gebhart/patrepeval huggingface dataset:
Lack of terminally differentiated tumor-specific CD8+ T cells at tumor site in spite of antitumor immunity to self-antigens in human metastatic melanoma. (2003)

Activation of CTL-mediated antitumor immunity to self-epitopes expressed by neoplastic cells is thought to be prevented, at any stage of tumor progression, by tolerance mechanisms. In contrast, in 74 American Joint Committee on Cancer stages I-IV melanoma patients, we found that development of lymph node metastases is a key event triggering CD8(+) T-cell-mediated immunity to self-epitopes encoded by melanocyte differentiation antigens. This was shown by the increased peripheral precursor frequency to Melan-A/Mart-1, gp100, and tyrosinase epitopes in stage III and IV compared with stage I and II patients, and by accumulation of functional memory T cells directed to Melan-A/Mart-1(26-35) in tumor-invaded lymph nodes. However, in tumor-invaded lymph nodes of most patients, CD8(+) T cells directed to melanocyte differentiation antigens or to tumor-restricted antigens (MAGE-3 and NY-ESO-1 epitopes), showed a CCR7(+) CD45RA(+) CD27(+) CD28(+) perforin(-) "precursor" phenotype. Only in 7 of 23 cases antigen-specific CD8(+) T cells in invaded lymph nodes showed a predominant CCR7(-) CD45RA(-) CD27(+) CD28(-) perforin(+) "preterminally differentiated" phenotype. In the latter subset of patients, by immunohistochemistry in lymph node lesions, we found that CD8(+) T lymphocytes intermingling with the neoplastic tissue expressed a CCR7(-) CD45RO(+)/RA(-) phenotype, whereas CD4(+) lymphocytes did not infiltrate the tumor. Furthermore, perforin and granzyme B were expressed on a higher fraction of the CD8(+) cells surrounding the invading tumor compared with the lymphocytes infiltrating the neoplastic tissue. In addition, no evidence for tumor regression was found in such metastatic lesions, as documented by absence of neoplastic cell necrosis or apoptosis. These data indicate that neoplastic cells in the lymph nodes and/or increased tumor burden in metastatic disease activate CD8(+) T-cell-mediated antitumor immunity to self-epitopes. However, the paucity of terminally differentiated CD8(+) T cells at tumor site suggests that immunotherapy strategies may require not only the boosting of tumor immunity, but also effective means to promote CD8(+) T-cell differentiation in the neoplastic tissue.
Proteolysis of Fodrin (Non-erythroid Spectrin) during Apoptosis (1995)

Several recent studies have implicated proteases as important triggers of apoptosis. Thus far, substrates that are cleaved during apoptosis have been elusive. In this report we demonstrate that cleavage of alpha-fodrin (non-erythroid spectrin) accompanies apoptosis, induced by activation via the CD3/T cell receptor complex in a murine T cell hybridoma, ligation of the Fas (CD95) molecule on a human T cell lymphoma line and other Fas-expressing cells, or treatment of cells with staurosporine, dexamethasone, or synthetic ceramide. Furthermore, inhibition of activation-induced apoptosis by pretreatment of T hybridoma cells with antisense oligonucleotides directed against c-myc also inhibited fodrin proteolysis, confirming that this cleavage process is tightly coupled to apoptosis. Fodrin cleavage during apoptosis may have implications for the membrane blebbing seen during this process.
A Novel Approach to the Discovery of Small‐Molecule Ligands of CDK2 (2012)

In an attempt to identify novel small-molecule ligands of cyclin-dependent kinase 2 (CDK2) with potential as allosteric inhibitors, we have devised a robust and cost-effective fluorescence-based high-throughput screening assay. The assay is based on the specific interaction of CDK2 with the extrinsic fluorophore 8-anilino-1-naphthalene sulfonate (ANS), which binds to a large allosteric pocket adjacent to the ATP site. Hit compounds that displace ANS directly or indirectly from CDK2 are readily classified as ATP site binders or allosteric ligands through the use of staurosporine, which blocks the ATP site without displacing ANS. Pilot screening of 1453 compounds led to the discovery of 12 compounds with displacement activities (EC(50) values) ranging from 6 to 44 μM, all of which were classified as ATP-site-directed ligands. Four new type I inhibitor scaffolds were confirmed by X-ray crystallography. Although this small compound library contained only ATP-site-directed ligands, the application of this assay to large compound libraries has the potential to reveal previously unrecognized chemical scaffolds suitable for structure-based design of CDK2 inhibitors with new mechanisms of action.
3D photonic metamaterials and invisibility cloaks: The making of (2011)

