gebhart/patrepeval huggingface dataset:
Tau avoids the GTP cap at growing microtubule plus ends (2020)

Abstract Plus-end tracking proteins (+TIPs) are a group of proteins that associate with the growing end of microtubules and mediate important cellular functions including neural development and cell division. Work in recent years has shown that the majority of +TIPs are directed to the plus-end through a family of end binding proteins (EBs), which preferentially bind the stabilizing cap of GTP-tubulin present during microtubule growth, versus weaker binding to GDP-tubulin in the proximal microtubule. One question yet to be addressed is whether there may exist other microtubule associated proteins (MAPs) that preferentially bind specific nucleotide states of tubulin. Here we report that the neuronal MAP tau, which is enriched in axons where it promotes microtubule growth and bundling, preferentially binds GDP-tubulin ( K D = 0.26 µM) over GMPCPP-tubulin ( K D = 1.1 µM) in vitro as well as GTP-tubulin at the tips of growing microtubules in vitro and in vivo . This nucleotide preference causes tau binding to lag behind the growing microtubule plus-end by about 100-200 nm both in vitro and in live cells. Thus, tau is a microtubule tip avoiding protein, establishing a new class of tip avoiding MAPs, and acts primarily by suppressing microtubule shortening rather than promoting growth. We speculate that neurological disease-relevant tau mutations may exert their phenotype by their failure to properly recognize GDP-tubulin, thus displacing +TIPs, such as EB3, and their associated activities into abnormal locations in the neuron.
Isolation of Mouse Peritoneal Cavity Cells (2010)

The peritoneal cavity is a membrane-bound and fluid-filled abdominal cavity of mammals, which contains the liver, spleen, most of the gastro-intestinal tract and other viscera. It harbors a number of immune cells including macrophages, B cells and T cells. The presence of a high number of naïve macrophages in the peritoneal cavity makes it a preferred site for the collection of naïve tissue resident macrophages (1). The peritoneal cavity is also important to the study of B cells because of the presence of a unique peritoneal cavity-resident B cell subset known as B1 cells in addition to conventional B2 cells. B1 cells are subdivided into B1a and B1b cells, which can be distinguished by the surface expression of CD11b and CD5. B1 cells are an important source of natural IgM providing early protection from a variety of pathogens (2-4). These cells are autoreactive in nature (5), but how they are controlled to prevent autoimmunity is still not understood completely. On the contrary, CD5+ B1a cells possess some regulatory properties by virtue of their IL-10 producing capacity (6). Therefore, peritoneal cavity B1 cells are an interesting cell population to study because of their diverse function and many unaddressed questions associated with their development and regulation. The isolation of peritoneal cavity resident immune cells is tricky because of the lack of a defined structure inside the peritoneal cavity. Our protocol will describe a procedure for obtaining viable immune cells from the peritoneal cavity of mice, which then can be used for phenotypic analysis by flow cytometry and for different biochemical and immunological assays.
Adsorption of vitronectin, collagen and immunoglobulin-G to plasma polymer surfaces by enzyme linked immunosorbent assay (ELISA) (2002)

Polymeric functional thin films have been deposited from plasmas of allyl alcohol, acrylic acid, allylamine and octa-1,7-diene onto polystyrene microwells and aluminium foil, and analysed by X-ray photoelectron spectroscopy (XPS) and water contact angle measurement. The films were found to be conformal and pin-hole free. Advancing and receding water contact angles measured in air showed that the surfaces had a range of hydrophilicities. The adsorption of human vitronectin, human immunoglobulin G (IgG) and heat-denatured bovine type II collagen to the different plasma polymer surfaces from single solutions was compared by enzyme linked immunosorbent assay (ELISA). Results demonstrate that the adsorption of proteins depends not only on the chemistry of the surface, but also on the nature of the protein. Vitronectin adsorbed most extensively to the acrylic acid-deposited surface, while immunoglobulin G adsorbed more readily to the allylamine deposited surface. The functionalised surfaces performed poorly in terms of collagen binding, with much higher levels of adsorption to the hydrocarbon (octa-1,7-diene) plasma polymer, and the uncoated polystyrene control wells. The amount of adsorbed protein detected on a surface is often explained in terms of surface hydrophilicity/hydrophobicity. The results of this study show that adsorption of these proteins is not simply a matter of wettability, but relates more to the chemical functionality of the surface, which in turn affects a number of surface properties, including wettability, surface charge and pKa.
Review of Various Herbal Supplements as Complementary Treatments for Oral Cancer (2016)

