gebhart/patrepeval huggingface dataset:
DNA‐binding proteins as site‐specific nucleases (1994)

DNA-binding proteins can be converted into site-specific nucleases by linking them to the chemical nuclease 1,10-phenanthroline-copper. This can be readily accomplished by converting a minor groove-proximal amino acid to a cysteine residue using site-directed mutagenesis and then chemically modifying the sulphydryl group with 5-iodoacetamido-1,10-phenanthroline-copper. These chimeric scission reagents can be used as rare cutters to analyse chromosomal DNA, to test predictions based on high-resolution nuclear magnetic resonance and X-ray crystal structures, and to locate binding sites of proteins within genomes.
Image-guided robotic navigation system for neurosurgery (2000)

This paper presents an image-guided robotic navigation system for neurosurgery, which can be applied to the electro-stimulation treatment of Parkinson's leisure, the biopsy of deep tumors, and haematoma evacuation. The system integrates a computer containing CT images for surgical planning, a magnetic tracking device for measuring the coordinates of the markers and surgical instruments, and a robot manipulator for guiding surgical instruments to the preplanned position and orientation. The computer display of brain anatomy offers a convenient tool for surgeons to diagnose brain diseases and to plan safe surgical paths, while the tracking device guides the robot manipulator to automatically move surgical instruments to the preplanned position and orientation. An experiment of using a skull model for simulating a robotic biopsy of brain tumor has been done to verify the performance of the robotic navigation system. The results show that the positioning accuracy of the robot relative to the tracker frame is only related to the positioning resolution of the robot manipulator and the positioning accuracy of the tracking device. In other words, the positioning accuracy of the robot manipulator does not affect the final positioning accuracy of the surgical instruments. Therefore, using a robot manipulator for precise surgical navigation is feasible and reliable. © 2000 John Wiley & Sons, Inc.
The prognostic significance of PD-L1 in bladder cancer (2015)

Immunotherapy is a promising strategy for the treatment of various types of cancer. An antibody that targets programmed death ligand-1 (PD-L1) pathway has been shown to be active towards various types of cancer, including melanoma and lung cancer. MPDL3280A, an anti-PD-L1 antibody, has shown clear clinical activity in PD-L1-overexpressing bladder cancer with an objective response rate of 40-50%, resulting in a breakthrough therapy designation granted by FDA. These events pronounce the importance of targeting the PD-L1 pathway in the treatment of bladder cancer. In the present study, we investigated the prognostic significance of the expression of three genes in the PD-L1 pathway, including PD-L1, B7.1 and PD-1, in three independent bladder cancer datasets in the Gene Expression Omnibus database. PD-L1, B7.1 and PD-1 were significantly associated with clinicopathological parameters indicative of a more aggressive phenotype of bladder cancer, such as a more advanced stage and a higher tumor grade. In addition, a high level expression of PD-L1 was associated with reduced patient survival. Of note, the combination of PD-L1 and B7.1 expression, but not other combinations of the three genes, were also able to predict patient survival. Our findings support the development of anti-PD-L1, which blocks PD-L1-PD-1 and B7.1-PD-L1 interactions, in treatment of bladder cancer. The observations were consistent in the three independent bladder cancer datasets consisting of a total of 695 human bladder specimens. The datasets were then assessed and it was found that the expression levels of the chemokine CC-motif ligand (CCL), CCL3, CCL8 and CCL18, were correlated with the PD-L1 expression level, while ADAMTS13 was differentially expressed in patients with a different survival status (alive or deceased). Additional investigations are required to elucidate the role of these genes in the PD-L1-mediated immune system suppression and bladder cancer progression. In conclusion, findings of this study suggested that PD-L1 is an important prognostic marker and a therapeutic target for bladder cancer.
Dependence of the Laser Two-Photon Ionization Process in Solution on the Laser Pulse Width (2001)

The laser two-photon ionization process has been investigated using simultaneous irradiation of an UV beam and an IR beam. When the laser pulse width was 300 ps, it proceeded through a geminate pair state (a stepwise process), as indicated by the signal enhancement with simultaneous irradiation of the two laser beams. Although no signal enhancement was observed when the laser pulse width was 100 fs, and because molecules with no absorption at the laser wavelength showed an intense signal, the two-photon ionization excited by a femtosecond laser should proceed through a simultaneous two-photon process. The detection limit was quite susceptible to the laser fluctuations.
The in situ carcinomas of the breast. (1993)

