gebhart/patrepeval huggingface dataset:
Diverse Glycosylation of MUC1 and MUC2: Potential Significance in Tumor Immunity (1999)

Mucins are major epithelial luminal surface proteins and function as a physical and biological barrier protecting mucous epithelia. Diverse glycosylation of mucins potentially provides a basis for tissue-specific interaction with the milieu. When mucins are associated with malignant epithelial cells, they not only protect these cells from a host environment during metastatic dissemination but also generate immunogenic epitopes which are used by the host in the detection and immunological elimination of carcinoma cells potentially depending upon their status of glycosylation. Diverse mucin structures are generated by the combination of different core peptides, of which 10 have been reported so far, multiple types of UDP-GalNAc: polypeptide N-acetylgalactosaminyltransferases (pp-GalNAc-Ts), and the consequences of stepwise glycosylation events. For example, the mucin 1 (MUCl) associated with malignant cells was previously believed to exhibit unique features with a lower percentage of threonine and serine residues attached to 2V-acetylgalactosamine and/ or without extension through core 2 structures. Some of MUCl-specific monoclonal antibodies and cytotoxic lymphocytes recognize the peptide sequences PDTR within the tandem repeat portion exposed by decreased degree of glycosylation. The specific arrangement of N-acetylgalactosamine residues is shown to be generated by a combination of pp-GalNAc-Ts with different specificities. The role of core 2 branching is somewhat confusing because well-known carcinoma-associated carbohydrate epitopes such as sialyl-Lex, sialyl-Lea, LeY, and others are often expressed when O-glycans are extended through core 2 branching. The other series of well-known carcinoma-associated carbohydrate structures are truncated O-glycans, conventionally called Tn and sialyl-Tn antigens. Interestingly, these are often found to be aligned on core polypeptides, resulting in three or more consecutive truncated O-glycans. MUC2 and other mucins, but not MUCl, have unique tandem repeats containing three or more consecutive serine or threonine residues, which potentially serve as a scaffold for trimeric Tn and sialyl-Tn epitopes. We recently found, using the MUC2 tandem repeat, that trimeric Tn is a high-affinity receptor for a calcium-type lectin expressed on the surface of histiocytic macrophages. The biosynthesis of trimeric Tn was strictly regulated by the acceptor specificity of pp-GalNAc-Ts. These results strongly suggest that variation in both glycan structures and distribution of glyeans on the core polypeptides give mucins unique and diverse biological functions that play essential roles in carcinoma-host and other cellular interactions.
An in vitro method for detecting infectious Cryptosporidium oocysts with cell culture (1997)

Current assay methods to detect Cryptosporidium oocysts in water are generally not able to evaluate viability or infectivity. A method was developed for low-level detection of infective oocysts by using HCT-8 cells in culture as hosts to C. parvum reproductive stages. The infective foci were detected by labeling intracellular developmental stages of the parasite in an indirect-antibody assay with a primary antibody specific for reproductive stages and a secondary fluorescein isothiocyanate-conjugated antibody. The complete assay was named the focus detection method (FDM). The infectious foci (indicating that at least one of the four sporozoites released from a viable oocyst had infected a cell) were enumerated by epifluorescence microscopy and confirmed under Nomarski differential interference contrast microscopy. Time series experiments demonstrated that the autoreinfective life cycle in host HCT-8 cells began after 12 h of incubation. Through dilution studies, levels as low as one infectious oocyst were detected. The cell culture FDM compared well to other viability assays. Vital stains and excystation demonstrated that oocyst populations less than 1% viable (by vital dyes) and having a low sporozoite yield following excystation could not infect host cells. Until now, the water industry has relied on an oocyst detection method (under an information collection regulation) that is unable to determine viability. The quantifiable results of the cell culture method described demonstrate two important applications: (i) an infectivity assay that may be used in conjunction with current U.S. Environmental Protection Agency-mandated detection methodologies, and (ii) a method to evaluate oocyst infectivity in survival and disinfection studies.
<i>Immunology and Cell Biology</i> publication of the year award 2008 (2009)