In the United States, nearly 44,000 people are diagnosed with oral or pharyngeal cancer annually. The life expectancy for those who are diagnosed have a survival rate of 57% after five years. Among them, oral cancer can be classified as benign or malignant tumors and is diagnosed at several stages in the development: premalignant conditions, premalignant lesions, and malignant cancer. The early signs of oral cancer often go unnoticed by the individual and are often discovered during routine dental examinations. Early detection and treatment may help to increase patient survival rates. The most widely used treatments for oral cancer include surgery, radiation, and chemotherapy-alone or in combination. Preclinical and clinical evidence for the use of green tea, raspberry, asparagus, and cannabis extracts is discussed in this review. Diet changes, supplementation with antioxidants, high-dose vitamin C therapy, and cannabinoid use have been suggested to decrease cancer cell replication and increase chance of remission. Early detection and lifestyle changes, including the use of dietary supplements in at-risk populations, are critical steps in preventing and successfully treating oral cancer. The main evidence for supplement use is currently in cancer prevention rather than treatment. Further research, determination, and mechanism of action for bioactive compounds such as epigallocatechin, epicatechin-3-gallate, and Bowman-Birk inhibitor concentrate, through in vitro, in vivo, and clinical trials need to be completed to support the use of natural products and their effectiveness in preventative care and supporting therapeutic approaches.
Action of Cis-dichlorodiammineplatinum(II) (NSC-119875) at ehe cellular level. (1976)

Asynchronous human lymphoma cells treated for 1 hour with increasing concentrations of cis-dichlorodiammineplatinum(II) revealed a marked decrease in survival as estimated by the colony-forming technique. When the treatmentwas extended for 8 hours at a concentration of 5micrograms/ml, a killing effect (greater than 3 log decades) was observed which was similar to that obtained when 50micrograms/ml is incubated with the cells for 1 hour. This finding suggests that better antitumor effects with fewer toxic effects may be obtained clinically by prolonged infusion of low doses of cis-dichlorodiammineplatinum (II). Synchronized lymphoma cells showed no significant degree of cell-cycle-stage sensitivity to cis-dichlorodiammineplatinum (II). The drug kills cells with similar efficiency in all stages of the cell cycle. No killing effect was elicited after incubation of the cells with spironolactone, a compound said to protect the kidneys from the toxic effects of heavy metals. However, simultaneous incubation of spironolactone and cis-dichlorodiammineplatinum (II) did not prevent the lethal action of the second drug. If spironolactone is proven to be an inhibitor of cis-dichlorodiammineplatinum (II) nephrotoxicity, it will become a valuable addition to the treatment of human neoplasia with this platinum compound. Lymphoma cells given a "priming" dose of 10 micrograms/ml of cis-dichlorodiammineplatinum (II) failed to repair the induced damage. A second exposure to 10 micrograms/ml of the drug at various subsequent intervals elicited greater killing effect than that produced by 20 micrograms/ml given at one time. A clear synergistic effect was noted when cis-dichlorodiammineplatinum (II) was given simultaneously with camptothecin or BCNU. The molecular mechanism by which this effect is accomplished is not presently apparent.
Nivolumab plus ipilimumab in patients with advanced non-clear cell renal cell carcinoma (nccRCC): Safety and efficacy from CheckMate 920. (2021)

