gebhart/patrepeval huggingface dataset:
Biology of Giardia lamblia. Detection of N-acetyl-D-glucosamine as the only surface saccharide moiety and identification of two distinct subsets of trophozoites by lectin binding. (1988)

Lectins and glycosidases of known sugar specificity were used as probes to analyze the surface carbohydrate moieties of G. lamblia trophozoites and in particular to determine whether chitin or oligomeric D-GlcNAc is present in the trophozoite form of the parasite as well as on the cyst. Of 13 lectins with varying sugar specificity, only D-GlcNAc-specific lectins bound specifically to the trophozoite surface as determined by light microscopy and EM. A striking finding was the identification of two distinct subsets of trophozoites, distinguished by reactivity with WGA and detected by light microscopy and EM as well as by flow cytometry. Unlike the cyst wall, the trophozoite D-GlcNAc residues were resistant to chitinase treatment. In contrast N-acetyl-beta-D-glucosaminidase abolished WGA binding suggesting that the lectin binds to terminal beta-linked D-GlcNAc residues. These residues were identified as being present on surface glycoproteins by Western blotting of parasite membrane proteins using WGA as a probe. This study identifies D-GlcNAc as the only saccharide moiety detectable by lectin binding on the surface of G. lamblia trophozoites and demonstrates that in contrast to the cyst, chitin is not present in the trophozoite. In addition two distinct subsets of trophozoites were identified based on reactivity with WGA and may represent varying stages of differentiation from trophozoite to cyst.
Cellular and Subcellular Localization of the Nramp2 Iron Transporter in the Intestinal Brush Border and Regulation by Dietary Iron (1999)

Genetic studies in animal models of microcytic anemia and biochemical studies of transport have implicated the Nramp2 gene in iron transport. Nramp2 generates two alternatively spliced mRNAs that differ at their 3' untranslated region by the presence or absence of an iron-response element (IRE) and that encode two proteins with distinct carboxy termini. Antisera raised against Nramp2 fusion proteins containing either the carboxy or amino termini of Nramp2 and that can help distinguish between the two Nramp2 protein isoforms (IRE: isoform I; non-IRE: isoform II) were generated. These antibodies were used to identify the cellular and subcellular localization of Nramp2 in normal tissues and to study possible regulation by dietary iron deprivation. Immunoblotting experiments with membrane fractions from intact organs show that Nramp2 is expressed at low levels throughout the small intestine and to a higher extent in kidney. Dietary iron starvation results in a dramatic upregulation of the Nramp2 isoform I in the proximal portion of the duodenum only, whereas expression in the rest of the small intestine and in kidney remains largely unchanged in response to the lack of dietary iron. In proximal duodenum, immunostaining studies of tissue sections show that Nramp2 protein expression is abundant under iron deplete condition and limited to the villi and is absent in the crypts. In the villi, staining is limited to the columnar absorptive epithelium of the mucosa (enterocytes), with no expression in mucus-secreting goblet cells or in the lamina propria. Nramp2 expression is strongest in the apical two thirds of the villi and is very intense at the brush border of the apical pole of the enterocytes, whereas the basolateral membrane of these cells is negative for Nramp2. These results strongly suggest that Nramp2 is indeed responsible for transferrin-independent iron uptake in the duodenum. These findings are discussed in the context of overall mechanisms of iron acquisition by the body.
Combining and measuring the benefits of bimanual pen and direct-touch interaction on horizontal interfaces (2008)

Many research projects have demonstrated the benefits of bimanual interaction for a variety of tasks. When choosing bimanual input, system designers must select the input device that each hand will control. In this paper, we argue for the use of pen and touch two-handed input, and describe an experiment in which users were faster and committed fewer errors using pen and touch input in comparison to using either touch and touch or pen and pen input while performing a representative bimanual task. We present design principles and an application in which we applied our design rationale toward the creation of a learnable set of bimanual, pen and touch input commands.
Influence of Fatigue on the Efficiency of Men During Exhausting Runs (1958)

