gebhart/patrepeval huggingface dataset:
Stem Cell Niches in the Mouse Airway (2001)

Stem cell research has progressed to new levels of understanding over the last decade. Many adult tissues undergo continuous self-renewal and hence require resident stem cells with the capacity for multipotent differentiation in that organ (1). Such adult stem cells are permanently established in an organ following embryogenesis. Stem cells are most often slow-cycling and give rise to transient amplifying cells (TAC), which impart the majority of tissue renewal in the setting of injury. Unlike stem cells, which by definition have unlimited proliferative capacity, TAC are restricted in their capacity to divide and cannot proliferate indefinitely. Although stem cells and TAC are both selfrenewing populations, TAC are primarily thought to be the major progenitor population which gives rise to terminally differentiated cell types of an adult organ. While the concept of lineage restricted stem cells in adult organs has a long history, recent research isolating stem cells from different organs with multipotent capacity for “trans-differentiation” into various tissue lineages has begun to redefine “stem cell” characteristics (2). For example, neural stem cells have been found to have the capacity to cross tissue-specific lineages in the production of blood derived hematopoietic cell types (3). Similarly, bone marrow-derived myogenic progenitors have also been demonstrated to have the capacity to regenerate muscle (4, 5). These findings have reorganized thinking in the field beyond the traditional viewpoint that stem cells of adult tissues are limited to cell lineages present only in the organ from which they are derived. The concept of whether all organs retain stem cells with multipotent capacity for trans-differentiation across tissue lineages remains to be determined. However, these findings suggest that stem cells can respond to the unique biochemical cues of a niche in which they reside.
Coalescence of the Sites of Cowpea Mosaic Virus RNA Replication into a Cytopathic Structure (2002)

Cowpea mosaic virus (CPMV) replication induces an extensive proliferation of endoplasmic reticulum (ER) membranes, leading to the formation of small membranous vesicles where viral RNA replication takes place. Using fluorescent in situ hybridization, we found that early in the infection of cowpea protoplasts, CPMV plus-strand RNA accumulates at numerous distinct subcellular sites distributed randomly throughout the cytoplasm which rapidly coalesce into a large body located in the center of the cell, often near the nucleus. The combined use of immunostaining and a green fluorescent protein ER marker revealed that during the course of an infection, CPMV RNA colocalizes with the 110-kDa viral polymerase and other replication proteins and is always found in close association with proliferated ER membranes, indicating that these sites correspond to the membranous site of viral replication. Experiments with the cytoskeleton inhibitors oryzalin and latrunculin B point to a role of actin and not tubulin in establishing the large central structure. The induction of ER membrane proliferations in CPMV-infected protoplasts did not coincide with increased levels of BiP mRNA, indicating that the unfolded-protein response is not involved in this process.
Bis(chelated) palladium(II) complexes with a diphosphine and a dinitrogen ligand: very efficient catalyst precursors in the co- and ter-polymerisation of CO and olefins (1996)

A new series of palladium(II) complexes of general formula [Pd(dppp)(L–L)][PF6]2 has been synthesised and characterised [dppp = Ph2P(CH2)3PPh2, L–L = 2,2′-bipyridine (bipy), 4,4′-dimethyl-2,2′-bipyridine, phenanthroline or 3,4,7,8-tetramethyl-1,10-phenanthroline]. The crystal structure of [Pd(dppp)(bipy)][PF6]2 has been determined. The chemical behaviour of the complexes in solution has been studied by NMR spectroscopy. Depending on the nature of the solvent, the chemical environment of palladium in solution can be either the same as in the solid state or different. Whereas in CD2Cl2 the co-ordination sphere remains intact, partial dissociation of the nitrogen ligand occurs in co-ordinating solvents. The complexes were found to be very active catalyst precursors in the CO–olefin co- and ter-polymerisation reactions. Detailed investigation of their catalytic activity allowed the catalyst precursor to be considered as the result of the assembly of different parts, each with a well defined role. In particular, the dissociated N-donor modulates the proton concentration, thus affecting the length of the polymeric chain.
Bone morphogenetic protein signaling regulation of AMPK and PI3K in lung cancer cells and C. elegans (2022)