A small committee, consisting of the Editor-in-Chief of ICB, the current ASI President and a past President of ASI, selects the best eligible paper based on the sole criterion of scientific excellence. This year, I am pleased to announce that Dr Scott Byrne (pictured) was chosen by the committee as the winner of the 2008 ICB Publication of the Year Award. Dr Byrne's winning paper is entitled ‘TGFβ is responsible for skin tumour infiltration by macrophages enabling the tumours to escape immune destruction’ and was published in the January 2008 issue of ICB.1 There is increasing evidence from many laboratories that evasion of immune attack by the host's immune system is an important stage in tumour progression. In his award-winning paper, Dr Byrne and his colleagues show that, in the case of skin cancer, tumour growth factor (TGF)β-mediated recruitment of macrophages into tumours has a key role in immune escape, the cytokine being capable of converting a regressing tumour to a progressing tumour. Analysis of the tumour-associated macrophages (TAMs) recruited by TGFβ revealed that they are highly phagocytic, poor at antigen presentation (based on major histocompatibility complex-II and CD86 expression) and are associated with a decreased number of tumour-infiltrating dendritic cells. The authors conclude that TGFβ-recruited TAMs dramatically reduce the ability of dendritic cells to present tumour-associated antigens to the immune system, and suggest that TGFβ represents a good target for cancer immunotherapy. Dr Byrne completed his PhD degree at the University of Sydney in 2002, part of his PhD studies forming the basis of his award-winning paper. He then worked at The MD Anderson Cancer Center in Houston, TX as a CJ Martin Research Fellow. There, he continued his studies, which commenced during his PhD, into the cellular mechanisms underlying ultraviolet-induced immunosuppression. He discovered that one mechanism by which ultraviolet causes immune suppression is through the activation of suppressor B cells in the lymph nodes draining the irradiated skin site. Currently Dr Byrne is a Cancer Institute NSW Senior Research Fellow and cellular immunologist at The University of Sydney. His research group is interested in analysing how the ultraviolet part of the solar spectrum alters the immune outcome in such a way that immune regulation or suppression occurs instead of immune activation. These studies are important because immune suppression is one of the main contributors to the development of skin cancer. Understanding the cellular and molecular mechanisms underlying ultraviolet-induced immune regulation is also important for the study of diseases such as autoimmune disorders and for the success of immunization strategies. There is no doubt that Dr Byrne's award-winning paper highlights the high standard of papers being published in ICB and, I hope, will encourage others to submit their outstanding research to the journal.
A Human-Aware Manipulation Planner (2012)

With recent advances in safe and compliant hardware and control, robots are close to finding their places in our homes. As the safety barrier between humans and robots is beginning to fade, the necessity to design pertinent robot behavior in human environments is becoming a crucial step. In order to obtain a safe, comfortable, and socially acceptable interaction, the robot should be engineered from top to bottom by considering the presence of the human. In this paper, we present a manipulation planning framework and its implementation human-aware manipulation planner. This planner generates paths not only safe but comfortable and “socially acceptable” as well by reasoning explicitly on human's kinematics, vision field, posture, and preferences. The planner, which is applied into “robot handing over an object” scenarios, breaks the human centric interaction that depends mostly on human effort and allows the robot to take initiative by computing automatically where the interaction takes place, thus decreasing the cognitive weight of interaction on human side.
Palladium-Catalyzed Carbon Dioxide Elimination−Fixation Reaction of 4-Methoxycarbonyloxy-2-buten-1-ols (2004)

A new type of palladium-catalyzed CO(2) recycling reaction using allylic carbonates is described. Reaction of trans-4-methoxycarbonyloxy-2-buten-1-ols in the presence of a palladium catalyst produces cyclic carbonates having a vinyl group via a CO(2) elimination-fixation process. A variety of allylic carbonates participate in the reaction giving cyclic carbonates with high efficiencies. Stereoselective construction of trans-cyclic carbonates is achieved by using nonsymmetric substrates. An enantiospecific reaction proceeds to give chiral cyclic carbonate when a chiral methyl-substituted substrate is subjected to the reaction conditions.
Rabbit Ig <i>kappa</i> 1b6 gene structure. (1990)