In three experiments a man ran on the treadmill at 6.84 yd/sec. for the exact times of 1 minute, 2 minutes and 2.58 minutes, respectively. In previous trial runs this speed was found to exhaust the runner in 2.58 minutes. For each run his O2 intake and O2 debt were determined and samples of venous blood drawn before and 4 minutes after work were analyzed for lactic acid. The runner's O2 requirement was found to decrease in the 2nd minute of the 2.58-minute run at constant speed and then to increase markedly in the last half minute as he approached exhaustion. The rate of accumulation of lactic acid was also greatly accelerated in the last half minute of the run. These results are confirmed by similar experiments on two other subjects. In other experiments it was found that a runner who was exhausted in 3.37 minutes of running at a constant speed of 6.84 yd/sec. could cover the same distance (1382 yd.) in the same total time with a lower O2 requirement and less elevation of lactic acid if he ran the first 2.37 minutes at 6.63 yd/sec. and the last minute at 7.33 yd/sec.; whereas, if he ran the 1st minute at 7.33 yd/sec. and the last 2.37 minutes at 6.63 yd/sec. both his O2 requirement and blood lactate were higher than when he ran at constant speed. It is clear from the data that in order to run a given middle distance race in minimum time the runner should follow a pace which will delay until near the end of the race the sudden change in physiological state in which the energy cost of running and the development of fatigue are so greatly accelerated, i.e. he should run the first part of his race a little slower than the average speed and make a faster finish in order to utilize the O2 debt to the maximum. Submitted on November 10, 1957
2-Alkynyl Derivatives of Adenosine-5'-N-ethyluronamide: Selective A2 Adenosine Receptor Agonists with Potent Inhibitory Activity on Platelet Aggregation (1994)

A series of new 2-alkynyl and 2-cycloalkynyl derivatives of adenosine-5'-N-ethyluronamide (NECA) and of N-ethyl-1'-deoxy-1'-(6-amino-2-hexynyl-9H-purin-9-yl)-beta-D- ribofuranuronamide (1, HE-NECA), bearing hydroxy, amino, chloro, and cyano groups in the side chain, were synthesized. The compounds were studied in binding and functional assays to assess their potency for the A2 compared to A1 adenosine receptor. The presence of an alpha-hydroxyl group in the alkynyl chain of NECA derivatives accounts for the A2 agonist potency, leading to compounds endowed with sub-nanomolar affinity in binding studies. However, these analogues also possess good A1 receptor affinity resulting in low A2 selectivity. From functional experiments the 4-hydroxy-1-butynyl (6) and the 4-(2-tetrahydro-2H-pyranyloxy)-1-butynyl (16) derivatives appear to be very potent in inducing vasorelaxation without appreciable effect on heart rate. The new compounds were also tested as inhibitors of platelet aggregation induced by ADP. Introduction of an alpha-hydroxyl group in the alkynyl side chain caused a greater increase in antiaggregatory activity than either NECA or HE-NECA, resulting in the most potent inhibitors of platelet aggregation so far known in the nucleoside series. The presence of an alpha-quaternary carbon such as the 3-hydroxy-3,5-dimethyl-1-hexynyl (12) and the 3-hydroxy-3-phenyl-1-butynyl (15) derivatives markedly reduced the antiaggregatory potency without affecting the A2 affinity. The hydrophobicity index (k') of the new nucleosides barely correlated with the binding data, whereas high k' values were associated with increased A2 vs A1 selectivity but with reduced activity in all functional assays. Some of the compounds synthesized possess interesting pharmacological properties. Compounds having an appropriate balance between vasorelaxation and antiplatelet activity, if confirmed in vivo, deserve further development for the treatments of cardiovascular disorders.
Synthesis of n-Type Poly(benzotriazole)s Having p-Conducting and Polymerizable Carbazole Pendants (2006)

Poly(benzotriazole)s, P(BTz)s, having an n-type benzotriazole-π-conjugated main chain and p-type and electrochemically polymerizable carbazole (CBz) pendant groups, −(CH2)m−CBz (m = 12 or 6) groups, were synthesized by Ni− (for homopolymers) and Pd-promoted (for a copolymer) organometallic polycondensations. The copolymer between benzotriazole with the −(CH2)12−CBz pendant and p-phenylene was soluble in organic solvents and showed a number-average molecular weight (Mn) of 27000 in the GPC analysis. The homopolymers (m = 12, 6) were less soluble, and about half of the polymer was soluble in CHCl3 in the case of m = 12; the soluble part gave an Mn value of 4700. The polymers were photoluminescent with quantum yields of 50−70%. Cyclic voltammograms of the polymers revealed that the polymers were active in electrochemical n-doping in accord with the electron-accepting nature of the benzotriazole main chain. Application of electrochemical oxidation potential to the polymer made the polymer insoluble due to occurrence of electrochemical polymerization of the CBz unit.
Nanosensors for trace explosive detection (2008)

