gebhart/patrepeval huggingface dataset:
γδ T cells for immune therapy of patients with lymphoid malignancies (2003)

There is increasing evidence that gammadelta T cells have potent innate antitumor activity. We described previously that synthetic aminobisphosphonates are potent gammadelta T cell stimulatory compounds that induce cytokine secretion (ie, interferon gamma [IFN-gamma]) and cell-mediated cytotoxicity against lymphoma and myeloma cell lines in vitro. To evaluate the antitumor activity of gammadelta T cells in vivo, we initiated a pilot study of low-dose interleukin 2 (IL-2) in combination with pamidronate in 19 patients with relapsed/refractory low-grade non-Hodgkin lymphoma (NHL) or multiple myeloma (MM). The objectives of this trial were to determine toxicity, the most effective dose for in vivo activation/proliferation of gammadelta T cells, and antilymphoma efficacy of the combination of pamidronate and IL-2. The first 10 patients (cohort A) who entered the study received 90 mg pamidronate intravenously on day 1 followed by increasing dose levels of continuous 24-hour intravenous (IV) infusions of IL-2 (0.25 to 3 x 106 IU/m2) from day 3 to day 8. Even at the highest IL-2 dose level in vivo, gammadelta T-cell activation/proliferation and response to treatment were disappointing with only 1 patient achieving stable disease. Therefore, the next 9 patients were selected by positive in vitro proliferation of gammadelta T cells in response to pamidronate/IL-2 and received a modified treatment schedule (6-hour bolus IV IL-2 infusions from day 1-6). In this patient group (cohort B), significant in vivo activation/proliferation of gammadelta T cells was observed in 5 patients (55%), and objective responses (PR) were achieved in 3 patients (33%). Only patients with significant in vivo proliferation of gammadelta T cells responded to treatment, indicating that gammadelta T cells might contribute to this antilymphoma effect. Overall, administration of pamidronate and low-dose IL-2 was well tolerated. In conclusion, this clinical trial demonstrates, for the first time, that gammadelta T-cell-mediated immunotherapy is feasible and can induce objective tumor responses.
Use of a vector based on Potato virus X in a whole plant assay to demonstrate nuclear targeting of Potato spindle tuber viroid (2001)

Potato spindle tuber viroid (PSTVd) is a covalently closed circular RNA molecule of 359 nucleotides that replicates within the nucleus of host cells. To determine how this small, highly structured RNA enters the nucleus, we have developed a virus-based, whole plant in vivo assay that uses green fluorescent protein (GFP) as the reporter molecule. The coding region of GFP was interrupted by insertion of an intron derived from the intervening sequence 2 of the potato ST-LS1 gene. A cDNA copy of the complete PSTVd genome was, in turn, embedded within the intron, and this construct was delivered into Nicotiana benthamiana plants via a vector based on Potato virus X. The intron-containing GFP subgenomic RNA synthesized during virus infection cannot produce a functional GFP unless the RNA is imported into the nucleus, where the intron can be removed and the spliced RNA returned to the cytoplasm. The appearance of green fluorescence in leaf tissues inoculated with constructs containing a full-length PSTVd molecule embedded in the intron indicates that nuclear import and RNA splicing events did occur.
The Binding of Substrate Analogs to Phosphotriesterase (2000)

Phosphotriesterase (PTE) from <i>Pseudomonas diminuta</i> catalyzes the detoxification of organophosphates such as the widely utilized insecticide paraoxon and the chemical warfare agent sarin. The three-dimensional structure of the enzyme is known from high resolution x-ray crystallographic analyses. Each subunit of the homodimer folds into a so-called TIM barrel, with eight strands of parallel β-sheet. The two zinc ions required for activity are positioned at the C-terminal portion of the β-barrel. Here, we describe the three-dimensional structure of PTE complexed with the inhibitor diisopropyl methyl phosphonate, which serves as a mimic for sarin. Additionally, the structure of the enzyme complexed with triethyl phosphate is also presented. In the case of the PTE-diisopropyl methyl phosphonate complex, the phosphoryl oxygen of the inhibitor coordinates to the more solvent-exposed zinc ion (2.5 Å), thereby lending support to the presumed catalytic mechanism involving metal coordination of the substrate. In the PTE-triethyl phosphate complex, the phosphoryl oxygen of the inhibitor is positioned at 3.4 Å from the more solvent-exposed zinc ion. The two structures described in this report provide additional molecular understanding for the ability of this remarkable enzyme to hydrolyze such a wide range of organophosphorus substrates.
Dissecting eIF4E action in tumorigenesis (2007)