Previous studies employing Southern blot analyses have detected multiple kappa-homologous sequences within EcoRI-digested DNA isolated from kappa 1b6 homozygous rabbits and kappa 1b6 L chain secreting RMH H158 cell line. These results are very unexpected because the published partial protein sequence for the kappa 1b6 C region is incompatible with an EcoRI restriction endonuclease recognition sequence at the nucleotide level for this allotype. To determine their identity, the kappa-homologous sequences were isolated from DNA extracted from a kappa 1b6 L chain secreting RMH H158 cell line by molecular cloning. Structural analyses demonstrated these sequences to contain genetic information encoding the majority of the kappa 1b6 L chain gene locus. The protein sequence deduced from the kappa 1b6 C region gene was shown to differ from the published partial kappa 1b6 C region protein sequence at five amino acid positions. One of these differences results in a glycine to serine interchange that introduces an EcoRI restriction endonuclease recognition site within the kappa 1b6 C region gene. Subsequent genomic Southern blot analyses confirmed this structural assignment. Based on these data, the EcoRI-sensitive kappa-homologous fragments present within the genomes of the RMH H158 cell line and kappa 1b6 homozygous rabbits represent the nominal kappa 1 gene and not an alternative kappa isotype or kappa pseudogene. Rabbit Ig kappa 1 allelic nucleotide sequence homology comparisons have shown the isolated kappa 1b6 J-C gene locus to display common structural features previously identified in other kappa 1 alleles.
Comment (1973)

CALL IT what you will, serendipity, accident, fortuitous chance, but add it to coincidence and together they will take some beating. This was brought home to me recently when browsing through fifty year old files of The Nation and The Athenaeum . In a vague search for something entirely different my eye was attracted by the heading, ‘The woman librarian’, a somewhat inelegant title to a longish letter to the editor sent by Dr Ernest A Baker on the occasion of a discussion at University College London conducted by Miss Marian Frost. Librarian at Worthing, who was at that time one of the sixteen women chief librarians in the country. And then, the very next day, there appeared in the November issue of NLW a note about the potential qualities of women librarians first published in 1889.
GMP-Compliant, Large-Scale Expanded Allogeneic Natural Killer Cells Have Potent Cytolytic Activity against Cancer Cells In Vitro and In Vivo (2013)

Ex vivo-expanded, allogeneic natural killer (NK) cells can be used for the treatment of various types of cancer. In allogeneic NK cell therapy, NK cells from healthy donors must be expanded in order to obtain a sufficient number of highly purified, activated NK cells. In the present study, we established a simplified and efficient method for the large-scale expansion and activation of NK cells from healthy donors under good manufacturing practice (GMP) conditions. After a single step of magnetic depletion of CD3(+) T cells, the depleted peripheral blood mononuclear cells (PBMCs) were stimulated and expanded with irradiated autologous PBMCs in the presence of OKT3 and IL-2 for 14 days, resulting in a highly pure population of CD3(-)CD16(+)CD56(+) NK cells which is desired for allogeneic purpose. Compared with freshly isolated NK cells, these expanded NK cells showed robust cytokine production and potent cytolytic activity against various cancer cell lines. Of note, expanded NK cells selectively killed cancer cells without demonstrating cytotoxicity against allogeneic non-tumor cells in coculture assays. The anti-tumor activity of expanded human NK cells was examined in SCID mice injected with human lymphoma cells. In this model, expanded NK cells efficiently controlled lymphoma progression. In conclusion, allogeneic NK cells were efficiently expanded in a GMP-compliant facility and demonstrated potent anti-tumor activity both in vitro and in vivo.
Dibenzotropylidene phosphanes (TROPPs): synthesis and coinage metal complexes (1998)

