gebhart/patrepeval huggingface dataset:
Antigen Sensitivity of CD22-Specific Chimeric TCR Is Modulated by Target Epitope Distance from the Cell Membrane (2008)

We have targeted CD22 as a novel tumor-associated Ag for recognition by human CTL genetically modified to express chimeric TCR (cTCR) recognizing this surface molecule. CD22-specific cTCR targeting different epitopes of the CD22 molecule promoted efficient lysis of target cells expressing high levels of CD22 with a maximum lytic potential that appeared to decrease as the distance of the target epitope from the target cell membrane increased. Targeting membrane-distal CD22 epitopes with cTCR(+) CTL revealed defects in both degranulation and lytic granule targeting. CD22-specific cTCR(+) CTL exhibited lower levels of maximum lysis and lower Ag sensitivity than CTL targeting CD20, which has a shorter extracellular domain than CD22. This diminished sensitivity was not a result of reduced avidity of Ag engagement, but instead reflected weaker signaling per triggered cTCR molecule when targeting membrane-distal epitopes of CD22. Both of these parameters were restored by targeting a ligand expressing the same epitope, but constructed as a truncated CD22 molecule to approximate the length of a TCR:peptide-MHC complex. The reduced sensitivity of CD22-specific cTCR(+) CTL for Ag-induced triggering of effector functions has potential therapeutic applications, because such cells selectively lysed B cell lymphoma lines expressing high levels of CD22, but demonstrated minimal activity against autologous normal B cells, which express lower levels of CD22. Thus, our results demonstrate that cTCR signal strength, and consequently Ag sensitivity, can be modulated by differential choice of target epitopes with respect to distance from the cell membrane, allowing discrimination between targets with disparate Ag density.
Tissue microarray‐based analysis shows phospho‐β‐catenin expression in malignant melanoma is associated with poor outcome (2002)

Beyond depth of invasion, there are very few prognostic markers to predict outcome in melanoma. It has been shown recently that the beta-catenin oncogene is mutated or shows altered subcellular localization suggesting that activation of beta-catenin mediated signaling plays a role in oncogenesis. We hypothesize that assessment of activated beta-catenin, as detected by a phospho-specific antibody, may be useful to predict outcome in melanoma. We use immuno-histochemical analysis of beta-catenin and phospho-beta-catenin, first to verify the specificity of the phospho-beta-catenin antibody and then to assay expression in a tissue microarray-based study. The subcellular localization of beta-catenin is membranous in some cases and cytoplasmic and nuclear in others. We validate the specificity of a ser33/37/thr41 phospho-beta-catenin antibody in transfected cells and show that the expression is almost exclusively localized to the nucleus in both cultured cells and human tissue. Evaluation of both total and phospho-beta-catenin antibodies showed that cytoplasmic/nuclear staining was more common in primary lesions, whereas nuclear phospho-beta-catenin was more common in metastatic lesions. High levels of nuclear phospho-beta-catenin are associated with significantly worse overall survival (51% vs. 25% overall survival at 5 years, p = 0.046). These results suggest that phospho-specific antibodies to beta-catenin define a unique subset of cases and that monitoring of phospho-beta-catenin expression may be useful for assessing prognosis in malignant melanoma.
Defect of nephrogenesis induced by gentamicin in rat metanephric organ culture. (1994)

These results indicate that gentamicin induces a significant reduction in the number of nephrons in metanephric explants and that this effect is more important on less differentiated metanephroi. Metanephric organ culture combined with glomerular labeling represents a useful model to test the effect of various growth factors and other drugs on early nephrogenesis.
The ftsH gene of Bacillus subtilis is involved in major cellular processes such as sporulation, stress adaptation and secretion (1997)