These studies show that BMP signaling suppresses catabolic metabolism and stimulates anabolic metabolism. We identified feedback mechanisms where catabolic induced signaling mediated by AMPK negatively regulates BMP signaling, whereas anabolic signaling produces a positive feedback regulation of BMP signing through Akt. These mechanisms were conserved in both lung cancer cells and C. elegans. These studies suggest that aberrant BMP signaling causes dysregulation of metabolism that is a potential mechanism by which BMP promotes survival of cancer cells.
Incorporation of Different Types of n-3 Fatty Acids Into Tissue Lipids of Poultry (1992)

The objective of the present study was to compare the incorporation of different types of n-3 polyunsaturated fatty acids into thigh muscle lipids of poultry. Nine groups of broiler chicks were fed diets supplemented with three levels (1.0, 2.5, and 5.0%) of either corn, linseed, or menhaden oil. Birds supplemented with linseed oil, rich in linolenic acid (C18:3n-3), had significantly higher levels of n-3 fatty acids and higher n-3:n-6 ratios than those supplemented with the same level of menhaden oil, primarily due to an accumulation of C18:3n-3. Levels of eicosapentaenoic acid (C20:5n-3) were increased (P less than .05), compared with the controls fed the same level of corn oil, in the groups fed the two higher levels of linseed oil, and in all the groups fed menhaden oil. Linolenic acid is less susceptible to auto-oxidation, and is less likely to impart an off-flavor to the muscle. Thus, if it is desirable to increase the n-3:n-6 ratio in poultry, seed meals or oils with a high content of C18:3n-3 could be used in poultry feeds.
Supplemental Table 1 from A Phase I Trial of a Guadecitabine (SGI-110) and Irinotecan in Metastatic Colorectal Cancer Patients Previously Exposed to Irinotecan (2023)

&lt;p&gt;Pharmacokinetic parameters of guadecitabine and decitabine after guadecitabine injection&lt;/p&gt;
Structural Analysis of Oligosaccharides by Nuclear Magnetic Resonance Method (2003)

本レビューでは、NMRを用いた糖鎖の構造解析法として、糖鎖を構成する各糖残基の1Hシグナルの帰属、NOEの実験、およびパルスプログラムの構築法等について紹介する。
Poly(ethylene) brushes grafted to silicon substrates (2011)

A poly(glycidyl methacrylate) (PGMA) synthesized by RAFT polymerization was spin-coated onto a silicon substrate to yield, after annealing and rinsing unreacted chains, covalently attached epoxy-containing PGMA pseudo-brushes. A tailor-made ω-amino-poly(ethylene) (Mn = 1040 g mol−1, PDI = 1.3) was then grafted in melt at 130 °C for 24 h by reaction between amine chain-ends and surface-tethered epoxy groups. After discarding unreacted poly(ethylene) chains by sonication and Soxhlet rinsing, the resulting poly(ethylene) brushes were characterized by scanning probe microscopy, water contact angle and neutron reflectivity measurements. The grafting of poly(ethylene) brushes to silicon substrates has thus been demonstrated for the first time and resulted in nanostructured grafted layers with homogeneous surface coverage.
Simple method for quality factor estimation in resonating MEMS structures (2018)