Dibenzocycloheptatrienyl phosphanes (dibenzotropylidene phosphanes=TROPPR) 11a–c may be easily prepared from dibenzocycloheptatrienyl chloride 8 and the secondary phosphanes R2PH [9a: R=Ph; 9b: R=4-Me-C6H4; 9c: R=cyclohexyl (Cyc)] in good yields. Alternatively, the di(tert-butyl)phosphanyl substituted TROPPBut derivative 4 was obtained along with the phosphane 5 by a mechanistically still unknown rearrangement of a strained phosphorus ylide I. The conformations of these new phosphanes were established by X-ray analyses performed for the compounds TROPPBut4 and TROPPPh11a. The R2P moiety is bonded to an axial position of the central seven-membered ring, which adopts a boat conformation. Thereby a rigid concave binding site containing a phosphane and an olefin function is formed, which should allow the synthesis of a wide range of transition metal complexes. In order to test how far the particular shape of the TROPP-type ligands enforces metal–olefin interactions, the coinage metal complexes [(TROPPPh)Cu(µ2-Cl)]2, 13, [(TROPPPh)Ag(µ2-O2SOCF3)]2, 16, [(TROPPPh)2Ag][O3SCF3], 17 and [(TROPPPh)AuCl], 19 were prepared. These were completely characterized by multinuclear NMR experiments in solution and the solid state, as well as by X-ray analyses. The structural and NMR data show that the interaction between the metal center M and the olefin moiety of the TROPP ligand is weak and decreases in the order Cu>Ag>Au. Indeed, for 19 (M=Au) no interaction could be observed. In the silver complex 17, coupling between an Ag nucleus and a proton of a bonded olefin was determined for the first time [J(109/107AgH)=0.4 Hz]. In solution the complexes derived from TROPP-type ligands seem to have an enhanced (kinetic) stability.
Predominant Rab-GTPase amplicons contributing to oral squamous cell carcinoma progression to metastasis (2015)

Metastatic oral squamous cell carcinoma (OSCC) is frequently associated with recurrent gene abnormalities at specific chromosomal loci. Here, we utilized array comparative genomic hybridization and genome-wide screening of metastatic and non-metastatic tongue tumors to investigate genes potentially contributing to OSCC progression to metastasis. We identified predominant amplifications of chromosomal regions that encompass the RAB5, RAB7 and RAB11 genes (3p24-p22, 3q21.3 and 8p11-12, respectively) in metastatic OSCC. The expression of these Rab GTPases was confirmed by immunohistochemistry in OSCC tissues from a cohort of patients with a follow-up of 10 years. A significant overexpression of Rab5, Rab7 and Rab11 was observed in advanced OSCC cases and co-overexpression of these Rabs was predictive of poor survival (log-rank test, P = 0.006). We generated a Rab interaction network and identified central Rab interactions of relevance to metastasis signaling, including focal adhesion proteins. In preclinical models, mRNA and protein expression levels of these Rab members were elevated in a panel of invasive OSCC cell lines, and their down-regulation prevented cell invasion at least in part via inhibition of focal adhesion disassembly. In summary, our results provide insights into the cooperative role of Rab gene amplifications in OSCC progression and support their potential utility as prognostic markers and therapeutic approach for advanced OSCC.
A self-organised layered superstructure of arrayed [2]pseudorotaxanes (1994)

A [2]pseudorotaxane, built up from a macrocyclic cyclophane containing two atomatic π-acceptors and an acyclic molecular containing three aromatic π-donors, has the ability to undergo self-organisation on crystallisation to form a layered superstructure of arrayed [2]pseudorotaxanes.
Experimental Analysis of Vapor HF Etch Rate and Its Wafer Level Uniformity on a CMOS-MEMS Process (2016)

This paper presents the characterization results of the release step with vapor hydrofluoric acid on a Complementary Metal Oxide Semiconductor-Microelectromechanical Systems (CMOS-MEMS) process obtained with a new methodology for controlling the release etch process of CMOS-MEMS devices. The effect of release hole size on etch rate and uniformity was investigated. No appreciable effects were observed for release hole sizes between 0.48 and 1 μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . With-in-wafer uniformity better than 3% and wafer-to-wafer variability better than 2.5% were found, while achieving constant etch rates of ~0.25 μmmin <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> and maintaining the required selectivity. The new characterization methodology is based on monitoring capacitance values of a set of test structures distributed across the analyzed wafers rather than monitoring oxide undercuts. A new parameter defined as etch ratio greatly improved the accuracy of this methodology by removing undesirable contributions to the capacitance coming from sources not related to the release process itself. Results showed that this methodology provides a characterization accuracy one order of magnitude better than what was achieved with a method based on optical measurements of oxide lateral undercuts.
The Norepinephrine Transporter Inhibitor Reboxetine Reduces Stimulant Effects of MDMA (“Ecstasy”) in Humans (2011)