The ftsH gene of Bacillus subtilis has been identified as a general stress gene which is transiently induced after thermal or osmotic upshift. The FtsH protein exhibits 70.1% homology to FtsH of Escherichia coli which constitutes an essential ATP- and Zn(2+)-dependent protease anchored in the cytoplasmic membrane via two N-terminal transmembrane domains. This paper describes the isolation and functional characterization of an ftsH null mutant which was obtained by integration of a cat-cassette near the 5' end of ftsH, thereby preventing the synthesis of FtsH protein. In contrast to the situation in E. coli, ftsH is dispensable in B. subtilis but results in a pleiotropic phenotype. While the mutant cells grew mostly as large filaments under physiological conditions, they turned out to be extremely sensitive to heat and salt stress. Although ftsH is necessary for adaptation to heat, it is not involved in the regulation of the heat-shock response. The induction profiles of representative genes of the CIRCE and sigma-B regulon and class III heat-shock genes ion and clpC were identical in the wild type and the ftsH null mutant. Furthermore, the ftsH knockout strain was unable to sporulate, and this failure was probably due to the absence of Spo0A protein which is essential for entry into the sporulation programme. In addition, secretion of bulk exoproteins was severely impaired in the ftsH null mutant after entry into stationary phase. The alpha-amylase and subtilisin activity in the supernatant was specifically tested. Whereas the activity of alpha-amylase increased after entry into stationary phase in both the wild type and the ftsH mutant strain, that of subtilisin encoded by aprE was prevented at the level of transcription in the mutant. Most of these results can be explained by the failure to synthesize appropriate amounts of Spo0A protein in the ftsH null mutant and point to ftsH as a developmental checkpoint.
Sydney multicenter study of Parkinson's disease: Non‐L‐dopa–responsive problems dominate at 15 years (2004)

One-third of the 149 people recruited 15 to 18 years ago in the Sydney Multicenter Study of Parkinson's disease have survived. The original study compared low-dose levodopa with low-dose bromocriptine. We now report the problems experienced by people who survive 15 years from diagnosis. The standardized mortality ratio is significantly elevated at 1.86 and is not significantly different between treatment arms. Falls occur in 81% of patients, and 23% sustained fractures. Cognitive decline is present in 84%, and 48% fulfill the criteria for dementia. Hallucinations and depression are experienced by 50%. Choking has occurred in 50%, symptomatic postural hypotension in 35%, and urinary incontinence in 41%. No patient is still employed, and 40% of patients live in aged care facilities. Although approximately 95% have experienced L-dopa-induced dyskinesia/dystonia and end of dose failure of medication, in the majority, these symptoms are not disabling. Dyskinesia and dystonia were delayed by early use of bromocriptine, but end-of-dose failure appeared at a similar time once L-dopa was added. The rate of disease progression is similar in both arms of the study. We conclude that the most disabling long-term problems of Parkinson's disease relate to the emergence of symptoms that are not improved by L-dopa. Neuroprotective interventions in Parkinson's disease should be judged by their ability to improve non-L-dopa-responsive aspects of the disease, rather than just by their capacity to delay the introduction of L-dopa or reduce its associated side effects.
Effect of phenol and derivatives on atom transfer radical polymerization in the presence of air (2003)

Abstract The various phenolic compounds in conjunction with Cu(II) or Cu(I)‐ N , N , N ′, N ″, N ″‐pentamethyl diethylenetriamine (PMDETA) complexes are used to initiate atom transfer radical polymerization (ATRP) of methyl methacrylate, styrene, and methyl acrylate in the presence of a limited amount of air at temperatures in the range of 80–110 °C. Meanwhile, an effort is directed toward the elucidation of the role of phenol and derivatives in ATRP catalyzed by Cu(II)/PMDETA. The catalytic sequence involves the formation of Cu(I) by electron transfer from phenol to Cu(II); Cu(I) so formed can then react in two distinctly different ways: with organic halide to form a propagating radical or with oxygen to form copper salt in its higher oxidation state; and regeneration of Cu(I) by excess phenol. Such regeneration of Cu(I) would be expected to lead to polymerization as a result of the consumption of oxygen and phenol as well. The phenols with electron releasing groups tended to increase the conversion of the polymerization. In this respect, sodium phenoxide, a more effective additive was found, whereas p ‐nitro phenol was the least effective. The obtained polymers displayed the common features of a controlled polymerization such as molecular weight control and low polydispersity index value ( M w / M n &lt; 1.5). © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 351–359, 2004
Enantioselective Organocatalytic Michael Addition of Aldehydes to Nitroethylene: Efficient Access to γ2-Amino Acids (2008)