The quality factor of a packaged MEMS resonating structure depends on both the packaging pressure and the structure’s proximity to the walls. This type of mechanical constraints, which causes energy dissipation from the structure to the surrounding air, are applicable for oscillating energy harvesters and should be considered in the design process. However, the modelling of energy losses or the measurements of their direct influence inside a packaged chip is not trivial. In this paper, a simple experimental method to quantify the energy loss in an oscillating MEMS structures due to the surrounding air is described together with preliminary results. The main advantage of the method is the ability to characterize the damping contributions under different vacuum and packaging conditions without requiring any packaging of the harvester chip or fabrication of multiple devices with different cavity depths.
Data from Polysaccharide Krestin Is a Novel TLR2 Agonist that Mediates Inhibition of Tumor Growth via Stimulation of CD8 T Cells and NK Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Polysaccharide krestin (PSK) is a mushroom extract that has been long used in Asia and recently in Western countries as a treatment for cancer due to its presumed immune potentiating effects. Although there have been reports of clinical responses after patients have ingested PSK, the mechanism of action of the agent remains undefined. The current study was undertaken to investigate the mechanism of the antitumor actions of PSK.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; The immunostimulatory effect of PSK was first evaluated &lt;i&gt;in vitro&lt;/i&gt; using splenocytes from neu transgenic mice and Toll-like receptor (TLR) 2 knockout (TLR2&lt;sup&gt;−/−&lt;/sup&gt;) mice. Then the immunostimualtory and antitumor effect of PSK was determined using tumor-bearing neu transgenic mice, TLR2&lt;sup&gt;−/−&lt;/sup&gt;, and wild-type C57BL/6 mice.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We demonstrate that PSK is a selective TLR2 agonist, and the activation of dendritic cells (DC) and T cells by PSK is dependent on TLR2. Oral administration of PSK in neu transgenic mice significantly inhibits breast cancer growth. Selective depletion of specific cell populations suggests that the antitumor effect of PSK is dependent on both CD8&lt;sup&gt;+&lt;/sup&gt; T cell and NK cells, but not CD4&lt;sup&gt;+&lt;/sup&gt; T cells. PSK does not inhibit tumor growth in TLR2&lt;sup&gt;−/−&lt;/sup&gt; mice suggesting that the antitumor effect is mediated by TLR2.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; These results demonstrate that PSK, a natural product commonly used for the treatment of cancer, is a specific TLR2 agonist and has potent antitumor effects via stimulation of both innate and adaptive immune pathways. &lt;i&gt;Clin Cancer Res; 17(1); 67–76. ©2010 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Real-time electrical detection of the formation and destruction of lipid bilayers on silicon nanowire devices (2015)

Silicon nanowire (Si NW) two-terminal devices were fabricated to electrically probe the real-time formation and destruction of lipid bilayers. A liposome solution, containing the same ratio of zwitterionic/anionic lipids that are present in an Escherichia coli cell membrane, was applied to the NW devices. Lipid bilayer formation on the Si NWs was detected in-situ by observing electrical resistance changes complemented by confocal fluorescence microscopy imaging. The formation of lipid bilayers resulted in a 1% to 2% decrease in device current, consistent with the negative gating effect of the lipids on the NW surface. The devices demonstrated a ≈ 1 min electrical response time to lipid encapsulation. Removal of the lipid layer was achieved by exposing the devices to a detergent, which resulted in NW conductance returning to its original value with a ≈ 2 min recovery time. The lipid bilayer coated Si NWs demonstrate a novel platform to enable in-situ electrical probing of bacterial cell membrane mechanisms, interactions, and reactions.
Thyrostimulin, a heterodimer of two new human glycoprotein hormone subunits, activates the thyroid-stimulating hormone receptor (2002)

Human thyrotropin (TSH), luteotropin (LH), follitropin (FSH), and chorionic gonadotropin are members of the heterodimeric glycoprotein hormone family. The common α subunit forms noncovalent heterodimers with different β subunits. Two novel human glycoprotein hormonelike genes, α2 (A2) and β5 (B5), recently have been identified. Using a yeast two-hybrid assay, the two subunits were found as potential heterodimerization partners. Immunological analyses confirmed the heterodimerization of A2 and B5 in transfected cells and their colocalization in the anterior pituitary. Recombinant A2/B5 heterodimeric glycoproteins, purified using cation exchange and size fractionation chromatography, activated human TSH receptors, but not LH and FSH receptors, and showed high affinity to TSH receptors in a radioligand receptor assay. The heterodimer also stimulated cAMP production and thymidine incorporation by cultured thyroid cells and increased serum thyroxine levels in TSH-suppressed rats in vivo. This new heterodimeric glycoprotein hormone was named as thyrostimulin based on its thyroid-stimulating activity. The expression of thyrostimulin in the anterior pituitary known to express TSH receptors suggested a paracrine mechanism. The present discovery of a new ligand based on genomic approaches could facilitate the understanding of the physiological roles of extra-thyroid TSH receptor systems and the structural-functional basis of receptor signaling by related glycoprotein hormones.
Video delivery over next generation cellular networks (2013)

