gebhart/patrepeval huggingface dataset:
Plant cells recognize chitin fragments for defense signaling through a plasma membrane receptor (2006)

Chitin is a major component of fungal cell walls and serves as a molecular pattern for the recognition of potential pathogens in the innate immune systems of both plants and animals. In plants, chitin oligosaccharides have been known to induce various defense responses in a wide range of plant cells including both monocots and dicots. To clarify the molecular machinery involved in the perception and transduction of chitin oligosaccharide elicitor, a high-affinity binding protein for this elicitor was isolated from the plasma membrane of suspension-cultured rice cells. Characterization of the purified protein, CEBiP, as well as the cloning of the corresponding gene revealed that CEBiP is actually a glycoprotein consisting of 328 amino acid residues and glycan chains. CEBiP was predicted to have a short membrane spanning domain at the C terminus. Knockdown of CEBiP gene by RNA interference resulted in the suppression of the elicitor-induced oxidative burst as well as the gene responses, showing that CEBiP plays a key role in the perception and transduction of chitin oligosaccharide elicitor in the rice cells. Structural analysis of CEBiP also indicated the presence of two LysM motifs in the extracellular portion of CEBiP. As the LysM motif has been known to exist in the putative Nod-factor receptor kinases involved in the symbiotic signaling between leguminous plants and rhizobial bacteria, the result indicates the involvement of partially homologous plasma membrane proteins both in defense and symbiotic signaling in plant cells.
Transmitting Chinese Medicine (2013)

Historians of Chinese medicine acknowledge the plurality of Chinese medicine along both synchronic and diachronic dimensions. Yet, there remains a tendency to think of tradition as being defined by some unchanging features. The Chinese medical body is a case in point. This is assumed to have been formalised by the late Han dynasty around a system of internal organs, conduits, collaterals, and associated body structures. Although criticism was voiced from time to time, this body and the micro/macrocosmic cosmological resonances that underpin it are seen to persist until the present day. I challenge this view by attending to attempts by physicians in China and Japan in the period from the mid 16th to the late 18th century to reimagine this body. Working within the domain of cold damage therapeutics and combining philological scholarship, empirical observations, and new hermeneutic strategies these physicians worked their way towards a new territorial understanding of the body and of medicine as warfare that required an intimate familiarity with the body's topography. In late imperial China this new view of the body and medicine was gradually re-absorbed into the mainstream. In Japan, however, it led to a break with this orthodoxy that in the Republican era became influential in China once more. I argue that attending further to the innovations of this period from a transnational perspective - commonly portrayed as one of decline - may help to go beyond the modern insistence to frame East Asian medicines as traditional.
Ulcerative Colitis Practice Guidelines in Adults: American College of Gastroenterology, Practice Parameters Committee (2010)

Guidelines for clinical practice are aimed to indicate preferred approaches to medical problems as established by scientifically valid research. Double-blind placebo controlled studies are preferable, but compassionate-use reports and expert review articles are used in a thorough review of the literature conducted through Medline with the National Library of Medicine. When only data that will not withstand objective scrutiny are available, a recommendation is identified as a consensus of experts. Guidelines are applicable to all physicians who address the subject regardless of specialty training or interests and are aimed to indicate the preferable but not necessarily the only acceptable approach to a specific problem. Guidelines are intended to be flexible and must be distinguished from standards of care, which are inflexible and rarely violated. Given the wide range of specifics in any health-care problem, the physician must always choose the course best suited to the individual patient and the variables in existence at the moment of decision. Guidelines are developed under the auspices of the American College of Gastroenterology and its Practice Parameters Committee and approved by the board of trustees. Each has been intensely reviewed and revised by the Committee, other experts in the field, physicians who will use them, and specialists in the science of decision analysis. The recommendations of each guideline are therefore considered valid at the time of composition based on the data available. New developments in medical research and practice pertinent to each guideline will be reviewed at a time established and indicated at publication to assure continued validity. The recommendations made are based on the level of evidence found. Grade A recommendations imply that there is consistent level 1 evidence (randomized controlled trials), grade B indicates that the evidence would be level 2 or 3, which are cohort studies or case-control studies. Grade C recommendations are based on level 4 studies, meaning case series or poor-quality cohort studies, and grade D recommendations are based on level 5 evidence, meaning expert opinion.
An Assessment of the Feasibility of Fueling a Tokamak Reactor with Lithium Tritide Pellets (1992)