Selective and sensitive detection of explosives is very important in countering terrorist threats. Detecting trace explosives has become a very complex and expensive endeavor because of a number of factors, such as the wide variety of materials that can be used as explosives, the lack of easily detectable signatures, the vast number of avenues by which these weapons can be deployed, and the lack of inexpensive sensors with high sensitivity and selectivity. High sensitivity and selectivity, combined with the ability to lower the deployment cost of sensors using mass production, is essential in winning the war on explosives-based terrorism. Nanosensors have the potential to satisfy all the requirements for an effective platform for the trace detection of explosives.
An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies (2015)

Posttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain the diversity of their structures and functions. A significant fraction of RNA experimental structures available to date present modified nucleobases, with half of them being involved in H-bonding interactions with other bases, i.e. 'modified base pairs'. Herein we present a systematic investigation of modified base pairs, in the context of experimental RNA structures. To this end, we first compiled an atlas of experimentally observed modified base pairs, for which we recorded occurrences and structural context. Then, for each base pair, we selected a representative for subsequent quantum mechanics calculations, to find out its optimal geometry and interaction energy. Our structural analyses show that most of the modified base pairs are non Watson-Crick like and are involved in RNA tertiary structure motifs. In addition, quantum mechanics calculations quantify and provide a rationale for the impact of the different modifications on the geometry and stability of the base pairs they participate in.
Binding of Phosphonic Acids to CdSe Quantum Dots: A Solution NMR Study (2011)

We use 1H and 31P solution nuclear magnetic resonance spectroscopy to analyze the binding of phosphonic acid ligands to wurtzite CdSe quantum dots (CdSe QDs). CdSe QDs synthesized with phosphonic acids as a surfactant have a ligand shell composed of phosphonic acid and phosphonic acid anhydride moieties. Titrations of as-synthesized QDs with excess oleic acid do not induce desorption of phosphonic species, whereas titration of oleic-acid-exchanged QDs with excess phosphonic acid shows that the latter quantitatively replaces the oleic acid with a 1:1 stoichiometry. Both the stoichiometry of the oleic acid/phosponic acid exchange interaction and the ratio between the Cd surface excess and the ligand density indicate that phosponic acids bind as hydrogen phosphonates to the CdSe surface.
TIGIT and PD-1 dual checkpoint blockade enhances antitumor immunity and survival in GBM (2018)

The use of inhibitory checkpoint blockade in the management of glioblastoma has been studied in both preclinical and clinical settings. TIGIT is a novel checkpoint inhibitor recently discovered to play a role in cancer immunity. In this study, we sought to determine the effect of anti-PD-1 and anti-TIGIT combination therapy on survival in a murine glioblastoma (GBM) model, and to elucidate the underlying immune mechanisms. Using mice with intracranial GL261-luc<sup>+</sup> tumors, we found that TIGIT expression was upregulated on CD8<sup>+</sup> and regulatory T cells (Tregs) in the brain compared to draining cervical lymph nodes (CLN) and spleen. We then demonstrated that treatment using anti-PD-1 and anti-TIGIT dual therapy significantly improved survival compared to control and monotherapy groups. The therapeutic effect was correlated with both increased effector T cell function and downregulation of suppressive Tregs and tumor-infiltrating dendritic cells (TIDCs). Clinically, TIGIT expression on tumor-infiltrating lymphocytes was shown to be elevated in patient GBM samples, suggesting that the TIGIT pathway may be a valuable therapeutic target. Expression of the TIGIT ligand, PVR, further portended a poor survival outcome in patients with low-grade glioma. We conclude that anti-TIGIT is an effective treatment strategy against murine GBM when used in combination with anti-PD-1, improving overall survival via modifications of both the T cell and myeloid compartments. Given evidence of PVR expression on human GBM cells, TIGIT presents as a promising immune therapeutic target in the management of these patients.
Dissecting the Neutralizing Antibody Specificities of Broadly Neutralizing Sera from Human Immunodeficiency Virus Type 1-Infected Donors (2007)