309 Background: The long-term efficacy and tolerability of nivolumab (NIVO) 3 mg/kg + ipilimumab (IPI) 1 mg/kg Q3W × 4 doses followed by NIVO 3 mg/kg Q2W for previously untreated advanced RCC (aRCC) demonstrated in the registrational CheckMate 214 clinical trial was based on patients (pts) with a predominantly clear cell component. CheckMate 920 (NCT02982954) is a US community-based, multi-arm, phase IIIb/IV clinical trial of NIVO+IPI treatment in pts with previously untreated aRCC and clinical features mostly excluded from phase III trials. Here, we present the safety and efficacy results for the cohort of pts with nccRCC from CheckMate 920, a patient population with a poor prognosis and without a definitive effective treatment. Methods: Pts with previously untreated advanced/metastatic nccRCC, Karnofsky performance status ≥ 70%, and any International Metastatic Renal Cell Database Consortium risk received NIVO 3 mg/kg + IPI 1 mg/kg (NIVO3+IPI1) Q3W × 4 doses followed by NIVO 480 mg Q4W for ≤ 2 years or until disease progression/unacceptable toxicity. The primary endpoint was incidence of any-causality grade ≥ 3 immune-mediated adverse events (imAEs) within 100 days of last dose of study drug. Key secondary endpoints: progression-free survival (PFS) and objective response rate (ORR) by RECIST v1.1 (both per investigator), duration of response (DOR), and time to response (TTR). Exploratory endpoints included overall survival (OS). Results: Of 52 treated pts with nccRCC, 69.2% were men; median age was 64 years (range, 23–86), and 28.8% had sarcomatoid features. Histological subtypes were papillary (34.6%), chromophobe (13.5%), translocation associated (3.8%), collecting duct (3.8%), renal medullary (1.9%), or unclassified (42.3%). With 24.1 months minimum follow-up, median duration of therapy (range) was 3.5 months (0.0–25.8) for NIVO and 2.1 months (0.0–3.9) for IPI. Median (range) number of doses received was 4.5 (1–28) for NIVO and 4.0 (1–4) for IPI. No grade 5 imAEs occurred. Grade 3–4 imAEs (n = 52) by category were diarrhea/colitis (7.7%), rash (5.8%), nephritis and renal dysfunction (3.8%), hepatitis (1.9%), adrenal insufficiency (1.9%), and hypophysitis (1.9%). ORR (n = 46) was 19.6% (95% CI, 9.4–33.9). Two pts achieved complete response (papillary, n = 1; unclassified pathology, n = 1), 7 achieved partial response (papillary, n = 4; unclassified pathology, n = 3), and 17 pts had stable disease. Median TTR was 2.8 months (range, 2.1–4.8). Median DOR was not reached (range, 0.03+–27.8+); 8 of 9 responders remain without reported progression. Median PFS (n = 52) was 3.7 months (95% CI, 2.7–4.6). Median OS (n = 52) was 21.2 months (95% CI, 16.6–not reached). Conclusions: In pts with previously untreated nccRCC, a population with high unmet medical need, treatment with NIVO3+IPI1 Q3W followed by NIVO 480 mg Q4W showed no new safety signals, and encouraging antitumor activity. Clinical trial information: NCT02982954 .
Expression and Function of IL-7 Receptors in Marrow Stromal Cells (2004)

IL-7 was first isolated in 1988, when its role in early B lymphocyte development was noted [1-3]. It soon became apparent that IL-7 is a "stromal cytokine" produced by a variety of stromal tissues including those in bone marrow and thymus [4-10]. The production of IL-7 by bone marrow stromal cells is thought to be essential for early B lymphocyte development at least in the murine model, and secreted IL-7 from extra thymic sources including bone marrow is postulated to play a critical role in post-thymic T cell homeostasis [11-15]. Although IL-7 was thought to have effects mostly within the lymphoid populations, the demonstration of IL-7 receptors in non-lymphoid cells including primary marrow stromal cells has challenged this paradigm [15]. In this report, we present data showing that functional IL-7 receptors are expressed by marrow stroma and that IL-7 mediated signaling through this receptor is distinct from that mediated by IL-7 receptors expressed on lymphoid cells.
Study on Cell Proliferation of Oral Malignant Tumor with Transferrin Receptor. (1992)

Transferrin receptor (TfR) is found in the vigorous proliferating cells. The author performed an immunohistochemical study on the TfR expression in the oral tissues and a flow cytometric analysis of TfR in the Hela cells with and without an anticancer drug (CDDP). Immunohistochemically a strong reaction of the TfR was clearly found in the basal and parabasal layers of the normal epithelium and malignant tumors but rarely found in the benign tumors. In the well differentiated carcinomas, the degree of staining was not so high as compared with the poorly differentiated ones. The fluorescence intensity of the cells in the CDDP 0.5 micrograms/ml group was not different from that in the control group. The intensity in the 1.0 micrograms/ml, 24 hr group was almost the same as that in the control group, but in the 1.0 micrograms/ml, 48 hr group a decrease of 18% and in the 72 hr group a decrease of 23% were observed. The intensity in the 2.0 micrograms/ml, 24 hr group decreased by 10%, and in the 2.0 micrograms/ml, 48 and 72 hr groups, it decreased more radically but a number of dead cells was recognized. From these results, the quantity of the TfR seemed to be parallel to the degree of the proliferative ability of the cancer cells. Examination with TfR can be helpful for the diagnosis and the determination of the therapeutic effect on oral cancer.
The long lives of giant clumps and the birth of outflows in gas-rich galaxies at high redshift (2013)