The use of 6LiT pellet injection for the Burning Plasma Experiment (BPX), the International Thermonuclear Experimental Reactor (ITER), or reactor fueling using the low ion temperature catalyzed reaction 6LiT + D-D proposed by Krasnopol’skij et al. is investigated. Solid LiT has significant advantages as a pellet material over cryogenic deuterium-tritium because of its higher heat of sublimation, mechanical strength, attainable pellet velocity, and plasma penetration. The implications of this for ignition scenarios are discussed. Injection of LiT has the additional advantage of inherent lithium wall conditioning, which has been shown in the Tokamak Fusion Test Reactor (TFTR) and the Texas Experimental Tokamak (TEXT) to have effects similar to boronization. The injection of LiH pellets has been demonstrated in TEXT, and observed pellet penetration is compared with an ablation model, which is then used to predict LiT penetration in ITER and BPX.
Random Sequencing of Paramecium Somatic DNA (2002)

We report a random survey of 1 to 2% of the somatic genome of the free-living ciliate Paramecium tetraurelia by single-run sequencing of the ends of plasmid inserts. As in all ciliates, the germ line genome of Paramecium (100 to 200 Mb) is reproducibly rearranged at each sexual cycle to produce a somatic genome of expressed or potentially expressed genes, stripped of repeated sequences, transposons, and AT-rich unique sequence elements limited to the germ line. We found the somatic genome to be compact (>68% coding, estimated from the sequence of several complete library inserts) and to feature uniformly small introns (18 to 35 nucleotides). This facilitated gene discovery: 722 open reading frames (ORFs) were identified by similarity with known proteins, and 119 novel ORFs were tentatively identified by internal comparison of the data set. We determined the phylogenetic position of Paramecium with respect to eukaryotes whose genomes have been sequenced by the distance matrix neighbor-joining method by using random combined protein data from the project. The unrooted tree obtained is very robust and in excellent agreement with accepted topology, providing strong support for the quality and consistency of the data set. Our study demonstrates that a random survey of the somatic genome of Paramecium is a good strategy for gene discovery in this organism.
Two novel metal-independent long-chain alkyl alcohol dehydrogenases from Geobacillus thermodenitrificans NG80-2 (2009)

Two alkyl alcohol dehydrogenase (ADH) genes from the long-chain alkane-degrading strain Geobacillus thermodenitrificans NG80-2 were characterized in vitro. ADH1 and ADH2 were prepared heterologously in Escherichia coli as a homooctameric and a homodimeric protein, respectively. Both ADHs can oxidize a broad range of alkyl alcohols up to at least C(30), as well as 1,3-propanediol and acetaldehyde. ADH1 also oxidizes glycerol, and ADH2 oxidizes isopropyl alcohol, isoamylol, acetone, octanal and decanal. The best substrate is ethanol for ADH1 and 1-octanol for ADH2. For both ADHs, the optimum assay condition is at 60 degrees C and pH 8.0, and both NAD and NADP can be used as the cofactor. Sequence analysis reveals that ADH1 and ADH2 belong to the Fe-containing/activated long-chain ADHs. However, the two enzymes contain neither Fe nor other metals, and Fe is not required for the activity, suggesting a new type of ADH. The ADHs characterized here are potentially useful in crude oil bioremediation and other bioconversion processes.
Autoradiographic investigations of glial proliferation in the brain of adult mice. The DNA synthesis phase of neuroglia and endothelial cells (1973)

