gebhart/patrepeval huggingface dataset:
Proteolysis of Non-phosphorylated and Phosphorylated Tau by Thrombin (2004)

The microtubule-associated protein tau aggregates intracellularly by unknown mechanisms in Alzheimer's disease and other tauopathies. A contributing factor may be a failure to break down free cytosolic tau, thus creating a surplus for aggregation, although the proteases that degrade tau in brain remain unknown. To address this issue, we prepared cytosolic fractions from five normal human brains and from perfused rat brains and incubated them with or without protease inhibitors. D-Phenylalanyl-L-prolylarginyl chloromethyl ketone, a thrombin-specific inhibitor, prevented tau breakdown in these fractions, suggesting that thrombin is a brain protease that processes tau. We next exposed human recombinant tau to purified human thrombin and analyzed the fragments by N-terminal sequencing. We found that thrombin proteolyzed tau at multiple arginine and lysine sites. These include Arg(155)-Gly(156), Arg(209)-Ser(210), Arg(230)-Thr(231), Lys(257)-Ser(258), and Lys(340)-Ser(341) (numbering according to the longest human tau isoform). Temporally, the initial cleavage occurred at the Arg(155)-Gly(156) bond. Proteolysis of the resultant C-terminal tau fragment then proceeded bidirectionally. When tau was phosphorylated by glycogen synthase kinase-3beta, most of these proteolytic processes were inhibited, except for the first cleavage at the Arg(155)-Gly(156) bond. Furthermore, paired helical filament tau prepared from Alzheimer's disease brain was more resistant to thrombin proteolysis than following dephosphorylation by alkaline phosphatase. The results suggest a possible role for thrombin in proteolysis of tau under physiological and/or pathological conditions in human brains. They are consistent with the hypothesis that phosphorylation of tau inhibits proteolysis by thrombin or other endogenous proteases, leading to aggregation of tau into insoluble fibrils.
Human pancreatic cancer cells (MPANC-96) recognized by autologous tumor-infiltrating lymphocytes afterin vitro as well asin vivo tumor expansion (1997)

A human tumor line designated MPanc-96 has been established from a poorly differentiated primary pancreatic adenocarcinoma. MPanc-96 has a doubling time of 27 hr and grows as a confluent monolayer in various culture media. Cytogenetic analysis of in vitro-cultured tumor cells revealed a large number of clonal chromosomal aberrations, confirming their neoplastic origin. MPanc-96 grows in SCID mice when injected s.c. Xenografts established from the tumor line had a similar histology as the primary tumor. Tumor-infiltrating lymphocytes (TILs) were isolated from the primary tumor, and cytotoxic T lymphocytes (CTLs) were generated after activation on immobilized anti-CD3 monoclonal antibody (MAb) for 48 hr, expansion in low-dose IL-2 and repeated stimulation with irradiated MPanc-96 tumor cells. The generated CTLs lysed fresh autologous tumor cells as well as in vitro and in vivo expanded tumor cells from passages 9-53, suggesting that one or more tumor-associated antigens (TAAs) are stably expressed. CTLs lysed tumor cells in an HLA-class I-restricted fashion but showed no significant cytotoxicity against autologous fibroblasts, several allogeneic pancreatic cancer cell lines or K562. Our findings may be significant for the design of an animal model for studying the mechanisms of immunotherapy in human pancreatic cancer or for the identification of TAAs in pancreatic cancer.
Nivolumab versus Docetaxel in Advanced Nonsquamous Non–Small-Cell Lung Cancer (2015)

Among patients with advanced nonsquamous NSCLC that had progressed during or after platinum-based chemotherapy, overall survival was longer with nivolumab than with docetaxel. (Funded by Bristol-Myers Squibb; CheckMate 057 ClinicalTrials.gov number, NCT01673867.).
The EMBL sequence version archive (2003)

http://www.ebi.ac.uk/embl/sva/
An improved yeast transformation method for the generation of very large human antibody libraries (2010)