In situ carcinoma of the breast is being diagnosed with greater frequency on breast biopsies. Of the two types of CIS, lobular carcinoma in situ is considered a marker for increased risk of developing breast cancer in either breast, and treatment options are based on different philosophies of careful follow-up vs preventive surgery. Ductal carcinoma in situ is a direct precursor to invasive carcinoma and the variety of treatments available reflect the need to completely excise this lesion. Several trials are now in progress to define the roles of surgery, radiation, and hormonal manipulation in the treatment of both types of CIS.
High Frequencies of Functional Tumor-Reactive T Cells in Bone Marrow and Blood of Pancreatic Cancer Patients (2005)

Pancreatic cancer is characterized by aggressive growth and treatment resistance. New approaches include immunotherapeutic strategies but the type and extent of spontaneous immune responses against tumor antigens remains unclear. A dominance of TH2 cytokines in patients' sera reported previously suggests systemic tumor-induced immunosuppression, potentially inhibiting the induction of tumor-reactive T cells. We characterized the localization, frequencies, and functional potential of spontaneously induced memory T cells specific for individual tumor antigens or the tumor-associated antigen mucin-1 in the peripheral blood and bone marrow of 41 pancreatic cancer patients. We found high numbers of tumor-reactive T cells in all bone marrow samples and in 50% of the blood samples. These cells secreted the TH1 cytokine IFN-gamma rather than TH2 cytokines upon stimulation with tumor antigens. Although consistently induced during pancreatic cancer, T cells specific for pancreatic antigens were not detected during chronic pancreatitis, suggesting that their evaluation may be of diagnostic use in both diseases. Freshly isolated T cells from cancer patients recognized autologous tumor cells and rejected them in vitro and in a xenotransplant model in vivo, suggesting their therapeutic potential. Thus, tumor antigen-specific T cell responses occur regularly during pancreatic cancer disease and lead to enrichment of tumor cell-reactive memory T cells in the bone marrow. The bone marrow can therefore be considered an important organ for antitumor immune responses in pancreatic cancer.
Mode of action of 9-(4-hydroxy-3-hydroxymethylbut-1-yl)guanine (BRL 39123) against herpes simplex virus in MRC-5 cells (1989)

The metabolism and mode of action of 9-(4-hydroxy-3-hydroxymethylbut-1-yl)guanine (BRL 39123) were studied in herpes simplex virus type 1 (HSV-1)-infected and uninfected MRC-5 cells and compared with those of acyclovir. In uninfected cells incubated with 10 microM acyclonucleoside for 4 h, no phosphorylation of either BRL 39123 or acyclovir was detected. In contrast, in HSV-1-infected cells, both BRL 39123 and acyclovir were phosphorylated up to the triphosphate esters. Phosphorylation of BRL 39123 occurred much more rapidly and proceeded to a greater extent than did that of acyclovir. Furthermore, following the removal of acyclonucleoside from the culture medium, the intracellular triphosphate ester of BRL 39123 was much more stable than was that of acyclovir, the half-lives being about 10 and 0.7 h, respectively. BRL 39123 treatment effectively inhibited the formation of HSV-1 DNA in infected MRC-5 cells, 50% inhibitory concentrations of BRL 39123 and acyclovir being 0.04 microgram/ml (0.16 microM) and 0.15 microgram/ml (0.67 microM), respectively. In addition, BRL 39123 was shown to be more effective than acyclovir at inhibiting viral DNA synthesis following short treatment times, presumably reflecting the greater stability of BRL 39123 triphosphate. Neither BRL 39123 nor acyclovir inhibited cellular DNA synthesis in uninfected cells at concentrations of up to 100 micrograms/ml.
Learning human behaviors from motion capture by adversarial imitation (2017)