Attempts to elicit broadly neutralizing antibody responses by human immunodeficiency virus type 1 (HIV-1) vaccine antigens have been met with limited success. To better understand the requirements for cross-neutralization of HIV-1, we have characterized the neutralizing antibody specificities present in the sera of three asymptomatic individuals exhibiting broad neutralization. Two individuals were infected with clade B viruses and the third with a clade A virus. The broadly neutralizing activity could be exclusively assigned to the protein A-reactive immunoglobulin G (IgG) fraction of all three donor sera. Neutralization inhibition assays performed with a panel of linear peptides corresponding to the third hypervariable (V3) loop of gp120 failed to inhibit serum neutralization of a panel of HIV-1 viruses. The sera also failed to neutralize chimeric simian immunodeficiency virus (SIV) and HIV-2 viruses displaying highly conserved gp41-neutralizing epitopes, suggesting that antibodies directed against these epitopes likely do not account for the broad neutralizing activity observed. Polyclonal IgG was fractionated on recombinant monomeric clade B gp120, and the neutralization capacities of the gp120-depleted samples were compared to that of the original polyclonal IgG. We found that the gp120-binding antibody population mediated neutralization of some isolates, but not all. Overall, the data suggest that broad neutralization results from more than one specificity in the sera but that the number of these specificities is likely small. The most likely epitope recognized by the monomeric gp120 binding neutralizing fraction is the CD4 binding site, although other epitopes, such as the glycan shield, cannot be excluded.
LAT1 Is a Critical Transporter of Essential Amino Acids for Immune Reactions in Activated Human T Cells (2013)

Activation of T cells accompanies remarkable enhancement of metabolism. Sufficient and continuous nutrient supply is therefore important to support immune reaction in T cells. However, the mechanism of the promotion of nutrient incorporation in activated T cells has not been elucidated. In this study, we show that L-type amino acid transporter 1 (LAT1) is a major transporter for essential amino acids into activated human T cells. CD3/CD28 stimulation in primary human T cells triggered dramatic induction of LAT1 expression mediated by NF-κB and AP-1. Functional disturbance of LAT1 by a specific inhibitor and by small interfering RNA in human T cells suppressed essential amino acid uptake and induced a stress response mediated by DNA damage-inducible transcript 3 to attenuate cytokine production via inhibition of NF-κB and NFAT activities. These results uncover the previously unknown mechanism by which T cells accelerate essential amino acid uptake upon activation and adapt to essential amino acid starvation. Our results also raise the possibility for application of an LAT1 inhibitor as a new drug for therapy of disease caused by exaggerated immune response.
Inhibition of tumor cell proliferation in vitro and in vivo by exogenous p110RB, the retinoblastoma tumor suppressor protein. (1995)

Reconstitution of retinoblastoma gene (RB) deficient tumor cells with RB generally leads to growth suppression in vitro and/or reduced tumorigenicity in nude mice. An alternate approach to gene replacement is the delivery of the RB gene product (p110RB) into cells lacking its expression. In this report we demonstrate that exogenously added p110RB is taken up by and localized to the nucleus of cultured cells and has growth suppression properties similar to endogenous RB. RB-negative (RBneg) tumor cells are preferentially growth inhibited while most RB-positive (RBpos) tumor cells and normal cells are much less sensitive. We have extended these studies to relevant nude mouse xenograft models for human lung cancer. Local or systemic administration of p110RB inhibits tumor growth in treated animals. These results represent the first use of a tumor suppressor protein as a potential cancer therapeutic.
Induction of vascular endothelial growth factor expression by hypoxia and by glucose deficiency in multicell spheroids: implications for tumor angiogenesis. (1995)