Antibody library selection by yeast display technology is an efficient and highly sensitive method to identify binders to target antigens. This powerful selection tool, however, is often hampered by the typically modest size of yeast libraries (approximately 10(7)) due to the limited yeast transformation efficiency, and the full potential of the yeast display technology for antibody discovery and engineering can only be realized if it can be coupled with a mean to generate very large yeast libraries. We describe here a yeast transformation method by electroporation that allows for the efficient generation of large antibody libraries up to 10(10) in size. Multiple components and conditions including CaCl(2), MgCl(2), sucrose, sorbitol, lithium acetate, dithiothreitol, electroporation voltage, DNA input and cell volume have been tested to identify the best combination. By applying this developed protocol, we have constructed a 1.4 x 10(10) human spleen antibody library essentially in 1 day with a transformation efficiency of 1-1.5 x 10(8) transformants/microg vector DNA. Taken together, we have developed a highly efficient yeast transformation method that enables the generation of very large and productive human antibody libraries for antibody discovery, and we are now routinely making 10(9) libraries in a day for antibody engineering purposes.
Cardiac stem cells delivered intravascularly traverse the vessel barrier, regenerate infarcted myocardium, and improve cardiac function (2005)

The ability of cardiac stem cells (CSCs) to promote myocardial repair under clinically relevant conditions (i.e., when delivered intravascularly after reperfusion) is unknown. Thus, rats were subjected to a 90-min coronary occlusion; at 4 h after reperfusion, CSCs were delivered to the coronary arteries via a catheter positioned into the aortic root. Echocardiographic analysis showed that injection of CSCs attenuated the increase in left ventricular (LV) end-diastolic dimensions and impairment in LV systolic performance at 5 weeks after myocardial infarction. Pathologic analysis showed that treated hearts exhibited a smaller increase in LV chamber diameter and volume and a higher wall thickness-to-chamber radius ratio and LV mass-to-chamber volume ratio. CSCs induced myocardial regeneration, decreasing infarct size by 29%. A diploid DNA content and only two chromosomes 12 were found in new cardiomyocytes, indicating that cell fusion did not contribute to tissue reconstitution. In conclusion, intravascular injection of CSCs after reperfusion limits infarct size, attenuates LV remodeling, and ameliorates LV function. This study demonstrates that CSCs are effective when delivered in a clinically relevant manner, a clear prerequisite for clinical translation, and that these beneficial effects are independent of cell fusion. The results establish CSCs as candidates for cardiac regeneration and support an approach in which the heart's own stem cells could be collected, expanded, and stored for subsequent therapeutic repair.
PARP1 is required for chromosomal translocations (2013)

Chromosomal translocations are common contributors to malignancy, yet little is known about the precise molecular mechanisms by which they are generated. Sequencing translocation junctions in acute leukemias revealed that the translocations were likely mediated by a DNA double-strand break repair pathway termed nonhomologous end-joining (NHEJ). There are major 2 types of NHEJ: (1) the classical pathway initiated by the Ku complex, and (2) the alternative pathway initiated by poly ADP-ribose polymerase 1 (PARP1). Recent reports suggest that classical NHEJ repair components repress translocations, whereas alternative NHEJ components were required for translocations. The rate-limiting step for initiation of alternative NHEJ is the displacement of the Ku complex by PARP1. Therefore, we asked whether PARP1 inhibition could prevent chromosomal translocations in 3 translocation reporter systems. We found that 2 PARP1 inhibitors or repression of PARP1 protein expression strongly repressed chromosomal translocations, implying that PARP1 is essential for this process. Finally, PARP1 inhibition also reduced both ionizing radiation-generated and VP16-generated translocations in 2 cell lines. These data define PARP1 as a critical mediator of chromosomal translocations and raise the possibility that oncogenic translocations occurring after high-dose chemotherapy or radiation could be prevented by treatment with a clinically available PARP1 inhibitor.
Nanoscopic magnetic field sensor based on extraordinary magnetoresistance (2003)

The design, fabrication, and performance of a nanoscopic magnetic field sensor based on the newly discovered phenomenon of extraordinary magnetoresistance (EMR) are reported. It is shown that a sensor with an active volume of 35 nm length×30 nm width×20 nm height yields room temperature EMR values as high as 35% at an applied field of 0.05 T. The mesoscopic physics implications of these new results are discussed.
Animal Models as Tools for Screening Candidate Drugs (2005)

The Proceedings of the First International Symposium on Translational Clinical Research for Inherited and Orphan Retinal Diseases: Sponsored by the National Neurovision Research Institute Inc.: Advances in Basic Sciences in Inherited Orphan Retinal Diseases
Mapping of brain metabolite distributions by volumetric proton MR spectroscopic imaging (MRSI) (2008)