Enantioselective organocatalytic Michael addition of aldehydes to nitroethylene catalyzed by (S)-diphenylprolinol silyl ether provides beta-substituted-delta-nitroalcohols in nearly optically pure form (96-99% ee). The Michael adducts bear a single substituent adjacent to the carbonyl and can be efficiently converted to protected gamma2-amino acids, which are essential for the systematic conformational studies of gamma-peptide foldamers.
Phenotype, Function, and Gene Expression Profiles of Programmed Death-1hi CD8 T Cells in Healthy Human Adults (2011)

T cell dysfunction is an important feature of many chronic viral infections. In particular, it was shown that programmed death-1 (PD-1) regulates T cell dysfunction during chronic lymphocytic choriomeningitis virus infection in mice, and PD-1(hi) cells exhibit an intense exhausted gene signature. These findings were extended to human chronic infections such as HIV, hepatitis C virus, and hepatitis B virus. However, it is not known if PD-1(hi) cells of healthy humans have the traits of exhausted cells. In this study, we provide a comprehensive description of phenotype, function, and gene expression profiles of PD-1(hi) versus PD-1(lo) CD8 T cells in the peripheral blood of healthy human adults as follows: 1) the percentage of naive and memory CD8 T cells varied widely in the peripheral blood cells of healthy humans, and PD-1 was expressed by the memory CD8 T cells; 2) PD-1(hi) CD8 T cells in healthy humans did not significantly correlate with the PD-1(hi) exhausted gene signature of HIV-specific human CD8 T cells or chronic lymphocytic choriomeningitis virus-specific CD8 T cells from mice; 3) PD-1 expression did not directly affect the ability of CD8 T cells to secrete cytokines in healthy adults; 4) PD-1 was expressed by the effector memory compared with terminally differentiated effector CD8 T cells; and 5) finally, an interesting inverse relationship between CD45RA and PD-1 expression was observed. In conclusion, our study shows that most PD-1(hi) CD8 T cells in healthy adult humans are effector memory cells rather than exhausted cells.
Detailed Human Shape and Pose from Images (2007)

Much of the research on video-based human motion capture assumes the body shape is known a priori and is represented coarsely (e.g. using cylinders or superquadrics to model limbs). These body models stand in sharp contrast to the richly detailed 3D body models used by the graphics community. Here we propose a method for recovering such models directly from images. Specifically, we represent the body using a recently proposed triangulated mesh model called SCAPE which employs a low-dimensional, but detailed, parametric model of shape and pose-dependent deformations that is learned from a database of range scans of human bodies. Previous work showed that the parameters of the SCAPE model could be estimated from marker-based motion capture data. Here we go further to estimate the parameters directly from image data. We define a cost function between image observations and a hypothesized mesh and formulate the problem as optimization over the body shape and pose parameters using stochastic search. Our results show that such rich generative models enable the automatic recovery of detailed human shape and pose from images.
Efficient universal lossless data compression algorithms based on a greedy sequential grammar transform. I. Without context models (2000)

A grammar transform is a transformation that converts any data sequence to be compressed into a grammar from which the original data sequence can be fully reconstructed. In a grammar-based code, a data sequence is first converted into a grammar by a grammar transform and then losslessly encoded. In this paper, a greedy grammar transform is first presented; this grammar transform constructs sequentially a sequence of irreducible grammars from which the original data sequence can be recovered incrementally. Based on this grammar transform, three universal lossless data compression algorithms, a sequential algorithm, an improved sequential algorithm, and a hierarchical algorithm, are then developed. These algorithms combine the power of arithmetic coding with that of string matching. It is shown that these algorithms are all universal in the sense that they can achieve asymptotically the entropy rate of any stationary, ergodic source. Moreover, it is proved that their worst case redundancies among all individual sequences of length n are upper-bounded by c log log n/log n, where c is a constant. Simulation results show that the proposed algorithms outperform the Unix Compress and Gzip algorithms, which are based on LZ78 and LZ77, respectively.
Synthesis of (((Benzenesulfonamido)alkyl)phenyl)alkanoic Acid Derivatives Containing Pyridyl or Imidazolyl Groups and Their Thromboxane A2 Receptor Antagonistic and Thromboxane A2 Synthase Inhibitory Activities. (1996)