Perfusion insufficiency, and the resultant hypoxia, often induces a compensatory neovascularization to satisfy the needs of the tissue. We have used multicellular tumor spheroids, simulating avascular microenvironments within a clonal population of glioma tumor cells, in conjunction with in situ analysis of gene expression, to study stress inducibility of candidate angiogenic factors. We show that expression of vascular endothelial growth factor (VEGF) is upregulated in chronically hypoxic niches (inner layers) of the spheroid and that expression is reversed when hypoxia is relieved by hyperoxygenation. Acute glucose deprivation--another consequence of vascular insufficiency--also activates VEGF expression. Notably, glioma cells in two distinct regions of the spheroid upregulated VEGF expression in response to hypoxia and to glucose starvation. Experiments carried out in cell monolayers established that VEGF is independently induced by these two deficiencies. Upon implantation in nude mice, spheroids were efficiently neovascularized. Concomitant with invasion of blood vessels and restoration of normoxia to the spheroid core, VEGF expression was gradually downregulated to a constitutive low level of expression, representing the output of nonstressed glioma cells. These findings show that stress-induced VEGF activity may compound angiogenic activities generated through the tumor "angiogenic switch" and suggest that stress-induced VEGF should be taken into account in any attempt to target tumor angiogenesis.
Plasminogen activator system in human breast cancer (1992)

We measured antigen levels of 2 kinds of plasminogen activator, tissue-type plasminogen activator (t-PA) and urokinase-type plasminogen activator (UK), as well as those of their primary inhibitors, type-I plasminogen activator inhibitor (PAI-1) and type-2 plasminogen activator inhibitor (PAI-2), in tissue extracts from benign and malignant breast tumors. Tumor tissue samples from 40 fibroadenomas and 40 breast cancers were examined. t-PA antigen levels were the same in the 2 groups. Malignant tumors contained higher levels of UK antigen than did benign tumors. In the case of breast cancer, UK antigen levels of tumors with axillary lymph-node involvement were significantly higher than those of tumors without lymph-node involvement. PAI-1 and PAI-2 antigen levels of breast-cancer tissue samples were higher than those of fibroadenoma samples. PAI-1 antigen levels of carcinomas with lymph-node involvement were also significantly higher than those of carcinomas without node involvement. PAI-2 antigen levels, on the contrary, were higher in carcinomas without node involvement. UK, PAI-1 and PAI-2 antigen levels are potentially excellent independent factors for prediction of the metastatic potential of breast cancers.
CD44-related chondroitin sulfate proteoglycan, a cell surface receptor implicated with tumor cell invasion, mediates endothelial cell migration on fibrinogen and invasion into a fibrin matrix. (1996)

Microvascular endothelial cell invasion into the fibrin provisional matrix is an integral component of angiogenesis during wound repair. Cell surface receptors which interact with extracellular matrix proteins participate in cell migration and invasion. Malignant cells use CD44-related chondroitin sulfate proteoglycan (CSPG) as a matrix receptor to mediate migration and invasion. In this study, we examine whether cell surface CSPG can mediate similar events in nonmalignant wound microvascular endothelial cells or whether use of CSPG for migration and invasion is a property largely restricted to malignant cells. After inhibiting CSPG synthesis with p-nitrophenyl beta-d xylopyranoside (beta-d xyloside), wound microvascular endothelial cells were capable of attaching and spreading on the surface of a fibrin gel; however, their ability to invade the fibrin matrix was virtually eliminated. To begin to examine the mechanism by which endothelial cells use CSPG to invade fibrin matrices, cell adhesion and migration on fibrinogen was examined. Endothelial cell adhesion and migration on fibrinogen were inhibited by both beta-d xyloside and after cleavage of chondroitin sulfate from the core protein by chondroitinase ABC. We have determined that wound microvascular endothelial cells express the majority of their proteoglycan as CSPG and that the CSPG core protein is immunologically related to CD44. PCR studies show that these cells express both the "standard" (CD44H) isoform and an isoform containing the variably spliced exon V3. In addition, anti-CD44 antibody blocks endothelial cell migration on fibrinogen. Affinity chromatography studies reveal that partially purified microvascular endothelial cell CSPG binds fibrinogen. These findings suggest that CD44-related CSPG, a molecule implicated in the invasive behavior of tumor cells, is capable of binding fibrinogen/fibrin, thereby mediating endothelial cell migration and invasion into the fibrin provisional matrix during wound repair.