Distributions of proton MR-detected metabolites have been mapped throughout the brain in a group of normal subjects using a volumetric MR spectroscopic imaging (MRSI) acquisition with an interleaved water reference. Data were processed with intensity and spatial normalization to enable voxel-based analysis methods to be applied across a group of subjects. Results demonstrate significant regional, tissue, and gender-dependent variations of brain metabolite concentrations, and variations of these distributions with normal aging. The greatest alteration of metabolites with age was observed for white-matter choline and creatine. An example of the utility of the normative metabolic reference information is then demonstrated for analysis of data acquired from a subject who suffered a traumatic brain injury. This study demonstrates the ability to obtain proton spectra from a wide region of the brain and to apply fully automated processing methods. The resultant data provide a normative reference for subsequent utilization for studies of brain injury and disease.
Anti‐CD36 antibodies in thrombotic thrombocytopenic purpura (1994)

The membrane glycoprotein CD36 (GPIV, M(r) 88,000) is found on platelets, monocytes and endothelial cells of the microvasculature. In the present study, anti CD36 antibodies have been identified as occurring with high frequency in patients with thrombotic thrombocytopenic purpura. The presence of anti CD36 antibodies in 15 TTP plasma samples thought to contain them on the basis of an initial screening by protein blots was confirmed by re-screening against a standard of purified CD36, by immunoprecipitation from 125I-labelled control platelets and by dot blots against purified CD36. In a further 28 random samples examined, 23/27 (85%) were CD36-positive by immunoprecipitation, 21/28 (75%) by protein blotting, and 17/28 (60%) by dot blots against purified CD36. On protein blots following SDS-PAGE, immunoprecipitates produced from normal platelets by TTP plasma gave positive reactions with the anti CD36 monoclonal antibody 125I-Mo91. One half of the total TTP samples examined (21/42) caused approximately 70% release in control platelets loaded with 14C-serotonin. Of samples causing release > or = 70%, one-half (8/15) failed to cause release from Naka-negative platelets which constitutively lack CD36 showing that CD36 was the sole target for platelet activation in these TTP samples. These studies demonstrate that antibodies directed against CD36 occur frequently in TTP patients and could cause thrombotic complications and vascular damage by reacting with the parent antigen present in platelets and endothelial cells.
A New Subfamily of Polyphosphate Kinase 2 (Class III PPK2) Catalyzes both Nucleoside Monophosphate Phosphorylation and Nucleoside Diphosphate Phosphorylation (2014)

Inorganic polyphosphate (polyP) is a linear polymer of tens to hundreds of phosphate (Pi) residues linked by "high-energy" phosphoanhydride bonds as in ATP. PolyP kinases, responsible for the synthesis and utilization of polyP, are divided into two families (PPK1 and PPK2) due to differences in amino acid sequence and kinetic properties. PPK2 catalyzes preferentially polyP-driven nucleotide phosphorylation (utilization of polyP), which is important for the survival of microbial cells under conditions of stress or pathogenesis. Phylogenetic analysis suggested that the PPK2 family could be divided into three subfamilies (classes I, II, and III). Class I and II PPK2s catalyze nucleoside diphosphate and nucleoside monophosphate phosphorylation, respectively. Here, we demonstrated that class III PPK2 catalyzes both nucleoside monophosphate and nucleoside diphosphate phosphorylation, thereby enabling us to synthesize ATP from AMP by a single enzyme. Moreover, class III PPK2 showed broad substrate specificity over purine and pyrimidine bases. This is the first demonstration that class III PPK2 possesses both class I and II activities.
PU.1 and C/EBPα/β convert fibroblasts into macrophage-like cells (2008)

