gebhart/patrepeval huggingface dataset:
Significance of PELP1 in ER-Negative Breast Cancer Metastasis (2011)

Breast cancer metastasis is a major clinical problem. The molecular basis of breast cancer progression to metastasis remains poorly understood. PELP1 is an estrogen receptor (ER) coregulator that has been implicated as a proto-oncogene whose expression is deregulated in metastatic breast tumors and whose expression is retained in ER-negative tumors. We examined the mechanism and significance of PELP1-mediated signaling in ER-negative breast cancer progression using two ER-negative model cells (MDA-MB-231 and 4T1 cells) that stably express PELP1-shRNA. These model cells had reduced PELP1 expression (75% of endogenous levels) and exhibited less propensity to proliferate in growth assays in vitro. PELP1 downregulation substantially affected migration of ER-negative cells in Boyden chamber and invasion assays. Using mechanistic studies, we found that PELP1 modulated expression of several genes involved in the epithelial mesenchymal transition (EMT), including MMPs, SNAIL, TWIST, and ZEB. In addition, PELP1 knockdown reduced the in vivo metastatic potential of ER-negative breast cancer cells and significantly reduced lung metastatic nodules in a xenograft assay. These results implicate PELP1 as having a role in ER-negative breast cancer metastasis, reveal novel mechanism of coregulator regulation of metastasis via promoting cell motility/EMT by modulating expression of genes, and suggest PELP1 may be a potential therapeutic target for metastatic ER-negative breast cancer.
N-Methylsansalvamide A Peptide Analogues. Potent New Antitumor Agents (2005)

Sansalvamide A, a cyclic depsipeptide isolated from a marine fungus of the genus Fusarium, is composed of four hydrophobic amino acids (Phe, two Leu, Val) and one hydroxy acid ((S)-2-hydroxy-4-methylpentanoic acid; O-Leu) with five stereogenic centers all having S-stereochemistry. We have recently synthesized the corresponding cyclic peptide (Gu, W.; Liu, S.; Silverman, R. B. Organic Lett. 2002, 4, 4171−4174) and found that it too has antitumor activity. N-Methylation can enhance potency and selectivity for peptides. Consequently, here we synthesize 12 different N-methylated sansalvamide A peptide analogues and show that for several different tumor cell lines three of these analogues are more potent than the natural product; in pancreatic cells, sansalvamide A shows little activity, but the N-methylsansalvamide peptides are potent cytotoxic agents.
Mechanisms of the Sympathoadrenal Response to Hypoglycemia (1997)

The sympathoadrenal response to hypoglycemia plays a key role in glucose counterregulation. In insulin-dependent diabetes, its role becomes even more critical because the glucagon response to hypoglycemia is lost after a short duration of diabetes. Moreover, the sympathoadrenal responses may also become blunted in some patients, rendering them without appropriate subjective warning symptoms, without effective glucose counterregulation, and at potential risk of a greater insult to the central nervous system. The neural origin of the sympathoadrenal response to hypoglycemia has been an area of some interest because it is undoubtedly the critical site where glucose sensing occurs. A role for both cerebral and extracerebral glucose sensors has been studied, and although there is some evidence that the liver may play some role in activating sympathoadrenal activity during hypoglycemia, most data point to the central nervous system as the key center for sensing hypoglycemia. This view is supported by studies showing that infusion of glucose into carotid and vertebral arteries (maintaining brain glucose levels during systemic hypoglycemia) abolishes the neurohormonal response to hypoglycemia. These studies, however, do not define the precise region in the brain involved in glucose sensing.
Total Synthesis of the Antimicrotubule Agent (+)-Discodermolide Using Boron-Mediated Aldol Reactions of Chiral Ketones (2000)

Ein Wirkungsmechanismus ähnlich dem von Taxol macht die Titelverbindung 1 zu einem vielversprechenden Kandidaten für die Entwicklung als Cytostatikum. Die hier vorgestellte effiziente, auf stereokontrollierten Aldolreaktionen beruhende Synthese sollte einen erheblich leichteren Zugang zu 1 ermöglichen als aus der natürlichen Quelle, einem seltenen Meeresschwamm.
Biopsy of Soft Tissue Masses: Evidence-based Medicine for the Musculoskeletal Tumor Society (2009)