We review our recent experimental progress regarding fabricating truly three-dimensional photonic metamaterials and transformation optics structures using direct laser writing (DLW). Recently, stimulated-emission depletion (STED) inspired approaches have made DLW to an essentially diffraction-unlimited optical-lithography approach.
A New Robust Approach for Hole Cleaning to Improve Rate of Penetration (2018)

Abstract Hole cleaning evaluation and prediction presents a challenge in drilling industry. The optimization of hole cleaning can reduce the down time during drilling operations. Good hole cleaning means high rate of penetration and less drilling problems. In this paper, a robust hole cleaning model is presented. It is based on monitoring and controlling simultaneously the carrying capacity index (CCI) and the cuttings concentration in the annulus (CCA) to ensure perfect hole cleaning. The cost of drilling can increase tremendously if not enough attention is paid to ensure proper hole cleaning. The knowledge of the size of cuttings, size of annulus, flow pattern, and down hole fluid properties cannot be determined with high level of accuracy using hole cleaning indicators such as transport ratio, hole cleaning ratio or transport index. Cutting concentration in annulus (CCA) alone cannot reveal the drilling mud properties, while the application of CCI alone will not help in optimizing ROP to the desired limit. The drilling parameters and mud rheological properties in certain hole sections were collected and analyzed first to determine the effect of mud properties and drilling parameters on hole cleaning and ROP performance. The data selected are from the same hole size, formation type and mud type. The relationship between mud rheological properties and CCI was then evaluated to determine how strong they are. This step helps determine the significance of mud rheological properties on estimating CCI. CCI and CCA were then simultaneously monitored and controlled to ensure proper hole cleaning leading to optimization of the Drilling operations and reduction in the drilling time. The data analysis demonstrated a strong link between rheological parameters and CCI. The approach was then validated by trial testing it in the field. The results showed that efficient hole cleaning level was achieved, which facilitated improvement of rate of penetration. It was used to drill in challenging hole sections and improved the well drilling performance by more than 55%, mitigated stuck pipe incidents, and eliminated wiper trips, reaming trips, and pumping of sweeps. The new approach or hole cleaning model showed the importance of combining CCI and CCA to optimize the drilling operations and reduce the time. This is the first time to combine the two techniques for hole cleaning optimization. The new hole cleaning model will help the drilling engineers drill a clean, stable hole in short time, and hence reduce the total cost of the drilling operations.
THE ADJUVANT EFFECT OF MICROBIAL PRODUCTS ON THE IMMUNE RESPONSE (1976)

As the case currently stands, President Roosevelt does not believe that it will be necessary to dismiss Miller and would need stronger evidence of the matter between him and the trades union.
Application of menthol to the skin of whole trunk in mice induces autonomic and behavioral heat-gain responses (2007)

When ambient temperature is decreased in mammals, autonomic and behavioral heat-gain responses occur to maintain their core temperatures. However, what molecules in cutaneous sensory nerve endings mediate cooling-induced responses is unclear. Recently, transient receptor potential melastatin-8 (TRPM8) has been identified in cell bodies of sensory neurons as low-temperature and menthol-activated cation channel. We hypothesized that TRPM8 mediates cooling-induced autonomic and behavioral heat-gain responses. To activate TRPM8 specifically, we applied 1-10% menthol to the skin of whole trunk in mice instead of cooling and measured core temperatures and autonomic and behavioral heat-gain responses. Solvent of menthol (100% ethanol) was used as control. Significant elevation of core temperatures was observed between 20 and 120 min after menthol application. Pretreatment with diclofenac sodium, an antipyretic drug, did not affect this hyperthermia, indicating that the menthol-induced hyperthermia is not fever. Menthol application induced a rise in oxygen consumption, shivering-like muscle activity, tail skin vasoconstriction (autonomic responses), and heat-seeking behavior. All of them are typical heat-gain responses. These results support the hypothesis that TRPM8 mediates cooling-induced autonomic and behavioral heat-gain responses.
Signaling through Purinergic Receptors for ATP Induces Human Cutaneous Innate and Adaptive Th17 Responses: Implications in the Pathogenesis of Psoriasis (2013)