Rapid progress in deep reinforcement learning has made it increasingly feasible to train controllers for high-dimensional humanoid bodies. However, methods that use pure reinforcement learning with simple reward functions tend to produce non-humanlike and overly stereotyped movement behaviors. In this work, we extend generative adversarial imitation learning to enable training of generic neural network policies to produce humanlike movement patterns from limited demonstrations consisting only of partially observed state features, without access to actions, even when the demonstrations come from a body with different and unknown physical parameters. We leverage this approach to build sub-skill policies from motion capture data and show that they can be reused to solve tasks when controlled by a higher level controller.
Platelet adhesion onto segmented polyurethane surfaces modified by carboxybetaine (2003)

Polyurethanes are widely used as blood-contacting biomaterials due to their good biocompatibility and mechanical properties. Nevertheless, their blood compatibility is still not adequate for more demanding applications. Surface modification is an effective way to improve the hemocompatibility for biomaterials. The purpose of present study was to synthesize a novel nonthrombogenic biomaterial by modifying the surface of polyurethane with Zwitterions of carboxybetaine monomer. The films of polyurethane were grafted with two kinds of carboxybetaine by a three-step procedure. In the first step, the film surfaces were treated with hexamethylene diisocyanate (HDI) in toluene at 50 degrees C in the presence of di-n-butyl tin dilaurate (DBTDL) as a catalyst. The extent of the reaction was measured by ATR-FT-IR spectra: a maximum number of free NCO group was obtained after a reaction time of 90 min. In the second step, the hydroxyl group of N,N-dimethylethylethanolamine (DMEA) or 4-dimethylamino-1-butanol (DMBA) was allowed to react in toluene with isocyanate groups bound on surface. In the third step, carboxybetaines were formed in the surface through the ring-opening reaction between tertiary amine of DMEA or DMBA and beta-propiolactone (PL). It was characterized by ATR-FT-IR and XPS that the grafted surfaces were composed of carboxybetaine. The results of the contact angle measurements showed that they were strongly hydrophilic. Platelet adhesion tests showed that films grafted carboxybetaine have good blood compatibility, as featured by the low platelet adhesion.
Development of difluoromethylornithine as a chemoprevention agent for the management of colon cancer (1995)

Experimental studies have demonstrated that carcinogenesis is a multistep process in which inappropriate proliferation of cells is a critical determinant. Polyamines support sustained growth and are highly regulated in all cells. The rate limiting enzyme for this pathway is ornithine decarboxylase (ODC), an enzyme that exhibits rapid turnover, and converts the amino acid ornithine to putrescine, which in turn is converted to the longer chain amines spermidine and spermine. In animal models of colon carcinogenesis, inhibition of ODC by difluoromethylornithine (DFMO), an enzyme-activated irreversible inhibitor, reduces the number and size of colon adenomas and carcinomas. DFMO was first ineffective when used clinically to treat acute leukemia or melanoma and caused clinically significant but reversible ototoxicity. Subsequently, we performed a series of analyses demonstrating that hearing loss was rare below a total cumulative dose of 150 gm/m2 and increased with total cumulative dose of DFMO. The hearing loss was reversible with rapid reversion to baseline hearing. We and others have conducted Phase IIa trials to determine the lowest dose at which DFMO can decrease colon mucosa polyamine content, and found that an oral dose as low as 0.25 gm/m2 per day (perhaps lower) decreases colon tissue putrescine content and lowers the spermidine/spermine ratio. We are currently conducting a long-term randomized Phase IIb trial which serially measures the long-term effect of several low doses (and placebo) of DFMO on sustaining polyamine depletion in colon mucosa, as well as carefully monitoring hearing by audiometry and other sophisticated tests.(ABSTRACT TRUNCATED AT 250 WORDS)
Current status of SOD1 mutations in familial amyotrophic lateral sclerosis (2000)

Twenty percent of cases of familial amyotrophic lateral sclerosis (FALS) have identifiable mutations in the gene for Cu, Zn superoxide dismutase (SOD1) located on the long arm of chromosome 21. SOD1 mutations are thought to cause a yet unknown toxic gain of function resulting in motor neuron damage. Seventy-one mutations, located in all five exons of SOD1, have been reported. Identified mutations are predominantly heterozygous mis-sense mutations, although rare nonsense mutations, deletions, and insertions exist. While gene dosage has an effect on the age of onset, genotoype/phenotype correlation is better defined for progression of symptoms than for disease onset.
Puffs and PCR: the in vivo dynamics of early gene expression during ecdysone responses in Drosophila (1993)

