gebhart/patrepeval huggingface dataset:
The Automatic Creation of Literature Abstracts (1958)

Excerpts of technical papers and magazine articles that serve the purposes of conventional abstracts have been created entirely by automatic means. In the exploratory research described, the complete text of an article in machine-readable form is scanned by an IBM 704 data-processing machine and analyzed in accordance with a standard program. Statistical information derived from word frequency and distribution is used by the machine to compute a relative measure of significance, first for individual words and then for sentences. Sentences scoring highest in significance are extracted and printed out to become the “auto-abstract."
Generation of human monoclonal antibodies reactive with cellular antigens. (1983)

Human lymphocytes from lymph node, peripheral blood, spleen, and tumor specimens have been fused with the LICR-LON-HMy2 (LICR-2) or SKO-007 human cell lines or the NS-1 mouse myeloma line. Over 75 fusions with the three myeloma-lymphoblastoid lines have been performed. Several factors appeared to improve the fusion outcome, including maintenance of the myeloma-lymphoblastoid lines in logarithmic phase growth at greater than or equal to 95% viability, a delay of 24 hr in the introduction of aminopterin to the fused cells, and preselection of the fetal calf serum used in the medium. For a given number of lymphocytes, fusions with NS-1 produced 5-20 times more clones than fusions with LICR-2 or SKO-007, and LICR-2 produced 4 times as many clones as SKO-007. The percentage of clones secreting human immunoglobulin, the range of immunoglobulin production, and the proportion of IgM, IgA, and IgG secretors were comparable for clones derived from the three myeloma-lymphoblastoid lines. Stable Ig-secreting clones were isolated with approximately equal frequency from LICR-2 and NS-1 fusions. A number of stable clones producing human monoclonal antibodies reacting with cell-surface, cytoplasmic, or nuclear antigens have been isolated from tumor-bearing patients and normal individuals. A surface antigenic system present on normal and malignant cells has been defined with a human monoclonal antibody derived from a patient with breast cancer. Techniques for producing human monoclonal antibody now appear to be sufficiently advanced to initiate a serological dissection of the humoral immune response to cancer.
Fungal mycelial mats used as textile by indigenous people of North America (2021)

The indigenous people of the United States and Canada long have used forest fungi for food, tinder, medicine, paint, and many other cultural uses. New information about historical uses of fungi continues to be discovered from museums as accessions of fungi and objects made from fungi collected over the last 150+ years are examined and identified. Two textiles thought to be made from fungal mats are located in the Hood Museum of Art, Dartmouth College, and the Oakland Museum of California. Scanning electron microscopy and DNA sequencing were used to attempt to identify the fungus that produced the mats. Although DNA sequencing failed to yield a taxonomic identification, microscopy and characteristics of the mycelial mats suggest that the mats were produced by <i>Laricifomes officinalis</i>. This first report of fungal mats used for textile by indigenous people of North America will help to alert museum curators and conservators as well as mycological researchers to their existence and hopefully lead to more items being discovered that have been made from fungal fabric.
The Prognostic Value of FoxP3+ Tumor-Infiltrating Lymphocytes in Cancer: A Critical Review of the Literature (2012)

CD8+ tumor-infiltrating lymphocytes (TIL) are associated with survival in a variety of cancers. A second subpopulation of TIL, defined by forkhead box protein P3 (FoxP3) expression, has been reported to inhibit tumor immunity, resulting in decreased patient survival. On the basis of this premise, several groups are attempting to deplete FoxP3+ T cells to enhance tumor immunity. However, recent studies have challenged this paradigm by showing that FoxP3+ T cells exhibit heterogeneous phenotypes and, in some cohorts, are associated with favorable prognosis. These discrepant results could arise from differences in study methodologies or the biologic properties of specific cancer types. Here, we conduct the first systematic review of the prognostic significance of FoxP3+ T cells across nonlymphoid cancers (58 studies from 16 cancers). We assessed antibody specificity, cell-scoring strategy, multivariate modeling, use of single compared with multiple markers, and tumor site. Two factors proved important. First, when FoxP3 was combined with one additional marker, double-positive T cells were generally associated with poor prognosis. Second, tumor site had a major influence. FoxP3+ T cells were associated with poor prognosis in hepatocellular cancer and generally good prognosis in colorectal cancer, whereas other cancer types were inconsistent or understudied. We conclude that FoxP3+ T cells have heterogeneous properties that can be discerned by the use of additional markers. Furthermore, the net biologic effects of FoxP3+ T cells seem to depend on the tumor site, perhaps reflecting microenvironmental differences. Thus, depletion of FoxP3+ T cells might enhance tumor immunity in some patient groups but be detrimental in others.
Apache Hadoop YARN (2013)

The initial design of Apache Hadoop [1] was tightly focused on running massive, MapReduce jobs to process a web crawl. For increasingly diverse companies, Hadoop has become the data and computational agorá---the de facto place where data and computational resources are shared and accessed. This broad adoption and ubiquitous usage has stretched the initial design well beyond its intended target, exposing two key shortcomings: 1) tight coupling of a specific programming model with the resource management infrastructure, forcing developers to abuse the MapReduce programming model, and 2) centralized handling of jobs' control flow, which resulted in endless scalability concerns for the scheduler.
DNA transposon-based gene vehicles - scenes from an evolutionary drive (2013)