Genetically engineered mouse models are powerful tools for studying cancer genes and validating targets for cancer therapy. We previously used a mouse lymphoma model to demonstrate that the translation initiation factor eIF4E is a potent oncogene in vivo. Using the same model, we now show that the oncogenic activity of eIF4E correlates with its ability to activate translation and become phosphorylated on Ser 209. Furthermore, constitutively activated MNK1, an eIF4E Ser 209 kinase, promotes tumorigenesis in a manner similar to eIF4E, and a dominant-negative MNK mutant inhibits the in vivo proliferation of tumor cells driven by mutations that deregulate translation. Phosphorylated eIF4E promotes tumorigenesis primarily by suppressing apoptosis and, accordingly, the anti-apoptotic protein Mcl-1 is one target of both phospho-eIF4E and MNK1 that contributes to tumor formation. Our results provide insight into how eIF4E contributes to tumorigenesis and pinpoint a level of translational control that may be suitable for therapeutic intervention.
Progressive multifocal leukoencephalopathy: clinical and MR response to treatment. (1996)

Progressive multifocal leukoencephalopathy (PML) is a fatal demyelinating disease that occurs in immunocompromised hosts. We describe two patients with biopsy-proved PML who showed improvement clinically and radiologically after medical therapy. These cases reveal that interval improvement can in rare instances be consistent with a diagnosis of PML.
Catalytic consequences of ultrafine Pt clusters supported on SrTiO3 for photocatalytic overall water splitting (2019)

The metal cluster size in supported metal catalysts impacts the oxidation state of the metal atoms, coordination capability, and finally the catalytic activity-especially when the number of atoms becomes countable. The correlation between metal oxidation state and its catalytic consequences for ultrafine Pt was studied for photocatalytic overall water splitting using a Pt/SrTiO 3 (photo)catalyst. A distinctive change in catalytic behavior and oxidation state was observed below 100 Pt-atom clusters at $2 nm. Combining density functional theory (DFT) and experimental characterizations including X-ray absorption spectroscopy (XAS), X-ray photoelectron spectroscopy (XPS), and diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), the smaller Pt clusters obtained by the surface organometallic route (under 100 Pt atoms) were predominantly oxidized and selectively performed photocatalytic water splitting selectively without activation of the water-forming back-reaction from H 2 and O 2 . When the Pt clusters obtained by classical impregnation were larger than 2 nm, they remained metallic (Pt 0 ) and were active for both water splitting and the competing thermal water formation back reaction. In addition, Pt 0 clusters are poisoned in the presence of CO, whereas highly dispersed ultra-fine oxidized Pt clusters are insensitive to CO. This paper presents evidence of ultrafine PtO x (below approximately 2 nm clusters) that are insensitive to coordination of various gas identities (H 2 , O 2 , CO), resulting in efficient and selective photocatalytic overall water splitting.
Exploiting the data-rate potential of MIMO channels: multi-stratum space-time coding (2002)

There is a high potential with respect to Shannon capacity in having a multiple-input multiple-output (MIMO) channel. In this paper a new MIMO coding approach, called multi-stratum space-time coding (MSSTC) is presented The principle of MSSTC is to partition the data stream and to transmit the substreams on separate strata. The transmission on every stratum is based on space-time block coding (STBC) yielding full diversity. Orthogonal superposition of the strata results in independent transmit symbols and enables therefore a high data rate. Decoding may be done successively stratum by stratum yielding reasonable receiver complexity. The structural properties inherent in MSSTC make it a robust scheme for varying channel conditions. A Shannon capacity comparison to other MIMO schemes like V- and D-BLAST is presented showing the robustness of MSSTC in different environments.
Isolation of putative plant transcriptional coactivators using a modified two‐hybrid system incorporating a GFP reporter gene (1998)