Abstract The proliferation of glial cells outside the subependymal layer of the lateral ventricle as well as of endothelial cells was studied autoradiographically in the brain of the adult and untreated mouse. The double labeling method with 3 H‐ and 14 C‐thymidine was applied in order to show experimentally the existence of a DNA synthesis phase (S phase) and to measure its duration. Adult mice received a first injection of 14 C‐thymidine, two or four hours later a second injection of 3 H‐thymidine and were sacrificed one hour after the last injection by perfusion fixation. Double layer autoradiographs were made from serial sections of the region from the corpus callosum/commissura anterior up to the corpus callosum/commissura fornicis ventralis in order to register purely 3 H‐, doubly 3 H‐ and 14 C‐, and purely 14 C‐labeled nuclei. From the ratio of all 3 H‐labeled cells with and without 14 C to the purely 3 H‐labeled cells a DNA synthesis phase of 9.4 ± 0.5 hours for glial cells and one of 11.0 ± 2.2 hours for endothelial cells was obtained. Based on the first appearance of labeled mitoses and labeled pairs of glial cells after injections of labeled thymidine the G 2 phase was estimated to be &lt; three hours and G 2 + M about five hours. The duration of the measured S phase as well as the appearance of labeled mitoses about three hours after application of labeled thymidine are very similar to these cycle parameters in many other somatic cells in different kinds of animals. This has led to the conclusion that a well‐defined DNA synthesis phase with doubling of the DNA content and a successive mitosis also exists in glial and endothelial cells of the adult mouse brain.
Tolerogenic Dendritic Cells for Regulatory T Cell Induction in Man (2015)

Dendritic cells (DCs) are highly specialized professional antigen-presenting cells that regulate immune responses, maintaining the balance between tolerance and immunity. Mechanisms via which they can promote central and peripheral tolerance include clonal deletion, the inhibition of memory T cell responses, T cell anergy, and induction of regulatory T cells (Tregs). These properties have led to the analysis of human tolerogenic DCs as a therapeutic strategy for the induction or re-establishment of tolerance. In recent years, numerous protocols for the generation of human tolerogenic DCs have been developed and their tolerogenic mechanisms, including induction of Tregs, are relatively well understood. Phase I trials have been conducted in autoimmune disease, with results that emphasize the feasibility and safety of treatments with tolerogenic DCs. Therefore, the scientific rationale for the use of tolerogenic DCs therapy in the fields of transplantation medicine and allergic and autoimmune diseases is strong. This review will give an overview on efforts and protocols to generate human tolerogenic DCs with focus on IL-10-modulated DCs as inducers of Tregs and discuss their clinical applications and challenges faced in further developing this form of immunotherapy.
Formation and Self-Breaking Mechanism of Stable Atom-Sized Junctions (2007)

The self-breaking mechanism of gold junctions is studied by investigating stability of the atom-sized contacts. The single atom contact lifetime increases from about 0.02 to 200 s upon decreasing the junction stretching speed, while at the same time, the breaking force diminishes logarithmically. We find that the junction self-breaking processes involve sufficient atomic rearrangements, which thereby allow complete self-compensation of externally introduced strain at 0.8 pm/s. The present results have important implications on fabrication of stable single molecule junctions.
Ventilator-associated Pneumonia Caused by Potentially Drug-resistant Bacteria (1998)

To determine risk factors for ventilator-associated pneumonia (VAP) caused by potentially drug-resistant bacteria such as methicillin-resistant Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, and/or Stenotrophomonas maltophilia, 135 consecutive episodes of VAP observed in a single ICU over a 25-mo period were prospectively studied. For all patients, VAP was diagnosed based on results of bronchoscopic protected specimen brush (> or = 10(3) cfu/ml) and bronchoalveolar lavage (> or = 10(4) cfu/ml) specimens. Seventy-seven episodes were caused by "potentially resistant" bacteria and 58 episodes were caused by "other" organisms. According to logistic regression analysis, three variables among potential factors remained significant: duration of mechanical ventilation (MV) > or = 7 d (odds ratio [OR] = 6.0), prior antibiotic use (OR = 13.5), and prior use of broad-spectrum drugs (third-generation cephalosporin, fluoroquinolone, and/or imipenem) (OR = 4.1). Distribution of the 245 causative bacteria was analyzed according to four groups defined by prior duration of MV (< 7 or > or = 7 d) and prior use or lack of use (within 15 d) of antibiotics. Although 22 episodes of early-onset VAP in patients receiving no prior antibiotics were caused by antibiotic-susceptible bacteria, 84 episodes of late-onset VAP in patients receiving prior antibiotics were mainly caused by potentially resistant bacteria. Differences in the potential efficacies (ranging from 100% to 11%) against microorganisms of 15 antimicrobial regimens were studied according to classification into these four groups. These findings may provide a more rational basis for selecting the initial therapy of patients suspected of having VAP.
Myostatin and Sarcopenia: Opportunities and Challenges - A Mini-Review (2014)