Star-forming disk galaxies at high redshift are often subject to violent disk instability, characterized by giant clumps whose fate is yet to be understood. The main question is whether the clumps disrupt within their dynamical timescale (≤50 Myr), like the molecular clouds in today's galaxies, or whether they survive stellar feedback for more than a disk orbital time (300 Myr) in which case they can migrate inward and help building the central bulge. We present 3.5-7 pc resolution adaptive mesh refinement simulations of high-redshift disks including photoionization, radiation pressure, and supernovae feedback. Our modeling of radiation pressure determines the mass loading and initial velocity of winds from basic physical principles. We find that the giant clumps produce steady outflow rates comparable to and sometimes somewhat larger than their star formation rate, with velocities largely sufficient to escape the galaxy. The clumps also lose mass, especially old stars, by tidal stripping, and the stellar populations contained in the clumps hence remain relatively young (≤200 Myr), as observed. The clumps survive gaseous outflows and stellar loss, because they are wandering in gas-rich turbulent disks from which they can reaccrete gas at high rates compensating for outflows and tidal stripping, overall keeping realistic and self-regulated gaseous and stellar masses. The outflow and accretion rates have specific timescales of a few 108 yr, as opposed to rapid and repeated dispersion and reformation of clumps. Our simulations produce gaseous outflows with velocities, densities, and mass loading consistent with observations, and at the same time suggest that the giant clumps survive for hundreds of Myr and complete their migration to the center of high-redshift galaxies. These long-lived clumps are gas-dominated and contain a moderate mass fraction of stars; they drive inside-out disk evolution, thickening, spheroid growth, and fueling of the central black hole.
Parallelized Full Package Signal Integrity Analysis Using Spatially Distributed 3D Circuit Models (2006)

Full package signal integrity analysis is parallelized in a suite of tools called PATS (package analysis tool suite). PATS extracts sparse circuit models using a segment-to-segment BEM (boundary element method) algorithm for both capacitance and inverse inductance and uses a fixed-time step circuit simulator to create time-domain scattering models. Critical issues regarding the parallelization of PATS and segment-to-segment BEM circuit models are explored. Examples demonstrating the accuracy of this approach are presented for real packaging cases
THROMBOSIS OF A FUSIFORM INTRACRANIAL ANEURYSM INDUCED BY OVERLAPPING NEUROFORM STENTS (2007)

Overlapping Neuroform stents may induce spontaneous thrombosis of intracranial aneurysms and facilitate parent artery reconstruction through flow remodeling and stent endothelialization. Double stent placement may be a viable option in dissecting or fusiform intracranial aneurysms that are not amenable to open surgical treatment or endovascular coil embolization.
An ontology describing congenital heart defects data (2013)

Congenital heart defects (CHDs) are a group of diseases characterized by a structural anomaly of the heart that is present at birth. They are considered as the commonest cause of childhood death in developed countries. The causes of congenital heart disease are still under investigation, but their strongly presumed to be genetic or a combination of genetic and environmental factors. In order to store the derived knowledge, a collaborative knowledge base called CHDWiki has been developed, which collects all the information about the genetic basis of CHDs. However, this dedicated web resource suffers the same problems with similar portals where heterogeneous information is hosted. Further steps should be taken in order to ensure the interoperability of the available data. Also, the hosted data should be offered in a machine-readable format in order to direct be used by other Bioinformatic tools. In order to solve these problems, the life science scientific community tends to use semantic web technologies, which have proved their efficiency through numerous examples including VariO ontology, Gene Ontology (GO), Orphanet Ontology of rare diseases (OntoOrpha) and many more. In this contribution, we present an ontology, which describes CHD data, developed around three main data categories: genotype, phenotype (CHDs) and clinical reports. Retrieving data from CHDWiki, this ontology describes the relationships between genes and human phenotypes, derived from published data or single clinical cases, providing a useful tool to geneticists, molecular biologists and clinicians. This ontology hosts information about syndromic genes, chromosomal aberrations that may cause CHDs and associations between genes and CHDs. Further information is included such as structural variations and single point mutations.
Calcium Signaling by Cyclic ADP-ribose, NAADP, and Inositol Trisphosphate Are Involved in Distinct Functions in Ascidian Oocytes (1998)