Human cutaneous dendritic cells (DCs) have the ability to prime and bias Th17 lymphocytes. However, the factors that stimulate cutaneous DCs to induce Th17 responses are not well known. Alarmins, such as ATP, likely play a pivotal role in the induction and maintenance of cutaneous immune responses by stimulating DC maturation, chemotaxis, and secretion of IL-1β and IL-6, Th17-biasing cytokines. In this study, using a well-established human skin model, we have demonstrated that signaling purinergic receptors, predominantly the P2X7 receptor (P2X7R), via an ATP analog initiate innate proinflammatory inflammation, DC17 differentiation, and the subsequent induction of Th17-biased immunity. Moreover, our results suggest a potential role for P2X7R signaling in the initiation of psoriasis pathogenesis, a Th17-dependent autoimmune disease. In support of this, we observed the increased presence of P2X7R in nonlesional and lesional psoriatic skin compared with normal healthy tissues. Interestingly, there was also a P2X7R variant that was highly expressed in lesional psoriatic skin compared with nonlesional psoriatic and normal healthy skin. Furthermore, we demonstrated that psoriatic responses could be initiated via P2X7R signaling in nonlesional skin following treatment with a P2X7R agonist. Mechanistic studies revealed a P2X7R-dependent mir-21 angiogenesis pathway that leads to the expression of vascular endothelial growth factor and IL-6 and that may be involved in the development of psoriatic lesions. In conclusion, we have established that purinergic signaling in the skin induces innate inflammation, leading to the differentiation of human Th17 responses, which have implications in the pathogenesis and potential treatment of psoriasis.
Expression of proteinase-activated receptor-2 in human pancreatic cancer: A possible relation to cancer invasion and induction of fibrosis (2003)

The proteinase-activated receptor-2 (PAR-2) is a G protein-coupled receptor that is cleaved and activated by trypsin. To clarify the presence of PAR-2 in human pancreatic cancer, the expression of PAR-2 was analyzed by RT-PCR, immunoblotting and immunocytochemistry using 5 human pancreatic cancer cell lines. And to evaluate the biological significance, immunohistochemical expression of PAR-2 in malignant and non-malignant human pancreatic tissues was examined using paraffin-embedded sections. The presence of PAR-2 was confirmed in all 5 pancreatic cancer cell lines and all 21 paraffin-embedded specimens from human pancreatic cancer examined. The expression of PAR-2 was found to be higher in the tissues with infiltrative growth pattern than those with expansive growth pattern. Moreover, significantly higher expression of PAR-2 was observed in the tissues which were accompanied by severe fibrosis. Even in the same specimen, the intensity of immunoreactivity tended to be stronger in the part with severe fibrosis than that with mild fibrosis. Similarly, the higher expression of PAR-2 was observed in chronic pancreatitis with severe fibrosis than with mild fibrosis. Taken together, these results suggest that the activation of PAR-2 is involved in cancer invasion and the induction of fibrosis in human pancreatic cancer.
Decreased number of mast cells infiltrating into needle biopsy specimens leads to a better prognosis of prostate cancer (2007)

Mast cell infiltration is often observed around human tumours. Inflammatory cells such as macrophages, neutrophils and mast cells infiltrating around tumours are known to contribute to tumour growth; however, the clinical significance of mast cell invasion in prostate cancer (PCa) has not been investigated. Mast cell infiltration was evaluated in 104 patients (age range, 45-88 years; median, 72 years), who underwent needle biopsy of the prostate and were confirmed to have PCa. Needle biopsy specimens of prostate were sliced into 5-microm-thick sections and immunostained for mast cells with monoclonal antibody against mast cell-specific tryptase. Mast cells were counted systematically under a microscope (x 400 magnification), and the relations between mast cell numbers and clinicopathologic findings were evaluated. The mast cell count was evaluated for prognostic value by multivariate analysis. Mast cells were immunostained around the cancer foci. The median number of mast cells in each case was 16. The mast cell count was higher around cancer foci in patients with higher Gleason scores than in those with low Gleason scores. The mast cell number correlated well with clinical stage (P<0.001). Prostate-specific antigen-free survival of patients with higher mast cell counts was better than that in patients with lower mast cell counts (P<0.001). Multivariate analysis revealed that mast cell count was a significant prognostic factor (P<0.005). The number of mast cells infiltrating around cancer foci in prostate biopsy specimens can be a significant prognostic factor of PCa.
Imaging endogenous gene expression in brain cancer in vivo with 111In-peptide nucleic acid antisense radiopharmaceuticals and brain drug-targeting technology. (2004)