Dual hybrid interacting screening in yeast led to the identification of two proteins from Arabidopsis both exhibiting sequence similarity to a family of transcriptional coactivators from a diverse range of organisms. Their discovery constitutes the first description of such plant proteins. A modified yeast two-hybrid approach utilising the green fluorescent protein (GFP) of Aequora victoria was developed and used to clone one of the putative plant transcriptional coactivators from an Arabidopsis cDNA library. The two proteins, designated KIWI and KELP, can associate both hetero- and homomerically and their genes were cloned and mapped on the Arabidopsis genome. Both proteins are believed to play a role in gene activation during pathogen defence and plant development. The involvement of these proteins in general plant transcription as well as the advantages of using GFP as a reporter gene for detecting protein-protein interactions are discussed.
Dex-Net 1.0: A cloud-based network of 3D objects for robust grasp planning using a Multi-Armed Bandit model with correlated rewards (2016)

This paper presents the Dexterity Network (Dex-Net) 1.0, a dataset of 3D object models and a sampling-based planning algorithm to explore how Cloud Robotics can be used for robust grasp planning. The algorithm uses a Multi- Armed Bandit model with correlated rewards to leverage prior grasps and 3D object models in a growing dataset that currently includes over 10,000 unique 3D object models and 2.5 million parallel-jaw grasps. Each grasp includes an estimate of the probability of force closure under uncertainty in object and gripper pose and friction. Dex-Net 1.0 uses Multi-View Convolutional Neural Networks (MV-CNNs), a new deep learning method for 3D object classification, to provide a similarity metric between objects, and the Google Cloud Platform to simultaneously run up to 1,500 virtual cores, reducing experiment runtime by up to three orders of magnitude. Experiments suggest that correlated bandit techniques can use a cloud-based network of object models to significantly reduce the number of samples required for robust grasp planning. We report on system sensitivity to variations in similarity metrics and in uncertainty in pose and friction. Code and updated information is available at http://berkeleyautomation.github.io/dex-net/.
Electrical Stimulation of the Centromedian Thalamic Nucleus in Control of Seizures: Long‐Term Studies (1995)

Five patients with chronic incapacitating seizures averaging 15-5,000/month were selected for study. All patients had more than one seizure type and had received maximal doses of antiepileptic drugs (AEDs). The centromedian thalamic nucleus (CM) was stimulated electrically through bilateral multicontact platinum electrodes stereotaxically placed in CM and connected to internalized pulse generators. Electrophysiologic confirmation of electrode position included thalamically elicited recruiting responses and EEG desynchronization recorded at the scalp. Stimulation parameters were adjusted individually in the range of 450-800-microA intensity, 65 pps, 0.09 ms, in 1-min trains, alternating right and left side stimulation and with 4-min intervals delivered for 2 h/day. Quantitative evaluation included frequency of seizures/month, number of maximal interictal paroxysmal discharges, and frequency of background activities counted in selected scalp EEG samples, taken throughout the observation period (7-33 months). Significance of changes was evaluated by parametric Student's t test. Generalized tonic-clonic seizures (GTC) decreased dramatically, almost disappearing in all cases (p < 0.001), with a significant reduction in interictal paroxysmal discharges (p < 0.01) and a tendency toward an increase in EEG background frequency. Other generalized seizures (atypical absences) decreased significantly, but there was no change in the number of complex partial seizures (CPS). CM stimulation is useful in control of GTC, but its beneficial effect on other seizure types has not been established.
Diagnosis of Alzheimer's Disease (1985)

Early and accurate diagnosis of Alzheimer's disease (AD) has a major impact on the progress of research on dementia. To address the problems involved in diagnosing AD in its earliest stages, the National Institute on Aging, the American Association of Retired Persons, the National Institute of Neurological and Communicative Disorders and Stroke, and the National Institute of Mental Health jointly sponsored a workshop for planning research. The purpose of the meeting was to identify the most important scientific research opportunities and the crucial clinical and technical issues that influence the progress of research on the diagnosis of AD. The 37 participants included some of the most knowledgeable and eminent scientists and physicians actively involved in the study of AD. The participants were divided among six panels representing the disciplines of neurochemistry, neuropathology, neuroradiology, neurology, neuropsychology, and psychiatry. Within each of the panels, participants discussed specific areas of research requiring further
Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival (2011)