The steroid hormone ecdysone orchestrates insect development by regulating gene networks. In Drosophila the most detailed description of ecdysone action is the sequential activation of early and late puffs in the polytene chromosomes of the late larval salivary gland. A number of these early puffs (2B5, 74EF and 75B) contain complex transcription units (Broad-Complex, E74 and E75 respectively) encoding families of regulatory proteins which are expressed in most if not all tissues. In vitro, transcripts of the different isoforms of these early genes as well as the ecdysone receptor (EcR) present varying dose response characteristics (Karim and Thummel, 1992, EMBO J. 11, 4083-4093). We have developed an in vivo approach using a reverse transcription-polymerase chain reaction assay (RT-PCR) so as to visualise these transcripts in the RNA extracted from a single salivary gland. Using one salivary gland lobe for developmental puff staging and the sister lobe for RT-PCR, we have obtained precise developmental profiles for these transcripts and have extended our study to other tissues and stages where puffing studies were not possible. In the salivary gland we have characterised three distinct ecdysone responses. For the mid and late third larval instar responses our results confirm and extend the conclusions of the in vitro studies concerning the temporal expression of the early gene isoforms. The relatively brief prepupal response contains elements in common with each of the larval responses and all three can be explained by the profiles of the respective ecdysone peaks. Interestingly EcR transcripts respond differently during each response. The analysis of different tissues of the same animal reveals subtle differences in the timing of the ecdysone response and isoform expression and suggests that this may reflect tissue differences in the ecdysone profiles. As these molecules have homologues in vertebrates, our analysis may have general implications for the organisation of hormonal responses in vivo.
Neuroepithelial carcinomas in mice transgenic with human papillomavirus type 16 E6/E7 ORFs. (1993)

The effect of the human papillomavirus (HPV) oncogenes E6 and E7 was examined in transgenic mice with a construct containing the human beta-actin promoter regulating HPV16 E6 and E7 open reading frames. In the sole line of mice that transmitted the transgene, neuroepithelial tumors appeared at 2.5 months of life, and by 10 months, 87 of 122 (71%) of the animals were dead from brain tumors. The most frequent type of tumor (74%) was an anaplastic neuroepithelial tumor associated with the ependyma of the third and fourth ventricles, which locally invaded adjacent brain tissue and spread for considerable distances along the ventricular surface. The other two types of tumor were well-differentiated choroid plexus carcinomas (26%) and rare pituitary carcinomas (8.7%). HPV16 E6 RNA and E7 oncoprotein expression were demonstrated in tumor tissue and primary cell lines derived from the tumors. Examination of two tumor suppressor gene products, the retinoblastoma protein and p53, known to bind to HPV16 E7 and E6 oncoproteins, respectively, showed both were expressed in the primary tumor cell lines. These data support a causative role for the HPV oncoproteins in epithelial carcinogenesis.
Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing (2013)

Here we demonstrate the use of short-read massive sequencing systems to in effect achieve longer read lengths through hierarchical molecular tagging. We show how indexed and PCR-amplified targeted libraries are degraded, sub-sampled and arrested at timed intervals to achieve pools of differing average length, each of which is indexed with a new tag. By this process, indices of sample origin, molecular origin, and degree of degradation is incorporated in order to achieve a nested hierarchical structure, later to be utilized in the data processing to order the reads over a longer distance than the sequencing system originally allows. With this protocol we show how continuous regions beyond 3000 bp can be decoded by an Illumina sequencing system, and we illustrate the potential applications by calling variants of the lambda genome, analysing TP53 in cancer cell lines, and targeting a variable canine mitochondrial region.
Nanoelectrospray Emitter Arrays Providing Interemitter Electric Field Uniformity (2008)