Imaging endogenous gene expression in vivo with PNA antisense radiopharmaceuticals is possible if drug-targeting technology is used. Attachment of the PNA antisense agent to the targeting ligand enables the antisense radiopharmaceutical to traverse biologic membrane barriers and access intracellular target mRNA molecules.
N-TERMINAL AMINO ACID SEQUENCE OF HUMAN PREGNANCY-ASSOCIATED ENDOMETRIAL α-GLOBULIN, AN ENDOMETRIAL INSULINLIKE GROWTH FACTOR (IGF) BINDING PROTEIN - EVIDENCE FOR TWO SMALL MOLECULAR WEIGHT IGF BINDING PROTEINS* (1988)

We have previously demonstrated that quantitatively the major secretory protein of the human endometrium from the latter half of the first trimester of pregnancy, pregnancy-associated endometrial alpha 1-globulin (alpha 1-PEG), is a small mol wt insulin-like growth factor binding protein (IGF BP) and is detected at high levels in amniotic fluid. N-terminal amino acid sequences have been determined for this protein purified from both these sources and a single N-terminal amino acid sequence Ala Pro Trp Gln Cys Ala Pro Cys Ser Ala Glu Lys Leu Ala Leu Pro Pro was obtained. The first ten residues are identical to those previously reported for the small mol wt IGF BP isolated from amniotic fluid and HEPG2 culture medium. However it was different to that reported for the IGF BP isolated from term placenta, placental protein 12 (PP12), a protein previously suggested to originate in the endometrium. These data suggest that at least two distinct forms of the small mol wt IGF BP exist and supports the hypothesis that the amniotic fluid form originates from the pregnancy endometrium.
Bioinformatic analysis of expressed sequence tags derived from a compatible Alternaria brassicicola – Brassica oleracea interaction (2006)

SUMMARY Alternaria brassicicola is a necrotrophic fungal pathogen that causes black spot disease on members of the Brassicaceae plant family. In order to identify candidate fungal pathogenicity genes and characterize a compatible host response, a suppression subtractive hybridization (SSH) cDNA library enriched for A. brassicicola and Brassica oleracea genes expressed during the interaction was created, along with a fungal cDNA library representing genes expressed during nitrogen starvation (NS). A total of 3749 and 2352 expressed sequence tags (ESTs) were assembled into 2834 and 1264 unisequence sets for the SSH and NS libraries, respectively. We compared two methods to identify the origins (plant vs. fungal) of ESTs in the SSH library using different classification procedures, with and without the availability of a database representing the A. brassicicola whole genome sequence and Brassicaceae-specific genes. BLASTX analyses of the 2834 unisequence set using the GenBank non-redundant database identified 114 fungal genes. Further BLASTN analyses of the genes with unidentifiable origin using a database consisting of the 1264 fungal unisequence set from the nitrogen-starved library identified 94 additional fungal genes. By contrast, BLASTN analyses of the same SSH unisequence set using a partially assembled A. brassicicola whole genome draft sequence identified a total of 310 unisequenes of fungal origin. Our results indicated that even a small number of organism-specific EST sequences can be very helpful to identify pathogen genes in a library derived from infected tissue, partially overcoming the limitation of the public databases for little studied organisms. However, using the whole genome draft sequence of A. brassicicola we were able to identify approximately 30% more fungal genes in the SSH library than without utilizing this resource. The putative role of specific fungal and plant genes identified in this study in a compatible interaction is discussed.
A novel targeting modality to enhance adenoviral replication by vitamin D(3) in androgen-independent human prostate cancer cells and tumors. (2002)