ADP-ribosyl cyclase catalyzes the synthesis of two structurally and functionally different Ca2+ releasing molecules, cyclic ADP-ribose (cADPR) from beta-NAD and nicotinic acid-adenine dinucleotide phosphate (NAADP) from beta-NADP. Their Ca2+-mobilizing effects in ascidian oocytes were characterized in connection with that induced by inositol 1,4,5-trisphosphate (InsP3). Fertilization of the oocyte is accompanied by a decrease in the oocyte Ca2+ current and an increase in membrane capacitance due to the addition of membrane to the cell surface. Both of these electrical changes could be induced by perfusion, through a patch pipette, of nanomolar concentrations of cADPR or its precursor, beta-NAD, into unfertilized oocytes. The changes induced by beta-NAD showed a distinctive delay consistent with its enzymatic conversion to cADPR. The cADPR-induced changes were inhibited by preloading the oocytes with a Ca2+ chelator, indicating the effects were due to Ca2+ release induced by cADPR. Consistently, ryanodine (at high concentration) or 8-amino-cADPR, a specific antagonist of cADPR, but not heparin, inhibited the cADPR-induced changes. Both inhibitors likewise blocked the membrane insertion that normally occurred at fertilization consistent with it being mediated by a ryanodine receptor. The effects of NAADP were different from those of cADPR. Although NAADP induced a similar decrease in the Ca2+ current, no membrane insertion occurred. Moreover, pretreatment of the oocytes with NAADP inhibited the post-fertilization Ca2+ oscillation while cADPR did not. A similar Ca2+ oscillation could be artificially induced by perfusing into the oocytes a high concentration of InsP3 and NAADP could likewise inhibit such an InsP3-induced oscillation. This work shows that three independent Ca2+ signaling pathways are present in the oocytes and that each is involved in mediating distinct changes associated with fertilization. The results are consistent with a hierarchical organization of Ca2+ stores in the oocyte.
Epitaxially-grown germanium/silicon avalanche photodiodes for near infrared light detection (2009)

Avalanche Photodiodes (APDs) are widely used in fiber-optic communications as well as imaging and sensing applications where high sensitivities are needed. Traditional InP-based APD receivers typically offer a 10 dB improvement in sensitivity up to 10 Gb/s when compared to standard p-i-n based detector counterparts. As the data rates increase, however, a limited gain-bandwidth product (~100GHz) results in degraded receiver sensitivity. An increasing amount of research is now focusing on alternative multiplication materials for APDs to overcome this limitation, and one of the most promising is silicon. The difficulty in realizing a silicon-based APD device at near infrared wavelengths is that a compatible absorbing material is difficult to find. Research on germanium-on-silicon p-i-n detectors has shown acceptable responsivity at wavelengths as long as 1550 nm, and this work extends the approach to the more complicated APD structure. We are reporting here a germanium-on-silicon Separate Absorption Charge and Multiplication (SACM) APD which operates at 1310 nm, with a responsivity of 0.55A/W at unity gain with long dark current densities. The measured gain bandwidth product of this device is much higher than that of a typical III-V APD. Other device performances, like reliability, sensitivity and thermal stability, will also be discussed in this talk. This basic demonstration of a new silicon photonic device is an important step towards practical APD devices operating at 40 Gb/s, as well as for new applications which require low cost, high volume receivers with high sensitivity such as imaging and sensing.
Measurement of the tt¯ production cross section using dilepton events in pp¯ collisions (2011)

We present a measurement of the a production cross section sigma((u) over bar) in p (p) over bar collisions at root s = 1.96 TeV using 5.4 fb(-1) of integrated luminosity collected with the D0 detector. We consider final states with at least two jets and two leptons (ee, e mu, mu mu), and events with one jet for the e mu final state as well. The measured cross section is sigma((u) over bar) = 7.36(-0.79)(+0.90)(stat + syst) pb. This result combined with the cross section measurement in the lepton + jets final state yields sigma((u) over bar) = 7.56(-0.56)(+0.63)(stat + syst) pb, which agrees with the standard model expectation. The relative precision of 8% of this measurement is comparable to the precision of the latest theoretical calculations. (C) 2011 Elsevier B.V. All rights reserved.