The rapidly increasing use of mobile devices, such as smart phones and tablets, as well as the high popularity of mobile applications and especially video streaming incur an increasing traffic demand on mobile cellular systems. The cloud computing and the software defined networking (SDN) paradigms constitute suitable tools for mobile networks to efficiently handle the increasing video traffic. In this paper, we focus on content and, in particular, video delivery services on top of emerging and next generation cellular networks which employ SDN in their core, mainly from a business standpoint. We analyze the stakeholders and their business interests and relationships, also providing a value network and business model analysis for both existing and emerging use cases of interest.
Cancer testis (CT) antigen (Ag) expression in non-small cell lung carcinoma (NSCLC) paired primary (1°) and secondary (2°) tumours. (2010)

e21047 Background: The importance of CTAgs in NSCLC was recently highlighted with evidence that MAGE-A3 expression is not only a poor prognostic factor but also a promising target for adjuvant immunotherapy (Vansteenkiste, Proc ASCO 2007; abs 7554). With progressive stage, loss of or failure to acquire CTAg expression may indicate susceptibility of the tumor to immunoediting, where selective pressure from the host immune response results in Ag-negative variants that evade immune recognition. This may facilitate disease progression. This has implications for the effectiveness of cancer vaccination. We therefore compared expression of CTAgs in paired NSCLC 1° and metastatic 2° tumour tissue. Methods: 43 patients (pts) with histologically confirmed 1° NSCLC resected at Austin Hospital from April 1, 1992 to April 1, 2009, with available paired 2° lung or brain metastases were studied. Immunohistochemical staining was performed on tissue microarrays of formalin-fixed paraffin-embedded tissues, with human testis as the positive control. We examined the proportions of tumours expressing 4 CTAgs (MAGE-A3, MAGE-A1, NY-ESO-1, MAGE-C1) in the paired samples. Results: Among all 1° or 2° tumours MAGE-A3 was most frequently expressed in 65%, followed by MAGE-C1 in 56%, MAGE-A1 in 47% and NY-ESO-1 in 40%. Expression of any CTAg was seen in 22/27 (81.5%) 2° NSCLC brain metastases and in 10/16 (62.5%) 2° NSCLC lung metastases, p = 0.25. CTAg expression occurring in both 1° and 2° tumours was most common for MAGE-A3 (44%) and MAGE-C1 (26%). Acquisition of expression in 2° tumours occurred most commonly for MAGE-A1 (26%) and least commonly for NY-ESO-1 (9%), whereas loss of CTAg expression in 2° tumours was most common for NY-ESO-1 (19%) and MAGE-C1 (14%). Conclusions: With progression to metastatic NSCLC, NY-ESO-1 expression was most frequently lost and least frequently acquired. In contrast, MAGE-A1 was the CTAg most frequently acquired in 2° tumours. Results of this small series support previous observations in malignant melanoma that the highly immunogenic CTAg, NY-ESO-1 may be particularly susceptible to immunoediting, whereas MAGE-A1 may be less so (Barrow. Clin Cancer Res. 2006;12:764-71). No significant financial relationships to disclose.
Abstract TMP49: Translating Ribosome Affinity Purification for Qualitative Assessment of Human Neural Stem Cells Transcripts in the Ischemic Rat Brain (2016)

Introduction: Neural stem cell (NSC) transplantation is being explored as a potential therapy for ischemic stroke (IS). Although research has shown the efficacy of NSCs in IS, little is known about the gene expression profile of the NSCs after transplantation. To date this has been challenging due to the issue of trying to distinguish factors expressed by the transplanted cells from that of surrounding host cells. We have overcome this critical barrier by adapting the novel TRAP (Translating Ribosome Affinity Purification) approach to selectively purify mRNA from transplanted NSCs. Hypothesis: Application of TRAP technology can enrich isolation of human NSC transcripts from IS rats and enabling identification of the in vivo gene expression profile of transplanted NSCs. Methods: Nude rats were subjected to permanent distal cerebral artery occlusion and after 7 days fetal human NSCs expressing GFP under RPL10a promoter were transplanted into the motor cortex of IS and non-ischemic (NI) rats. Seven days post-transplantation, the graft site was dissected and processed using the TRAP methodology. Seven housekeeping genes (HKG) were analyzed by qPCR in TRAP and non-TRAP samples to determine the level of enrichment of human transcripts. The RNA isolated was converted to cDNA libraries and analyzed using RNAseq technology. Results: The expression level of HKG was consistent between samples and groups when analyzed by the Pearson correlation (r ≥ 8.7), indicating that TRAP samples are compatible between them for sequencing analysis. Furthermore, the average enrichment of human HKG was 22.7-fold (range: 3.37-22.76) and 58.8-fold (range: 1.31-154.94) in IS and NI rats, respectively. Preliminary data from MiSeq analysis detected 317 genes differentially expressed between IS and NI rats. Gene ontology analysis of these genes showed enrichment of genes involved in the intracellular process, stem cell biology, extracellular region, and signaling and secreted proteins. Conclusion: Our data demonstrate that the application of TRAP is feasible to enrich human NSC transcripts from rat cortex, making analysis of their expression profile in the stroke brain possible. This sets the stage to probe the molecular mechanism of action of transplanted stem cells.
Recent Advances in Electrochemical Biosensors: Applications, Challenges, and Future Scope (2021)