The progressive loss of skeletal muscle mass, strength and/or function with advancing age, termed sarcopenia, poses a major threat to independence and quality of life. Therefore, there is significant merit in better understanding the biology of sarcopenia and developing therapeutic interventions to prevent, slow or reverse its progression. Since the discovery of myostatin, a potent negative regulator of growth that is highly enriched in skeletal muscle, there has been great interest in it as a potential mediator of sarcopenia as well as a therapeutic target. The complex biology of myostatin, the promise of myostatin inhibition as an effective means to counter sarcopenia, and the challenges facing its clinical translation are reviewed herein.
mRNA expression profiles of primary high-grade central osteosarcoma are preserved in cell lines and xenografts (2011)

Based on the preservation of mRNA expression profiles that are characteristic for the histological subtype we propose that these model systems are representative for the primary tumor from which they are derived.
Quantitative Expression of Toll-Like Receptor 1–10 mRNA in Cellular Subsets of Human Peripheral Blood Mononuclear Cells and Sensitivity to CpG Oligodeoxynucleotides (2002)

The Toll-like receptor (TLR)9 is critical for the recognition of immunostimulatory CpG motifs but may cooperate with other TLRs. We analyzed TLR1-10 mRNA expression by using quantitative real-time PCR in highly purified subsets of human PBMC and determined the sensitivity of these subsets to CpG oligodeoxynucleotides (ODN). TLR1 and TLR6 were expressed in all cell types examined. TLR10 was highly expressed in B cells and weakly expressed in plasmacytoid dendritic cells (PDC). High expression of TLR2 was characteristic for monocytes. PDC and B cells expressed marked levels of TLR7 and TLR9 and were directly sensitive to CpG ODN. In CpG ODN-stimulated PDC and B cells, TLR9 expression rapidly decreased, as opposed to TLR7, which was up-regulated in PDC and decreased in B cells. In monocytes, NK cells, and T cells, TLR7 was absent. Despite low expression of TLR9, monocytes, NK cells, and T cells did not respond to CpG ODN in the absence of PDC but were activated in the presence of PDC. In conclusion, our studies provide evidence that PDC and B cells, but not monocytes, NK cells, or T cells, are primary targets of CpG ODN in peripheral blood. The characteristic expression pattern of TLR1-10 in cellular subsets of human PBMC is consistent with the concept that TLR9 is essential in the recognition of CpG ODN in PDC and B cells. In addition, selective regulation of TLR7 expression in PDC and B cells by CpG ODN revealed TLR7 as a candidate TLR potentially involved in modulating the recognition of CpG motifs.
How repertoire data are changing antibody science (2020)

Antibodies are vital proteins of the immune system that recognize potentially harmful molecules and initiate their removal. Mammals can efficiently create vast numbers of antibodies with different sequences capable of binding to any antigen with high affinity and specificity. Because they can be developed to bind to many disease agents, antibodies can be used as therapeutics. In an organism, after antigen exposure, antibodies specific to that antigen are enriched through clonal selection, expansion, and somatic hypermutation. The antibodies present in an organism therefore report on its immune status, describe its innate ability to deal with harmful substances, and reveal how it has previously responded. Next-generation sequencing technologies are being increasingly used to query the antibody, or B-cell receptor (BCR), sequence repertoire, and the amount of BCR data in public repositories is growing. The Observed Antibody Space database, for example, currently contains over a billion sequences from 68 different studies. Repertoires are available that represent both the naive state (<i>i.e.</i> antigen-inexperienced) and that after immunization. This wealth of data has created opportunities to learn more about our immune system. In this review, we discuss the many ways in which BCR repertoire data have been or could be exploited. We highlight its utility for providing insights into how the naive immune repertoire is generated and how it responds to antigens. We also consider how structural information can be used to enhance these data and may lead to more accurate depictions of the sequence space and to applications in the discovery of new therapeutics.
Conjugated Polymer/Photochromophore Binary Nanococktails: Bistable Photoswitching of Near‐Infrared Fluorescence for In Vivo Imaging (2013)