Level III, therapeutic study. See Guidelines for Authors for a complete description of levels of evidence.
Erratum to: Seroprevalence of Borrelia burgdorferi sensu lato and Anaplasma phagocytophilum in Danish horses (2010)

The seroprevalence of A. phagocytophilum in Europe varies from 83.
Supplementary Data 6 from Inhibition of EphB4–Ephrin-B2 Signaling Reprograms the Tumor Immune Microenvironment in Head and Neck Cancers (2023)

&lt;p&gt;Total number of CD4+T cells remain unchanged following Control-Fc and ephrin-B2-Fc (20 μg/ml) treatment of T cells (A). Correlation analysis was also performed between TGF-β and EFNB2, EphB4 on R2 analysis platform (B-C). Alterations of cell growth and survival markers in western blots performed using lysates of T cells treated with ephrin-B2-Fc and control-Fc (D). These samples were run on the same gel.&lt;/p&gt;
Gene Expression of a Novel Defensin Antimicrobial Peptide in the Silkworm,Bombyx mori (2008)

cDNA encoding a novel defensin (BmDefensinB) was cloned from the fat body of the silkworm, Bombyx mori, and gene expression was analyzed. BmDefensinB showed typical structural characteristics of invertebrate defensins. Phylogenetic and bootstrap analyses indicated that it has no orthologs, whereas previously reported BmDefensinA is the ortholog of Spodoptera frugiperda (Sf)Spodoptericin. The BmDefensinB gene was expressed tissue-specifically in the fat body and was strongly activated by bacteria such as Escherichia coli and Bacillus subtilis, and by an entomopathogenic fungus Beauveria bassiana. In contrast, the BmDefensinA gene was expressed to a much lesser extent. Expression of the BmDefensinB gene was strongly stimulated by B. mori Rel proteins RelB and Relish, supporting the observation that this gene is activated by E. coli, B. subtilis, and B. bassiana. These results suggest that BmDefensinB gene expression is controlled through both the Toll and the Imd pathway, and that this gene plays an important role in B. mori immune reactions against infection by bacteria and fungi.
Minimum TR radiofrequency‐pulse design for rapid gradient echo sequences (2021)

The TR-optimal framework designs RF pulses for a range of pulse parameters, specifically to minimize sequence TR.
Cucurbit[n]uril (n = 6, 7) Based Carbon-Gold Hybrids with Peroxidase-Like Activity (2018)

Despite the combination of molecular recognition and local electric field enhancement endowing cucurbit[<i>n</i>]uril-capped metallic nanoparticles, indicating great potential in a variety of areas, prior work has paid little attention to carbonizing cucurbit[n]uril on the surface of gold nanoparticles, which may propose new carbon-gold hybrid materials with interesting applications. In this work, we developed a simple and cost-effective method to prepare carbon-gold hybrids by carbonizing cucurbit[n]uril modified gold nanoparticles. The as-prepared cucurbit[n]uril based carbon and carbon-gold hybrid materials have shown to possess peroxidase-like activity. All cucurbit[n]uril based nanomaterials exhibited high catalytic activity over a pH range 2⁻6 and more tolerant to high temperature (up to 60 °C) when compared to natural horseradish peroxidase.
Surface Antigens Common to Mouse Cleavage Embryos and Primitive Teratocarcinoma Cells in Culture (1973)

Syngeneic antisera have been produced in mouse strain 129/Sv-CP males against the primitive cells of teratocarcinoma. These sera react specifically with the primitive cells and are negative on various types of differentiated teratoma cells derived from the same original tumor. They are negative on all other mouse cells tested, with the exception of male germ cells and cleavage-stage embryos. Thus, teratoma cells possess cell-surface antigens in common with normal cleavage-stage embryos.
Principles of Development (2019)