Earlier work has shown that the transcription factor C/EBPalpha induced a transdifferentiation of committed lymphoid precursors into macrophages in a process requiring endogenous PU.1. Here we have examined the effects of PU.1 and C/EBPalpha on fibroblasts, a cell type distantly related to blood cells and akin to myoblasts, adipocytes, osteoblasts, and chondroblasts. The combination of the two factors, as well as PU.1 and C/EBPbeta, induced the up-regulation of macrophage/hematopoietic cell surface markers in a large proportion of NIH 3T3 cells. They also up-regulated these markers in mouse embryo- and adult skin-derived fibroblasts. Based on cell morphology, activation of macrophage-associated genes, and extinction of fibroblast-associated genes, cell lines containing an attenuated form of PU.1 and C/EBPalpha acquired a macrophage-like phenotype. The lines also display macrophage functions: They phagocytose small particles and bacteria, mount a partial inflammatory response, and exhibit strict CSF-1 dependence for growth. The myeloid conversion is primarily induced by PU.1, with C/EBPalpha acting as a modulator of macrophage-specific gene expression. Our data suggest that it might become possible to induce the transdifferentiation of skin-derived fibroblasts into cell types desirable for tissue regeneration.
Identifying the vector of Lyme disease. (2004)

Lyme disease is the most common vector-borne illness in the United States. It is caused by the spirochete Borrelia burgdorferi, which is transmitted by the deer tick. Deer ticks have a four-stage life cycle (egg, larva, nymph, and adult), and nymphal ticks transmit B. burgdorferi to humans more frequently than adult ticks. Transmission of this spirochete typically requires a minimum of 24 to 48 hours of tick attachment. Early stages of Lyme disease are characterized by a hallmark rash, erythema migrans. The overall risk of acquiring Lyme disease is low in a person who has a deer tick bite. If erythema migrans develops at the site of the bite, treatment may include doxycycline in persons who are at least eight years of age. Administration of amoxicillin is appropriate for pregnant women or children younger than eight years. For those who are allergic to these medications, cefuroxime axetil may be used.
Detection of Epstein–Barr Viral Genomes in Reed–Sternberg Cells of Hodgkin's Disease (1989)

We used slot blot hybridization, Southern blot hybridization, and in situ hybridization to investigate the presence of Epstein-Barr virus (EBV) genomes in biopsy tissues from patients with Hodgkin's disease. Slot blot hybridization performed on DNA of tissue specimens from 16 patients revealed that biopsy tissue from 3 (19 percent) contained EBV DNA. Southern blot hybridization with a DNA probe containing the 500-base-pair tandem repeated sequences located at the termini of the EBV genome confirmed the findings of the slot blot hybridization in the three positive tissue specimens and indicated the monoclonality of the EBV-infected cells in such tissues. In situ hybridization performed on the three positive specimens and on two from a previous study localized EBV nucleic acid to the Reed-Sternberg cells and variants in all specimens, with intense hybridization to Reed-Sternberg cells in two, less intense but consistent hybridization to Reed-Sternberg cells in two, and focal hybridization to Reed-Sternberg cells in one. We conclude that EBV genomes are present within Reed-Sternberg cells and variants in some patients with Hodgkin's disease and that the infected cells are monoclonal.
Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery (2013)

The discovery of new or divergent viruses using metagenomics and high-throughput sequencing has become more commonplace. The preparation of a sample is known to have an effect on the representation of virus sequences within the metagenomic dataset yet comparatively little attention has been given to this. Physical enrichment techniques are often applied to samples to increase the number of viral sequences and therefore enhance the probability of detection. With the exception of virus ecology studies, there is a paucity of information available to researchers on the type of sample preparation required for a viral metagenomic study that seeks to identify an aetiological virus in an animal or human diagnostic sample. A review of published virus discovery studies revealed the most commonly used enrichment methods, that were usually quick and simple to implement, namely low-speed centrifugation, filtration, nuclease-treatment (or combinations of these) which have been routinely used but often without justification. These were applied to a simple and well-characterised artificial sample composed of bacterial and human cells, as well as DNA (adenovirus) and RNA viruses (influenza A and human enterovirus), being either non-enveloped capsid or enveloped viruses. The effect of the enrichment method was assessed by both quantitative real-time PCR and metagenomic analysis that incorporated an amplification step. Reductions in the absolute quantities of bacteria and human cells were observed for each method as determined by qPCR, but the relative abundance of viral sequences in the metagenomic dataset remained largely unchanged. A 3-step method of centrifugation, filtration and nuclease-treatment showed the greatest increase in the proportion of viral sequences. This study provides a starting point for the selection of a purification method in future virus discovery studies, and highlights the need for more data to validate the effect of enrichment methods on different sample types, amplification, bioinformatics approaches and sequencing platforms. This study also highlights the potential risks that may attend selection of a virus enrichment method without any consideration for the sample type being investigated.
Cytokine Storm in a Phase 1 Trial of the Anti-CD28 Monoclonal Antibody TGN1412 (2006)