The electrochemical biosensors are a class of biosensors which convert biological information such as analyte concentration that is a biological recognition element (biochemical receptor) into current or voltage. Electrochemical biosensors depict propitious diagnostic technology which can detect biomarkers in body fluids such as sweat, blood, feces, or urine. Combinations of suitable immobilization techniques with effective transducers give rise to an efficient biosensor. They have been employed in the food industry, medical sciences, defense, studying plant biology, etc. While sensing complex structures and entities, a large data is obtained, and it becomes difficult to manually interpret all the data. Machine learning helps in interpreting large sensing data. In the case of biosensors, the presence of impurity affects the performance of the sensor and machine learning helps in removing signals obtained from the contaminants to obtain a high sensitivity. In this review, we discuss different types of biosensors along with their applications and the benefits of machine learning. This is followed by a discussion on the challenges, missing gaps in the knowledge, and solutions in the field of electrochemical biosensors. This review aims to serve as a valuable resource for scientists and engineers entering the interdisciplinary field of electrochemical biosensors. Furthermore, this review provides insight into the type of electrochemical biosensors, their applications, the importance of machine learning (ML) in biosensing, and challenges and future outlook.
Dissecting the allosteric FXR modulation: a chemical biology approach using guggulsterone as a chemical tool (2019)

Guggulsterone is a promiscuous ligand for endocrine and metabolic lipid receptors traditionally used to treat a number of diseases including diabesity, hyperlipidemia, atherosclerosis, and osteoarthritis. Although relatively weak, its activity at the farnesoid X receptor (FXR) is particularly intriguing as guggulsterone acts as an antagonist with a peculiar ability of gene selective modulation. We report here a chemical biology study with the aim to further characterize the biological action of guggulsterone at the FXR and to obtain further insights into the functional role played by noncanonical FXR binding pockets S2 and S3. Our results suggest that the FXR accessory pockets might act as potential targets for small molecules able to modulate the metabolic activation of the receptor without affecting the anti-inflammatory activity thus revealing a new approach for disclosing selective FXR modulators that might bypass potential side-effects from chronic treatments.
A novel electrostatic actuator for micro deformable mirrors: fabrication and test (2004)

High performance adaptive optics systems for both astronomy and ophthalmology require deformable mirrors with a continuous membrane, a high actuator density and a stroke of several microns CEA/LETI and LAOG are collaborating to develop such devices, using a new kind of electrostatic actuator based on the so-called zipping effect. These new actuators can reach a large vertical force (more than 100 /spl mu/N for an active area of 800/spl times/800 /spl mu/m/sup 2/), and a large vertical stroke (more than 6 /spl mu/m). An innovative process based on SOI wafer bonding is used for the actuator array. The quasi-static response matches the FEM simulations, showing a good linearity. The dynamic response presents a clean non-resonant behaviour, with 1dB gain and 20/spl deg/ phase error at 2 kHz. A modulated control voltage is used to minimize the charging effects in the dielectric layer. A continuous membrane is manufactured separately, and a first assembly test was made on a single actuator. This promising test shows that an inter-actuator stroke of 2 /spl mu/m is possible with a continuous membrane and a voltage of 150 V. The peak to peak deflexion of the whole mirror should be larger than 6 /spl mu/m.
Table S2 from Validation of a Plasma-Based Comprehensive Cancer Genotyping Assay Utilizing Orthogonal Tissue- and Plasma-Based Methodologies (2023)

&lt;p&gt;Detailed results of Digital Sequencing and clinical ddPCR comparison. Results shown in individual 2x2 tables for each biomarker tested. *Note, all discordances were below DFCI ddPCR's reportable range. Detailed clinical information for each is presented in Supplemental Table 3.&lt;/p&gt;