance.
Front Cover: Photoactivatable Mussel‐Based Underwater Adhesive Proteins by an Expanded Genetic Code (ChemBioChem 18/2017) (2017)

The cover picture shows a new concept for producing DOPA-rich underwater adhesive proteins from marine mussels by genetic code expansion. By using computational design and genetic selection methods, a novel Methanocaldococcus jannaschii tyrosyl-tRNA synthetase-based enzyme was engineered. It activates the photocaged DOPA derivative ortho-nitrobenzyl (ONB)-DOPA for incorporation into proteins in response to amber stop codons through orthogonal translation. In this way, mussel proteins are equipped with ONB-DOPA at multiple sites, and this introduces spatiotemporal control over their adhesive properties. Exposure to UV light triggers cleavage of the ONB photocage, liberating the adhesive catechol side chain of DOPA. This strategy provides new ways for producing DOPA-based wet adhesives for application in industry and biomedicine. More information can be found in the communication by N. Budisa et al. on page 1819 in Issue 18, 2017 (DOI: 10.1002/cbic.201700327).
Recursive feature elimination for brain tumor classification using desorption electrospray ionization mass spectrometry imaging (2012)

The metabolism and composition of lipids is of increasing interest for understanding and detecting disease processes. Lipid signatures of tumor type and grade have been demonstrated using magnetic resonance spectroscopy. Clinical management and ultimate prognosis of brain tumors depend largely on the tumor type, subtype, and grade. Mass spectrometry, a well-known analytical technique used to identify molecules in a given sample based on their mass, can significantly improve the problem of tumor type classification. This work focuses on the problem of identifying lipid features to use as input for classification. Feature selection could result in improvements in classifier performance, discovery of biomarkers, improved data interpretation, and patient treatment.
Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicornis (2015)

Rising seawater temperature associated with global climate change is a significant threat to coral health and is linked to increasing coral disease and pathogen-related bleaching events. We performed heat stress experiments with the coral Pocillopora damicornis, where temperature was increased to 31°C, consistent with the 2-3°C predicted increase in summer sea surface maxima. 16S rRNA amplicon sequencing revealed a large shift in the composition of the bacterial community at 31°C, with a notable increase in Vibrio, including known coral pathogens. To investigate the dynamics of the naturally occurring Vibrio community, we performed quantitative PCR targeting (i) the whole Vibrio community and (ii) the coral pathogen Vibrio coralliilyticus. At 31°C, Vibrio abundance increased by 2-3 orders of magnitude and V. coralliilyticus abundance increased by 4 orders of magnitude. Using a Vibrio-specific amplicon sequencing assay, we further demonstrated that the community composition shifted dramatically as a consequence of heat stress, with significant increases in the relative abundance of known coral pathogens. Our findings provide quantitative evidence that the abundance of potential coral pathogens increases within natural communities of coral-associated microbes as a consequence of rising seawater temperature and highlight the potential negative impacts of anthropogenic climate change on coral reef ecosystems.
A Homogeneous Chemiluminescent Immunoassay Method (2013)

A new homogeneous chemiluminescent immunoassay method featuring the use of specific binding members separately labeled with an acridan-based chemiluminescent compound and a peroxidase is reported. Formation of an immunocomplex brings the chemiluminescent compound and the peroxidase into close proximity. Without any separation steps, a chemiluminescent signal is generated upon addition of a trigger solution, and the intensity is directly correlated to the quantity of the analyte.
Raman silicon nanocavity laser with efficient light emission from the edge of an adjacent waveguide (2023)

A Raman nanocavity laser can emit light into free space and into a properly designed waveguide adjacent to the cavity by mode coupling. In common device designs, the emission from the edge of this waveguide is relatively weak. However, a Raman silicon nanocavity laser with strong emission from the waveguide edge would be advantageous for certain applications. Here we investigate the increase in the edge emission that can be achieved by adding photonic mirrors to the waveguides adjacent to the nanocavity. We experimentally compare devices with and without photonic mirrors: the edge emission for devices with mirrors is 4.3 times stronger on average. This increase is analyzed using coupled-mode theory. The results indicate that the control of the round-trip phase shift (between the nanocavity and the mirror) and an increase of the quality factors of the nanocavity are important for further enhancement.
Synthesis of phenylated phthalimides. The diels‐alder reaction of tetraphenylcyclopentadienone with maleimides (1972)

Abstract A series of phenylated dihydrophthalimides has been synthesized by the Diels‐Alder reaction of tetraphenylcyclopentadienone with maleimide, N ‐phenylmaleimide, and N,N' ‐ o ‐, ‐ m ‐, and ‐ p ‐phenylenedimaleimide. Subsequent dehydrogenation of these compounds yielded the corresponding phenylated phthalimides. These phthalimides were also obtained in one step when the initial reactions were carried out in refluxing nitrobenzene.
Data from CTLA-4 Blockade with Ipilimumab: Long-term Follow-up of 177 Patients with Metastatic Melanoma (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Treatment with ipilimumab can cause objective tumor responses in patients with metastatic melanoma. We have treated 177 evaluable patients in three clinical trials and have long-term follow-up to evaluate the durability of responses.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Patients with metastatic melanoma were treated in three trials from 2002 to 2005. In protocol 1, 56 patients received ipilimumab with gp100 peptides. In protocol 2, 36 patients received ipilimumab with interleukin-2. In protocol 3, 85 patients received ipilimumab with intrapatient dose-escalation and were randomized to receive gp100 peptides. We have analyzed their long-term follow-up and survival data.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; With median follow-up for protocols 1, 2, and 3 being 92, 84, and 71 months, median survival was 14, 16, and 13 months with 5-year survival rates being 13%, 25%, and 23%, respectively. Patients in protocol 2 had a 17% complete response (CR) rate, compared with 7% in protocol 1 and 6% in protocol 3. These CR rates are higher than previously reported for the same trials because some patients who eventually became complete responders had continual tumor regression months to years after therapy. All but one of the 15 complete responders are ongoing at 54+ to 99+ months.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; This report provides the longest follow-up of patients with melanoma treated with ipilimumab and shows that ipilimumab can induce durable, potentially curative tumor regression in a small percentage of patients with metastatic melanoma. The combination of ipilimumab and interleukin-2 seems to have an increased CR rate, but this needs to be tested in a randomized trial. &lt;i&gt;Clin Cancer Res; 18(7); 2039–47. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Short Cationic Antimicrobial Peptides Interact with ATP (2010)

The mode of action of short, nonhelical antimicrobial peptides is still not well understood. Here we show that these peptides interact with ATP and directly inhibit the actions of certain ATP-dependent enzymes, such as firefly luciferase, DnaK, and DNA polymerase. α-Helical and planar or circular antimicrobial peptides did not show such interaction with ATP.