This study assessed the pharmacodynamic and pharmacokinetic effects of the interaction between the selective norepinephrine (NE) transporter inhibitor reboxetine and 3,4-methylenedioxymethamphetamine (MDMA, "ecstasy") in 16 healthy subjects. The study used a double-blind, placebo-controlled crossover design. Reboxetine reduced the effects of MDMA including elevations in plasma levels of NE, increases in blood pressure and heart rate, subjective drug high, stimulation, and emotional excitation. These effects were evident despite an increase in the concentrations of MDMA and its active metabolite 3,4-methylenedioxyamphetamine (MDA) in plasma. The results demonstrate that transporter-mediated NE release has a critical role in the cardiovascular and stimulant-like effects of MDMA in humans.
Locked versus Nonlocked Plate Fixation for Hallux MTP Arthrodesis (2011)

As locked plate technology continues to gain popularity for procedures in the foot, it is important that clinical outcomes are reported. Locked titanium plates were associated with higher nonunion rates. Improved plate design, patient selection, and an understanding of plate biomechanics in this unique loading environment may optimize future outcomes for hallux MTP arthrodesis.
Molecular cloning of a human histocompatibility antigen cDNA fragment. (1980)

A clone (pHLA-1) containing HLA-specific cDNA was constructed by reverse transcription of partially purified HLA mRNA from the human lymphoblastoid cell line LKT. The identity of pHLA-1 was established by its ability to hybridize to HLA heavy chain mRNA and by nucleotide sequence analysis. The pHLA-1 cDNA insert (approximately 525 base pairs) corresponds to the COOH-terminal 46 amino acids of an HLA-A, -B, or -C antigen (15 residues from the hydrophobic region and the remainder from the COOH-termial hydrophilic region), together with a portion of the 3' untranslated region of the mRNA.
Safety and immunogenicity of oral killed whole cell recombinant B subunit cholera vaccine in Barranquilla, Colombia. (1995)

In January and February 1992, an assessment was conducted of the safety and immunogenicity of two doses of a new oral cholera vaccine prepared from the recombinant B subunit of the toxin and from killed whole cells (rBS/WC) in 1,165 individuals between the ages of 12 months and 64 years in Barranquilla, Colombia. This was a randomized, double-blind placebo-controlled study. Participants received two doses of either the vaccine or a placebo (killed Escherichia coli K12) over a two-week interval. Few symptoms were detected during the three days following administration of the initial dose and even fewer following the second. Sera obtained upon administration of the first dose and two weeks after administration of the second were tested for Vibrio cholerae 01 Inaba vibriocidal antibodies and antitoxins. Geometric mean titers (GMT) of vibriocidal antibodies were found to increase two-fold in subjects receiving the vaccine. In the paired samples taken from vaccinated subjects, two-fold or greater increases were observed in 44% and four-fold or greater increases were observed in 34%, as compared to similar increases in 9.2% and 2.2% of the sera taken from those receiving the placebo (P < 0.05). The GMTs of IgG and IgA antitoxins, as determined by ELISA, increased by factors of 4 and 3.2, respectively, in those receiving the vaccine, as compared to factors of 1.1 and 1.1 in those given the placebo (P < 0.001 for IgG, P < 0.01 for IgA). Approximately 80% of the paired samples from the vaccinated group showed an increase of both IgG and IgA antitoxins > or = 1.5, as compared to only about 20% of those in the placebo group (P < 0.000001). Belonging to the O blood group did not significantly affect the immune response. Children under age four tended to show a weaker vibriocidal antibody response and a stronger antitoxin response than older subjects. The two doses of oral vaccine were found to be safe and without attributable side-effects. The vibriocidal antibody and antitoxin responses were similar to those obtained previously with the conventional oral killed whole cell B subunit cholera vaccine.