Nanoscopic dense integration between solid-state emission and photochromism provides nanoprobes capable of photoswitching of bright NIR fluorescence with high on/off contrast, bistability and improved signal identification, being suitable for imaging applications in autofluorescence-rich in vivo environments.
Noncanonical NF-κB Activation Mediates STAT3-Stimulated IDO Upregulation in Myeloid-Derived Suppressor Cells in Breast Cancer (2014)

Immunotherapy for cancer treatment is achieved through the activation of competent immune effector cells and the inhibition of immunosuppressive cells, such as myeloid-derived suppressor cells (MDSCs). Although MDSCs have been shown to contribute to breast cancer development, the mechanism underlying MDSC-mediated immunosuppression is unclear. We have identified a poorly differentiated MDSC subset in breast cancer-suppressing T cell function through STAT3-dependent IDO upregulation. In this study we investigated the mechanisms underlying aberrant expression of IDO in MDSCs. MDSCs were induced by coculturing human CD33(+) myeloid progenitors with MDA-MB-231 breast cancer cells. Increased STAT3 activation in MDSCs was correlated with activation of the noncanonical NF-κB pathway, including increased NF-κB-inducing kinase (NIK) protein level, phosphorylation of cytoplasmic inhibitor of NF-κB kinase α and p100, and RelB-p52 nuclear translocation. Blocking STAT3 activation with the small molecule inhibitor JSI-124 significantly inhibited the accumulation of NIK and IDO expression in MDSCs. Knockdown of NIK in MDSCs suppressed IDO expression but not STAT3 activation. RelB-p52 dimers were found to directly bind to the IDO promoter, leading to IDO expression in MDSCs. IL-6 was found to stimulate STAT3-dependent, NF-κB-mediated IDO upregulation in MDSCs. Furthermore, significant positive correlation between the numbers of pSTAT3(+) MDSCs, IDO(+) MDSCs, and NIK(+) MDSCs was observed in human breast cancers. These results demonstrate a STAT3/NF-κB/IDO pathway in breast cancer-derived MDSCs, which provides insight into understanding immunosuppressive mechanisms of MDSCs in breast cancer.
Wavelet based OFDM for wireless channels (2002)

The main objective of this paper is to replace the conventional Fourier based complex exponential carriers of the OFDM system with some orthonormal wavelets in order to reduce the level of interference. The wavelets are derived from multistage tree-structured Haar and Daubechies orthonormal quadrature mirror filter (QMF) bank. Compared with the conventional OFDM, it is found that the Haar and Daubechies-based orthonormal wavelets are capable of reducing the power of intersymbol interference (ISI) and intercarrier interference (ICI), which are caused by the loss in orthogonality between the carriers as a result of the multipath wireless channel.
Discovery of the First Potent Inhibitors of Mutant IDH1 That Lower Tumor 2-HG in Vivo (2012)

Optimization of a series of R132H IDH1 inhibitors from a high throughput screen led to the first potent molecules that show robust tumor 2-HG inhibition in a xenograft model. Compound 35 shows good potency in the U87 R132H cell based assay and ∼90% tumor 2-HG inhibition in the corresponding mouse xenograft model following BID dosing. The magnitude and duration of tumor 2-HG inhibition correlates with free plasma concentration.
Lacosamide in Painful Diabetic Peripheral Neuropathy (2007)

Lacosamide seems to attenuate pain in diabetic neuropathy in doses up to 400 mg/d and improves quality of life issues.
Interleukin 2 prevents graft-versus-host disease while preserving the graft-versus-leukemia effect of allogeneic T cells. (1990)

We have recently demonstrated that interleukin 2 (IL-2), when administered in high doses for several days beginning on the day of allogeneic bone marrow transplantation (BMT), markedly diminishes graft-versus-host disease (GVHD) mortality in lethally irradiated mice. An optimal anti-GVHD effect was attained by coadministering T-cell-depleted (TCD) syngeneic marrow. We demonstrate here that the full graft-versus-leukemia effect of allogeneic T lymphocytes is obtained even when GVHD is markedly diminished by the coadministration of IL-2 and TCD syngeneic marrow. This methodology represents an approach to the treatment of leukemia in which the beneficial effects of allogeneic T cells can be exploited while their major deleterious effect, GVHD, is avoided. These results may thus have an impact on the clinical use of BMT for the treatment of hematologic malignancies.