As part of our search for a dual inhibitor possessing both thromboxane A2 (TXA2) receptor antagonistic and TXA2 synthase inhibitory activities, some [[(benzenesulfonamido)alkyl]phenyl]alkanoic acid derivatives possessing a pyridyl or imidazolyl group were synthesized. Their TXA2 receptor antagonistic and TXA2 synthase inhibitory activities were evaluated in terms of the inhibitory effects on U-46619-induced guinea-pig platelet aggregation and on thromboxane B2 (TXB2) production in human platelets, respectively. It was found that 3-[4-[2-(1-imidazolyl)-1-(4-chlorobenzenesulfonamido)ethyl]phenyl] propionic acid (22a), containing an imidazolyl group, is a well-balanced dual inhibitor having both TXA2 receptor antagonistic activity (IC50 = 0.31 microM) and TXA2 synthase inhibitory activity (IC50 = 0.39 microM).
Discovery of 1-Methyl-1H-imidazole Derivatives as Potent Jak2 Inhibitors (2013)

Structure based design, synthesis, and biological evaluation of a novel series of 1-methyl-1H-imidazole, as potent Jak2 inhibitors to modulate the Jak/STAT pathway, are described. Using the C-ring fragment from our first clinical candidate AZD1480 (24), optimization of the series led to the discovery of compound 19a, a potent, orally bioavailable Jak2 inhibitor. Compound 19a displayed a high level of cellular activity in hematopoietic cell lines harboring the V617F mutation and in murine BaF3 TEL-Jak2 cells. Compound 19a demonstrated significant tumor growth inhibition in a UKE-1 xenograft model within a well-tolerated dose range.
Human Immunodeficiency Virus Type 1 Is Trapped by Acidic but Not by Neutralized Human Cervicovaginal Mucus (2009)

To reliably infect a primate model for human immunodeficiency virus (HIV), approximately 10,000-fold more virus must be delivered vaginally than intravenously. However, the vaginal mechanisms that help protect against HIV are poorly understood. Here, we report that human cervicovaginal mucus (CVM), obtained from donors with normal lactobacillus-dominated vaginal flora, efficiently traps HIV, causing it to diffuse more than 1,000-fold more slowly than it does in water. Lactobacilli acidify CVM to pH approximately 4 by continuously producing lactic acid. At this acidic pH, we found that lactic acid, but not HCl, abolished the negative surface charge on HIV without lysing the virus membrane. In contrast, in CVM neutralized to pH 6 to 7, as occurs when semen temporarily neutralizes the vagina, HIV maintained its native surface charge and diffused only 15-fold more slowly than it would in water. Thus, methods that can maintain both a high lactic acid content and acidity for CVM during coitus may contribute to both vaginal and penile protection by trapping HIV before it can reach target cells. Our results reveal that CVM likely plays an important but currently unappreciated role in decreasing the rate of HIV sexual transmission.
Protein design and folding: template trapping of self‐assembled helical bundles (2001)

An experimental system is described, permitting a detailed and systematic analysis of the factors governing self-assembly of amphipathic helices, e.g. to a four-helical bundle, a subject of major relevance for tertiary structure formation, protein folding and design. Following the Template Assembled Synthetic Proteins (TASP) approach, helices of different packing potential are competitively assembled in solution with a preformed two-helix TASP molecule, and after equilibration are covalently attached ('template trapping') via chemoselective thioether formation. The quantitative analysis of the individual TASP molecules by high performance liquid chromatography (HPLC) and electrospray mass spectrometry (ES-MS) allows the delineation of the role of complementary packing in helix bundle formation. The procedure established represents a general tool for the experimental verification of modern concepts in molecular recognition.
Dosing Regimen Has a Significant Impact on the Efficiency of Morpholino Oligomer-Induced Exon Skipping in mdx Mice (2009)