We report the development of a novel replication-competent adenoviral vector, Ad-hOC-E1, containing a single bidirectional human osteocalcin (hOC) promoter to drive both the early viral E1A and E1B gene. This vector selectively replicated in OC-expressing but not non-OC-expressing cells, with viral replication enhanced at least 10-fold on vitamin D(3) exposure. Both the artificial TATA-box and hOC promoter element in this bidirectional promoter construct were controlled by a common OC regulatory element which selectively activated OC expression in cells. The expression ofE1A and E1B gene by Ad-hOC-E1 can be markedly induced by vitamin D(3). Unlike Ad-sPSA-E1, an adenoviral vector with viral replication controlled by a strong super prostate-specific antigen (sPSA) promoter which only replicates in PSA-expressing cells with androgen receptor (AR), Ad-hOC-E1 retarded the growth of both androgen-dependent and androgen-independent prostate cancer cells irrespective of their basal level of AR and PSA expression. A single i.v. administration of 2 x 10(9) plaque-forming units of Ad-hOC-E1 inhibited the growth of previously established s.c. DU145 tumors (an AR- and PSA-negative cell line). Viral replication is highly enhanced by i.p. administration of vitamin D(3). Ultimately, enhancing Ad-hOC-E1 viral replication by vitamin D(3) may be used clinically to treat localized and osseous metastatic prostate cancer in men.
A Conformational Change in the Adeno-Associated Virus Type 2 Capsid Leads to the Exposure of Hidden VP1 N Termini (2005)

The complex infection process of parvoviruses is not well understood so far. An important role has been attributed to a phospholipase A2 domain which is located within the unique N terminus of the capsid protein VP1. Based on the structural difference between adeno-associated virus type 2 wild-type capsids and capsids lacking VP1 or VP2, we show via electron cryomicroscopy that the N termini of VP1 and VP2 are involved in forming globules inside the capsids of empty and full particles. Upon limited heat shock, VP1 and possibly VP2 become exposed on the outsides of full but not empty capsids, which is correlated with the disappearance of the globules in the inner surfaces of the capsids. Using molecular modeling, we discuss the constraints on the release of the globularly organized VP1-unique N termini through the channels at the fivefold symmetry axes outside of the capsid.
Comparison of non-canonical PAMs for CRISPR/Cas9-mediated DNA cleavage in human cells (2014)

CRISPR/Cas9-mediated DNA cleavage (CCMDC) is becoming increasingly used for efficient genome engineering. Proto-spacer adjacent motif (PAM) adjacent to target sequence is one of the key components in the design of CCMDC strategies. It has been reported that NAG sequences are the predominant non-canonical PAM for CCMDC at the human EMX locus, but it is not clear whether it is universal at other loci. In the present study, we attempted to use a GFP-reporter system to comprehensively and quantitatively test the efficiency of CCMDC with non-canonical PAMs in human cells. The initial results indicated that the effectiveness of NGA PAM for CCMDC is much higher than that of other 14 PAMs including NAG. Then we further designed another three pairs of NGG, NGA and NAG PAMs at different locations in the GFP gene and investigated the corresponding DNA cleavage efficiency. We observed that one group of NGA PAMs have a relatively higher DNA cleavage efficiency, while the other groups have lower efficiency, compared with the corresponding NAG PAMs. Our study clearly demonstrates that NAG may not be the universally predominant non-canonical PAM for CCMDC in human cells. These findings raise more concerns over off-target effects in CRISPR/Cas9-mediated genome engineering.
A Simple And Calibratable Method For The Determination Of Optimal Focus (1989)

Achieving a proper focus setting in sub-micron optical lithography is extremely important. A technique has been developed for the determination of optimal focus setting on production lots. Using aerial image simulation the dimensions of the test structure studied have been optimized. With a simple optical microscope a judgement can be made about the focus setting. As the depth of focus becomes comparable to the resist thickness, it was observed that different methods of focus determination do not give the same results.
Botulinum toxin (Dysport(R)) treatment of hip adductor spasticity in multiple sclerosis: a prospective, randomised, double blind, placebo controlled, dose ranging study (2000)

Dysport reduced the degree of hip adductor spasticity associated with multiple sclerosis, and this benefit was evident despite the concomitant use of oral antispasticity medication and analgesics. Although evidence for a dose response effect was not statistically significant, there was a clear trend towards greater efficacy and duration of effect with higher doses of Dysport. Dysport treatment was well tolerated, with no major side effects seen at doses up to 1500 Units. The optimal dose for hip adductor spasticity seems to be 500-1000 Units, divided between both legs.
INTRAVASCULAR LEUKOCYTE THROMBI AND AGGREGATES AS A CAUSE OF MORBIDITY AND MORTALITY IN LEUKEMIA (1974)

From Departments of Medicine and Pathology, Vanderbilt School of Medicine and Veterans Administration Hospital, Nashville, Tennessee 37203