Breast cancer is a heterogeneous disease with known expression-defined tumor subtypes. DNA copy number studies have suggested that tumors within gene expression subtypes share similar DNA Copy number aberrations (CNA) and that CNA can be used to further sub-divide expression classes. To gain further insights into the etiologies of the intrinsic subtypes, we classified tumors according to gene expression subtype and next identified subtype-associated CNA using a novel method called SWITCHdna, using a training set of 180 tumors and a validation set of 359 tumors. Fisher's exact tests, Chi-square approximations, and Wilcoxon rank-sum tests were performed to evaluate differences in CNA by subtype. To assess the functional significance of loss of a specific chromosomal region, individual genes were knocked down by shRNA and drug sensitivity, and DNA repair foci assays performed. Most tumor subtypes exhibited specific CNA. The Basal-like subtype was the most distinct with common losses of the regions containing RB1, BRCA1, INPP4B, and the greatest overall genomic instability. One Basal-like subtype-associated CNA was loss of 5q11-35, which contains at least three genes important for BRCA1-dependent DNA repair (RAD17, RAD50, and RAP80); these genes were predominantly lost as a pair, or all three simultaneously. Loss of two or three of these genes was associated with significantly increased genomic instability and poor patient survival. RNAi knockdown of RAD17, or RAD17/RAD50, in immortalized human mammary epithelial cell lines caused increased sensitivity to a PARP inhibitor and carboplatin, and inhibited BRCA1 foci formation in response to DNA damage. These data suggest a possible genetic cause for genomic instability in Basal-like breast cancers and a biological rationale for the use of DNA repair inhibitor related therapeutics in this breast cancer subtype.
Immunotherapy of cancer with genetically modified tumor vaccines. (1996)

Distant metastasis is the major cause for therapeutic failures in Clinical oncology. Active immunotherapy in the adjuvant setting of patients with low tumor volume would contribute to further reduction of the remaining tumor and establish long-lasting immunity that could protect the patient from recurrence of disease. Studies employing rodent tumor models with little or no intrinsic immunogenicity have shown that genetically modified tumor cell preparations consisting of irradiated tumor cells transduced with and expressing cytokines, such as interleukin-2 (IL-2), IL-6, interferon-gamma (IFNgamma), or granulocyte-macrophage colony stimulating factor (GM-CSF), or co-stimulatory molecules, such as B7-I, were capable of inducing the regression of preexisting tumors and cure animals from their disease. Moreover, in some instances, the cured animals have retained immunological memory, as indicated by the fact that animals have resisted a second challenge with the parental tumor cells. Induction of potent immune responses in tumor-bearing animals against nonimmunogenic or weakly immunogenic tumors supports the view that active immunization of cancer patients deserves consideration despite lack of demonstrable immunogenicity in many human tumors.
Vaccination with Theratope® (STn-KLH) as treatment for breast cancer (2004)

Cancer vaccines have demonstrated that they can stimulate antibody and cell-mediated immune responses against tumor-associated antigens in the laboratory. However, few clinical studies with cancer vaccines have demonstrated convincing clinical responses. Sialyl-Tn is a carbohydrate associated with MUC1. It is a unique tumor-associated antigen, present on many adenocarcinomas including breast, ovarian, colorectal, gastric and pancreatic. Consequently, Sialyl-TN is an ideal candidate for boosting the patient's immune system specifically against a unique tumor-associated antigen. The cancer vaccine Theratope was developed by Biomira, Inc. using a synthetic Sialyl-Tn antigen that emulates the unique carbohydrate on human cancer. Clinical trials have predominantly been carried out in breast cancer patients and these trials are outlined in this profile.
Genetic diversity and molecular epidemiology of respiratory syncytial virus over four consecutive seasons in South Africa: identification of new subgroup A and B genotypes (2001)