Duchenne muscular dystrophy (DMD) is a myodegenerative disorder caused primarily by mutations that create premature termination of dystrophin translation. The antisense oligonucleotide approach for skipping dystrophin exons allows restoration of the correct reading frame in the dystrophin transcript, thus producing a shorter protein. A similar approach in humans would result in the conversion of DMD to the milder Becker muscular dystrophy. It has been demonstrated previously that repeated intravascular injection of phosphorodiamidate morpholino oligomers (PMOs) in the mdx mouse induces more dystrophin expression than a single injection, but this approach is costly, and data demonstrating the safety of high doses of systemically injected PMO are unavailable. Furthermore, several publications have demonstrated the efficacy of peptide-conjugated PMOs, but the clinical applicability of such compounds is unclear at this stage. Here, we report that multiple intravascular injections of low doses of naked PMO show significantly more dystrophin-positive fibers in a variety of muscle groups, 8 weeks after administration compared with a single dose of the same total amount. After administration of a total of 200 mg of PMO per kilogram, histological features, such as the cross-sectional area, centronucleation index, and expression of the dystrophin-associated protein complex, showed significant improvement in mice treated by repeated injection. Furthermore, four administrations of just 5 mg/kg induced a significant amount of dystrophin expression. These results clearly demonstrate the key role of the optimization of dosing regimen for the systemic administration of PMO in patients, and support the clinical feasibility of this approach with naked PMO.
A fully human anti-CD47 blocking antibody with therapeutic potential for cancer (2016)

CD47/SIRPα interaction serves as an immune checkpoint for macrophage-mediated phagocytosis. Mouse anti-CD47 blocking antibodies had demonstrated potent efficacy in the treatment of both leukemic and solid tumors in preclinical experimentations, and therefore had moved forward rapidly into clinical trials. However, a fully human blocking antibody, which meets clinical purpose better, has not been reported for CD47 up to date. In this study, we reported the isolation of a fully human anti-CD47 blocking antibody, ZF1, from a phage display library. ZF1 displayed high specificity and affinity for CD47 protein, which were comparable to those for humanized anti-CD47 blocking antibody B6H12. Importantly, ZF1 treatment could induce robust, or even stronger than B6H12, phagocytosis of leukemic cancer cells by macrophage in vitro, and protect BALB/c nude mice from cancer killing by engrafted leukemic cells (CCRF and U937) to a similar extent as B6H12 did. Thus, these data provide primary early pre-clinical support for the development of ZF1 as a fully human blocking antibody to treat human leukemia by targeting CD47 molecule.
Initiation of Germination of Bacterial Spores by Hydrostatic Pressure (1970)

SUMMARY: Hydrostatic pressure initiated germination of bacterial spores in nutrient-free media. Those spores which were most dormant towards chemical germinants at I atmosphere pressure were also the most resistant to germination by pressure treatment. Germination by high pressure treatment was characterized by temperature and pH optima, like germination at atmospheric pressure. Germination initiated by pressure was inhibited by metabolic poisons and was potentiated by low concentrations of various nutrients including some of those which are normally germinative (at higher concentrations) at atmospheric pressure. In particular, L-alanine and closely related α-amino acids, but not their breakdown products, potentiated germination initiated by pressure. Study of potentiation by D-alanine (which strongly inhibits germination initiated by L-alanine at I atmosphere pressure) revealed that high pressures caused an increase in the rate of racemization of alanine by spores. Germination by pressure probably resulted from acceleration of some germination reaction which is normally negligibly slow at a pressure of I atmosphere, and also from an increase in permeability of some barrier within the spore to L-alanine and related α-amino acids.
A Conditionally Immortalized Human Podocyte Cell Line Demonstrating Nephrin and Podocin Expression (2002)

Recent molecular insights have established the podocyte as a key component of the glomerular filtration barrier, and hence an important common pathway in proteinuric diseases. A conditionally immortalized human podocyte cell line has been developed by transfection with the temperature-sensitive SV40-T gene. These cells proliferate at the "permissive" temperature (33 degrees C). After transfer to the "nonpermissive" temperature (37 degrees C), they entered growth arrest and expressed markers of differentiated in vivo podocytes, including the novel podocyte proteins, nephrin, podocin, CD2AP, and synaptopodin, and known molecules of the slit diaphragm ZO-1, alpha-, beta-, and gamma-catenin and P-cadherin. The differentiation was accompanied by a growth arrest and the upregulation of cyclin-dependent kinase inhibitors, p27 and p57, as well as cyclin D(1), whereas cyclin A was downregulated. These data are consistent with cell cycle protein expression during podocyte maturation in vivo. In conclusion, the development of this cell line provides a new tool in the study of podocyte biology, which will enable accurate assessment of the behavior of these complex cells in health and disease.