<italic>Principles of Development</italic> starts off by presenting some background history and basic concepts. The next chapterIt then looks at is about the <italic>Ddrosophila</italic> life cycle and the development of the body plan. Other topics covered include vertebrate life cycles, experimental techniques and human development, and the vertebrate body plan for Xenopus and zebrafish and the chick and mouse. Other chapters look at the development of nematodes and sea urchins, morphogenesis, cell differentiation and stem cells, and germ cells, fertilization and sex. The text then goes on to look at organogenesis, the development of the nervous system, and the growth, post-embryonic development, and regeneration. Finally, the text looks at plant life cycle and development, evolution, and development.
The Dynamic Interplay Between Mast Cells, Aging/Cellular Senescence, and Liver Disease (2020)

Mast cells are key players in acute immune responses that are evidenced by degranulation leading to a heightened allergic response. Activation of mast cells can trigger a number of different pathways contributing to metabolic conditions and disease progression. Aging results in irreversible physiological changes affecting all organs, including the liver. The liver undergoes senescence, changes in protein expression, and cell signaling phenotypes during aging, which regulate disease progression. Cellular senescence contributes to the age-related changes. Unsurprisingly, mast cells also undergo age-related changes in number, localization, and activation throughout their lifetime, which adversely affects the etiology and progression of many physiological conditions including liver diseases. In this review, we discuss the role of mast cells during aging, including features of aging (e.g., senescence) in the context of biliary diseases such as primary biliary cholangitis and primary sclerosing cholangitis and nonalcoholic fatty liver disease.
Threats Identification and their Solution in Inter-Basestation Dynamic Resource Sharing IEEE-802.22 (2008)

Cognitive Radio based IEEE 802.22 deploys the concept of maximum resource utilization through dynamic resource sharing. Inter base station resource sharing is dynamic process in IEEE 802.22 and is accomplished by exchange of control messages between the neighboring base stations. Insecure transmission of control channels open vulnerable holes for the Denial of Service attacks on base station. First the paper identifies the rogue base station and replay attacks during the resource sharing between the base stations that can snatch the resources from the renter base station. Then paper presents a hybrid approach of timestamp, nonce and Digital Signature to authenticate the sender and avoid the attacks.
Design for manufacturing (DFM) in submicron VLSI design (2007)

As VLSI technology scales to 65nm and below, traditional communication between design and manufacturing becomes more and more inadequate. Gone are the days when designers simply pass the design GDSII ﬁle to the foundry and expect very good man¬ufacturing and parametric yield. This is largely due to the enormous challenges in the manufacturing stage as the feature size continues to shrink. Thus, the idea of DFM (Design for Manufacturing) is getting very popular. Even though there is no universally accepted deﬁnition of DFM, in my opinion, one of the major parts of DFM is to bring manufacturing information into the design stage in a way that is understood by designers. Consequently, designers can act on the information to improve both manufacturing and parametric yield. In this dissertation, I will present several attempts to reduce the gap between design and manufacturing communities: Alt-PSM aware standard cell designs, printability improve¬ment for detailed routing and the ASIC design ﬂow with litho aware static timing analysis. Experiment results show that we can greatly improve the manufacturability of the designs and we can reduce design pessimism signiﬁcantly for easier design closure.
Experimental Study on Combustion Characteristics of Porous Ceramic Liquid Fuel Combustor (1999)

Experimental study on a porous ceramic liquid fuel combustor is performed. Compact burner with low pollutant emission and high combustion efficiency is realized through the use of porous ceramic materials of high porosities. The use of porous ceramic materials in burner material results in rapid vaporization of liquid fuel and enhancement in mixing process, and thus nearly premixed combustion of liquid fuel is achieved instead of diffusion and partially premixed combustion method, which is often used and apt to produce high pollutant emissions such as CO, NOx and soot. With this enhanced vaporization and premixing method of liquid fuel vapor and air, it is found that enhanced combustion process with intense radiation output and better emission characteristics in NOx, CO and soot emission, compared to other conventional liquid fuel burning method, are possible.
High temperature stability, low coherence and low relative intensity noise semiconductor sources for interferometric sensors (2016)