The molecular epidemiology of respiratory syncytial virus (RSV) was studied over four consecutive seasons (1997-2000) in a single tertiary hospital in South Africa: 225 isolates were subgrouped by RT-PCR and the resulting products sequenced. Subgroup A predominated in two seasons, while A and B co-circulated approximately equally in the other seasons. The nucleotide sequences of the C-terminal of the G-protein were compared to sequences representative of previously defined RSV genotypes. South African subgroup A and subgroup B isolates clustered into four and five genotypes respectively. One new subgroup A and three new subgroup B genotypes were identified. Different genotypes co-circulated in every season. Different circulation patterns were identified for group A and B isolates. Subgroup A revealed more variability and displacement of genotypes while subgroup B remained more consistent.
Expression of neuroimmune semaphorins 4A and 4D and their receptors in the lung is enhanced by allergen and vascular endothelial growth factor (2011)

This study clearly shows that neuroimmune semaphorins Sema4A and Sema4D and their receptors might serve as potential markers for the allergic airway inflammatory diseases. Our current findings pave the way for further investigations of the role of immune semaphorins in inflammation and their use as potential therapeutic targets for the inflammatory lung conditions.
A robust soft hash algorithm for digital image signature (2004)

Watermarking is largely used for copyright protection and fast search of images in databases. Another method for securely identifying images is to use hash functions. Digital signature standard, used in cryptosystem to dispute authentication documents, is based on hash functions. A digital signature is a bit stream dependent on key and content of document. For each document, the digital signature algorithm provides a unique output bit stream. In order to be efficient in images, the digital signature should be different if and only if the image content, and not the input bit stream, is different. Our new method is a one-way function for images. Using the radon transform and principal component analysis, we extract characteristics robust against geometrical transformation (rotation and scaling) and image processing attacks (compression, filtering, blurring).
Reversible Photoinduced Magnetization (1997)

Reversible photoinduced magnetization was observed in a cobalt iron cyanide thin film. Magnetic properties of the prussian blue analog, , can be switched between ferrimagnetic and paramagnetic by visible and near‐IR light illumination. The critical temperature after illumination was about 26 K. This material, obtained via an electrochemical route in the form of thin films on an electrode, provides a new system whose magnetic properties can be controlled by both photochemical and electrochemical redox reactions.
The star user interface (1982)

In April 1981 Xerox announced the 8010 Star Information System, a new personal computer designed for office professionals who create, analyze, and distribute information. The Star user interface differs from that of other office computer systems by its emphasis on graphics, its adherence to a metaphor of a physical office, and its rigorous application of a small set of design principles. The graphic imagery reduces the amount of typing and remembering required to operate the system. The office metaphor makes the system seem familiar and friendly; it reduces the alien feel that many computer systems have. The design principles unify the nearly two dozen functional areas of Star, increasing the coherence of the system and allowing user experience in one area to apply in others.
The Membrane Anchor Influences Ligand Binding Two-dimensional Kinetic Rates and Three-dimensional Affinity of FcγRIII (CD16) (2000)

Kinetic rates and affinity are essential determinants for biological processes that involve receptor-ligand binding. By using a micropipette method, we measured the kinetics of human Fcgamma receptor III (CD16) interacting with IgG when the two molecules were bound to apposing cellular membranes. CD16 is one of only four eukaryotic receptors known to exist natively in both the transmembrane (TM, CD16a) and glycosylphosphatidylinositol (GPI, CD16b) isoforms. The biological significance of this anchor isoform coexistence is not clear. Here we showed that the anchor influenced kinetic rates; compared with CD16a-TM, CD16a-GPI bound faster and with higher affinities to human and rabbit IgGs but slower and with lower affinity to murine IgG2a. The same differential affinity patterns were observed using soluble IgG ligands. A monoclonal antibody bound CD16a-GPI with higher affinity than CD16a-TM, whereas another monoclonal antibody reacted strongly with CD16a-TM but weakly with CD16a-GPI. No major differential glycosylation between the two CD16a isoforms was detected by SDS-polyacrylamide gel electrophoresis analysis. We suggest a conformational difference as the mechanism underlying the observed anchor effect, as it cannot be explained by the differing diffusivity, flexibility, orientation, height, distribution, or clustering of the two molecules on the cell membrane. These data demonstrate that a covalent modification of an Ig superfamily receptor at the carboxyl terminus of the ectodomain can have an impact on ligand binding kinetics.