Six healthy young male volunteers at a contract research organization were enrolled in the first phase 1 clinical trial of TGN1412, a novel superagonist anti-CD28 monoclonal antibody that directly stimulates T cells. Within 90 minutes after receiving a single intravenous dose of the drug, all six volunteers had a systemic inflammatory response characterized by a rapid induction of proinflammatory cytokines and accompanied by headache, myalgias, nausea, diarrhea, erythema, vasodilatation, and hypotension. Within 12 to 16 hours after infusion, they became critically ill, with pulmonary infiltrates and lung injury, renal failure, and disseminated intravascular coagulation. Severe and unexpected depletion of lymphocytes and monocytes occurred within 24 hours after infusion. All six patients were transferred to the care of the authors at an intensive care unit at a public hospital, where they received intensive cardiopulmonary support (including dialysis), high-dose methylprednisolone, and an anti-interleukin-2 receptor antagonist antibody. Prolonged cardiovascular shock and acute respiratory distress syndrome developed in two patients, who required intensive organ support for 8 and 16 days. Despite evidence of the multiple cytokine-release syndrome, all six patients survived. Documentation of the clinical course occurring over the 30 days after infusion offers insight into the systemic inflammatory response syndrome in the absence of contaminating pathogens, endotoxin, or underlying disease.
The Impact of Influenza Epidemics on Hospitalizations (2000)

The traditional method for assessing the severity of influenza seasons is to estimate the associated increase (i.e., excess) in pneumonia and influenza (P&I) mortality. In this study, excess P&I hospitalizations were estimated from National Hospital Discharge Survey Data from 26 influenza seasons (1970-1995). The average seasonal rate of excess P&I hospitalization was 49 (range, 8-102) /100,000 persons, but average rates were twice as high during A(H3N2) influenza seasons as during A(H1N1)/B seasons. Persons aged <65 years had 57% of all influenza-related hospitalizations; however, the average seasonal risk for influenza-related P&I hospitalizations was much higher in the elderly than in persons aged <65 years. The 26 pairs of excess P&I hospitalization and mortality rates were linearly correlated. During the A(H3N2) influenza seasons after the 1968 pandemic, excess P&I hospitalizations declined among persons aged <65 years but not among the elderly. This suggests that influenza-related hospitalizations will increase disproportionately among younger persons in future pandemics.
Single-mode fiber microlens with controllable spot size (1991)

A novel method for fabricating microlenses on tapered single-mode fibers is shown to be able to control the lens spot size. The fiber cladding is first symmetrically tapered by etching it with an evaporating ammonium bifluoride solution. A hemispheric lens is then melted on the taper tip with a CO(2) laser. The lens can reduce the fiber mode radius to 40% of its original value. A theoretical calculation of the focused spot size agrees well with experimental results.
Mouse embryonic stem cells express the cardiac myosin heavy chain genes during development in vitro. (1990)

In the mouse embryo, early organogenesis is characterized by the formation of a functional cardiac muscle, such that 9-day embryos exhibit beating, although not fully developed hearts. In light of this observation, we found it intriguing that mouse embryoid bodies (EB), which can develop in vitro from totipotential embryonic stem cells, undergo spontaneous contractile activity. To determine if these cells are capable of recapitulating aspects of cardiogenesis, a cDNA library was prepared from beating EB and screened with a chicken skeletal myosin heavy chain cDNA. We found that the predominant myosin transcripts in the library encode the alpha- and beta-cardiac isoforms. In addition, an embryonic skeletal myosin cDNA was isolated. The myosin heavy chain transcripts in both EB and 9-day embryonic hearts were found to be the same. Transcript-specific primers were prepared, and polymerase chain reaction analyses on single EB were carried out. The data show that a single EB is capable of expressing both the alpha- and beta-isoforms as well as very low amounts of the embryonic skeletal transcript. These data indicate that EB transcribe the appropriate tissue- and developmental stage-specific myosin heavy chain genes and therefore serve as a model system for studying early cardiogenic processes at the molecular level.