We investigate self-seeded optical sources for interferometric sensing applications and show that they can, depending on optical filter bandwidth, provide high-output power, high wavelength temperature stability (<5 ppm/°C), low relative intensity noise (<-140 dBc/Hz) and low coherence lengths (<100 um). We characterize the key performance indicators for a range of optical filter bandwidths and provide insight into key design parameters of such sources for interferometric sensors.
An open-source platform to study uniaxial stress effects on nanoscale devices (2017)

We present an automatic measurement platform that enables the characterization of nanodevices by electrical transport and optical spectroscopy as a function of the uniaxial stress. We provide insights into and detailed descriptions of the mechanical device, the substrate design and fabrication, and the instrument control software, which is provided under open-source license. The capability of the platform is demonstrated by characterizing the piezo-resistance of an InAs nanowire device using a combination of electrical transport and Raman spectroscopy. The advantages of this measurement platform are highlighted by comparison with state-of-the-art piezo-resistance measurements in InAs nanowires. We envision that the systematic application of this methodology will provide new insights into the physics of nanoscale devices and novel materials for electronics, and thus contribute to the assessment of the potential of strain as a technology booster for nanoscale electronics.
Quantitative Proteomics Identifies Proteins Enriched in Large and Small Extracellular Vesicles (2022)

There is a long-held consensus that several proteins are unique to small extracellular vesicles (EVs), such as exosomes. However, recent studies have shown that several of these markers can also be present in other subpopulations of EVs to a similar degree. Furthermore, few markers have been identified as enriched or uniquely present in larger EVs, such as microvesicles. The aim of this study was to address these issues by conducting an in-depth comparison of the proteome of large and small EVs. Large (16,500g) and small EVs (118,000g) were isolated from three cell lines using a combination of differential ultracentrifugation and a density cushion and quantitative mass spectrometry (tandem mass tag-liquid chromatography-tandem mass spectrometry) was used to identify differently enriched proteins in large and small EVs. In total, 6493 proteins were quantified, with 818 and 1567 proteins significantly enriched in small and large EVs, respectively. Tetraspanins, ADAMs and ESCRT proteins, as well as SNAREs and Rab proteins associated with endosomes were enriched in small EVs compared with large EVs, whereas ribosomal, mitochondrial, and nuclear proteins, as well as proteins involved in cytokinesis, were enriched in large EVs compared with small EVs. However, Flotillin-1 was not differently expressed in large and small EVs. In conclusion, our study shows that the proteome of large and small EVs are substantially dissimilar. We validated several proteins previously suggested to be enriched in either small or large EVs (e.g., ADAM10 and Mitofilin, respectively), and we suggest several additional novel protein markers.
Spontaneous reporting of adverse drug reactions as an outlet for patient dismay? The case of Levothyrox® change of excipients (2022)

Following minor changes of excipients of Levothyrox®, the French Pharmacovigilance Database was overwhelmed by patients' spontaneous reports of adverse drug reactions associated with the new formula. After noticing that most of these reports differed from those related to other drugs, we aimed to characterize their features and compared them with spontaneous reports associated with other chronic treatments as comparators. We randomly sampled patient reports associated with either Levothyrox® new formula (n = 200) or comparator drugs (n = 200) from March 2017 till March 2018 from the National Pharmacovigilance Database. We evaluated the number of incriminated drugs and adverse drug reactions per report and verified whether they were "expected" or not according to the Summary of Product Characteristics. Levothyrox®-associated reports included, on average, more adverse drug reactions (8 ± 4) than comparators (2 ± 2, P < 0.01) and mentioned mostly one drug (98.5% of reports), whereas comparators mentioned two at least (P < 0.001). The quantitative distribution of adverse drug reactions per report differed quite significantly, appearing almost Gaussian for Levothyrox® whereas Poisson-like for comparators (P < 0.0001). Age did not differ significantly in the two groups (54.2 vs. 49.7, NS), but female predominated in Levothyrox® group (94.5%) as compared with comparators (60.8%, P < 0.001). A mere third of the Levothyrox®-associated adverse drug reactions were deemed "expected," versus two thirds for comparators (P < 0.001). The pattern of spontaneous reports associated with Levothyrox®, whether fueled by media or influenced by social networks, appears atypical, as compared with that of comparators. Such reports, by their abundance, may impair the automatic detection of relevant concomitant signals.
Effective etalon reflectors with high damage threshold for erbium laser development (1996)