Arrays of electrospray ionization (ESI) emitters have been reported previously as a means of enhancing ionization efficiency or signal intensity. A key challenge when working with multiple, closely spaced ESI emitters is overcoming the deleterious effects caused by electrical interference among neighboring emitters. Individual emitters can experience different electric fields depending on their relative position in the array, such that it becomes difficult to operate all of the emitters optimally for a given applied potential. In this work, we have developed multi-nanoESI emitters arranged with a circular pattern, which enable the constituent emitters to experience a uniform electric field. The performance of the circular emitter array was compared to a single emitter and to a previously developed linear emitter array, which verified that improved electric field uniformity was achieved with the circular arrangement. The circular arrays were also interfaced with a mass spectrometer via a matching multicapillary inlet, and the results were compared with those obtained using a single emitter. By minimizing interemitter electric field inhomogeneities, much larger arrays having closer emitter spacing should be feasible.
Dominant interfering alleles define a role for c-Myb in T-cell development. (1994)

The transcription activator c-Myb is expressed at high levels in immature thymocytes and during T-cell activation and may be a regulator of T-cell differentiation. To investigate the role of c-Myb in T-cell development, we generated transgenic mice in which two dominant interfering Myb alleles, one a competitive inhibitor of DNA binding, and the other, an active repressor comprising the Myb DNA-binding domain linked to the Drosophila Engrailed transcription repressor domain, were expressed from early times onward in T cells. Both alleles partially blocked thymopoiesis and inhibited proliferation of mature T cells. The Myb-En chimera was the more efficient repressor and might serve as an archetype for the manufacture of other dominant interfering transcription factor alleles.
Successful Parenteral Penicillin Therapy of Established Lyme Arthritis (1985)

In a double-blind placebo-controlled trial carried out from 1980 to 1982, 20 patients with established Lyme arthritis were assigned treatment with 2.4 million U of intramuscular benzathine penicillin weekly for three weeks (total, 7.2 million U) and 20 patients received saline. Seven of the 20 penicillin-treated patients (35 per cent) had complete resolution of arthritis soon after the injections and have remained well during a mean follow-up period of 33 months. In contrast, all 20 patients given placebo continued to have attacks of arthritis (P less than 0.02). In 1983, of 20 patients treated with intravenous penicillin G, 20 million U a day for 10 days, 11 (55 per cent) had complete resolution of arthritis and have remained well since. As compared with nonresponders, penicillin-responsive patients in both studies were more likely to have previously received antibiotics for erythema chronicum migrans (P less than 0.02) and less likely to have been given intraarticular corticosteroids during or at the conclusion of parenteral therapy (P less than 0.1). The Lyme spirochete was not cultured from synovium or joint fluid. We conclude that established Lyme arthritis can often be treated successfully with parenteral penicillin. However, neither of the regimens that we tested is uniformly effective, and further experience will be needed to determine the optimal course of therapy.
A Differential Role for Macropinocytosis in Mediating Entry of the Two Forms of Vaccinia Virus into Dendritic Cells (2010)

Vaccinia virus (VACV) is being developed as a recombinant viral vaccine vector for several key pathogens. Dendritic cells (DCs) are specialised antigen presenting cells that are crucial for the initiation of primary immune responses; however, the mechanisms of uptake of VACV by these cells are unclear. Therefore we examined the binding and entry of both the intracellular mature virus (MV) and extracellular enveloped virus (EV) forms of VACV into vesicular compartments of monocyte-derived DCs. Using a panel of inhibitors, flow cytometry and confocal microscopy we have shown that neither MV nor EV binds to the highly expressed C-type lectin receptors on DCs that are responsible for capturing many other viruses. We also found that both forms of VACV enter DCs via a clathrin-, caveolin-, flotillin- and dynamin-independent pathway that is dependent on actin, intracellular calcium and host-cell cholesterol. Both MV and EV entry were inhibited by the macropinocytosis inhibitors rottlerin and dimethyl amiloride and depended on phosphotidylinositol-3-kinase (PI(3)K), and both colocalised with dextran but not transferrin. VACV was not delivered to the classical endolysosomal pathway, failing to colocalise with EEA1 or Lamp2. Finally, expression of early viral genes was not affected by bafilomycin A, indicating that the virus does not depend on low pH to deliver cores to the cytoplasm. From these collective results we conclude that VACV enters DCs via macropinocytosis. However, MV was consistently less sensitive to inhibition and is likely to utilise at least one other entry pathway. Definition and future manipulation of these pathways may assist in enhancing the activity of recombinant vaccinia vectors through effects on antigen presentation.