Summary form only given. In summary, our results demonstrate that thin plates made from infrared materials like Si can be used as effective etalon reflectors with high damage threshold for Er-doped solid state lasers. High reflectivity mirrors consisting of several silicon plates are under development.
Engineered bacterial communication prevents Vibrio cholerae virulence in an infant mouse model (2010)

To investigate the possibility of using commensal bacteria as signal mediators for inhibiting the disease cholera, we stably transformed Escherichia coli Nissle 1917 (Nissle) to express the autoinducer molecule cholera autoinducer 1 (CAI-1) (shown previously to prevent virulence when present with another signaling molecule, autoinducer 2, at high concentrations) and determined the effect on Vibrio cholerae virulence gene expression and colonization in an infant mouse model. We found that pretreatment of mice for 8 h with Nissle engineered to express CAI-1 (Nissle-cqsA) greatly increased the mice's survival (92%) from ingestion of V. cholerae. Pretreatment with Nissle-cqsA for only 4 h increased survival by 77%, whereas ingesting Nissle-cqsA at the same time as V. cholerae increased survival rates by 27%. Immunostaining revealed an 80% reduction in cholera toxin binding to the intestines of mice pretreated for 8 h with Nissle-cqsA. Further, the numbers of V. cholerae in treated mouse intestines was reduced by 69% after 40 h. This finding points to an easily administered and inexpensive approach where commensal bacteria are engineered to communicate with invasive species and potentially prevent human disease.
Single‐molecule measurements with a single quantum dot (2007)

Recent progress of quantum dot (QD) applications in single-molecule measurements are reviewed in this paper. Bright fluorescence and anti-photobleaching properties of QDs have explored the way to conduct long-time trajectory tracking of transmembrane proteins both in vitro and in vivo. Coupled with diversities of chemical and biochemical modifications of QD surfaces, their application fields are expanding to multidiscipline fields including imaging on the basis of a single molecule. Currently, molecular interactions and conformational changes on the QD surface can be detected at a single-molecule level. These expansions of application fields also involve toxicity problems in cells since most commercially available QDs consist of cadmium selenide or cadmium telluride, which are inherently toxic. For widespread applications of QDs including in vivo and therapeutic use in place of current organic fluorophore, cytotoxicity is discussed as well in this paper. 10.1002/tcr.20128.
Structural basis for the crypticity of B cell epitopes of the Goodpasture autoantigen: The role of novel collagen IV crosslinks (2008)

The autoantigens of certain autoimmune diseases harbor B cell epitopes that are sequestered by the antigen's tertiary or quaternary structure. The exposure of such cryptic epitopes, prompted by pathophysiological conditions, may be an important feature in the etiology of autoimmune disease. Here, we investigated the structural basis for the crypticity of B cell epitopes of the autoantigen of Goodpasture disease, an autoimmune disorder that causes rapidly progressive glomerulonephritis and pulmonary hemorrhage. The native autoantigen is the α3α4α5 noncollagenous hexamer, a globular domain that connects two triple‐helical protomers within the collagen IV network of basement membranes. The complete crypticity of autoepitopes within the hexamer correlates with the presence of dimer subunits. Here, the chemical basis for dimer formation was determined. Mass spectrometry analyses demonstrate that the α3α5‐heterodimers are connected by s‐hydroxylysyl‐methionine crosslinks, whereas, the α4α4‐homodimers are connected by s‐lysyl‐methionine crosslinks. These crosslinks function as molecular fasteners that reinforce the hexamers and block the accessibility of autoantibodies rendering the epitopes completely cryptic. Perturbation of the assembly or cleavage of crosslinks may be a key factor in the etiology of Goodpasture disease
Synthesis of Novel Bis(benzoxazole) Derivatives by Tandem Claisen Rearrangement and Their Fluorescence Behavior. (2002)

Abstract For Abstract see ChemInform Abstract in Full Text.