DNA transposons are primitive genetic elements which have colonized living organisms from plants to bacteria and mammals. Through evolution such parasitic elements have shaped their host genomes by replicating and relocating between chromosomal loci in processes catalyzed by the transposase proteins encoded by the elements themselves. DNA transposable elements are constantly adapting to life in the genome, and self-suppressive regulation as well as defensive host mechanisms may assist in buffering 'cut-and-paste' DNA mobilization until accumulating mutations will eventually restrict events of transposition. With the reconstructed Sleeping Beauty DNA transposon as a powerful engine, a growing list of transposable elements with activity in human cells have moved into biomedical experimentation and preclinical therapy as versatile vehicles for delivery and genomic insertion of transgenes. In this review, we aim to link the mechanisms that drive transposon evolution with the realities and potential challenges we are facing when adapting DNA transposons for gene transfer. We argue that DNA transposon-derived vectors may carry inherent, and potentially limiting, traits of their mother elements. By understanding in detail the evolutionary journey of transposons, from host colonization to element multiplication and inactivation, we may better exploit the potential of distinct transposable elements. Hence, parallel efforts to investigate and develop distinct, but potent, transposon-based vector systems will benefit the broad applications of gene transfer. Insight and clever optimization have shaped new DNA transposon vectors, which recently debuted in the first DNA transposon-based clinical trial. Learning from an evolutionary drive may help us create gene vehicles that are safer, more efficient, and less prone for suppression and inactivation.
Crystal Structure of a Mammalian Voltage-Dependent Shaker Family K + Channel (2005)

Voltage-dependent potassium ion (K+) channels (Kv channels) conduct K+ ions across the cell membrane in response to changes in the membrane voltage, thereby regulating neuronal excitability by modulating the shape and frequency of action potentials. Here we report the crystal structure, at a resolution of 2.9 angstroms, of a mammalian Kv channel, Kv1.2, which is a member of the Shaker K+ channel family. This structure is in complex with an oxido-reductase beta subunit of the kind that can regulate mammalian Kv channels in their native cell environment. The activation gate of the pore is open. Large side portals communicate between the pore and the cytoplasm. Electrostatic properties of the side portals and positions of the T1 domain and beta subunit are consistent with electrophysiological studies of inactivation gating and with the possibility of K+ channel regulation by the beta subunit.
Cardiac myosin-Th17 responses promote heart failure in human myocarditis (2016)

In human myocarditis and its sequela dilated cardiomyopathy (DCM), the mechanisms and immune phenotype governing disease and subsequent heart failure are not known. Here, we identified a Th17 cell immunophenotype of human myocarditis/DCM with elevated CD4<sup>+</sup>IL17<sup>+</sup> T cells and Th17-promoting cytokines IL-6, TGF-<b>β</b>, and IL-23 as well as GM-CSF-secreting CD4<sup>+</sup> T cells. The Th17 phenotype was linked with the effects of cardiac myosin on CD14<sup>+</sup> monocytes, TLR2, and heart failure. Persistent heart failure was associated with high percentages of IL-17-producing T cells and IL-17-promoting cytokines, and the myocarditis/DCM phenotype included significantly low percentages of FOXP3<sup>+</sup> Tregs, which may contribute to disease severity. We demonstrate a potentially novel mechanism in human myocarditis/DCM in which TLR2 peptide ligands from human cardiac myosin stimulated exaggerated Th17-related cytokines including TGF-<b>β</b>, IL-6, and IL-23 from myocarditic CD14<sup>+</sup> monocytes in vitro, and an anti-TLR2 antibody abrogated the cytokine response. Our translational study explains how an immune phenotype may be initiated by cardiac myosin TLR ligand stimulation of monocytes to generate Th17-promoting cytokines and development of pathogenic Th17 cells in human myocarditis and heart failure, and provides a rationale for targeting IL-17A as a therapeutic option.
Electrode configuration and spread of neural excitation: compartmental models of spiral ganglion cells. (1995)

A compartmental model of spiral ganglion cells in a potential field was used to predict spike discharges to electrical stimuli. The field was generated by monopolar, bipolar, or quadrupolar point source electrode geometries. The discharges of a population of afferent neurons were modeled to compare the relative spread of excitation. At the same stimulus intensity the spread of excitation was least for the quadrupolar and greatest for the radial bipolar, and this ordering held after equating for maximal spike discharge rates over the three geometries. Excitation spread from quadrupolar stimulation was highly dependent on stimulus intensity.
A BIOGEOGRAPHIC COMPARISON ON ATHYRIUM ROTH IN TAIWAN AND MAINLAND OF CHINA (2001)

Athyrium Roth is a typical Eastern Asiatic genus. There are about 160 species in the world. However, except a few species, most of them occur in the subtropical mountains of eastern Asia, and small part of them occurs in the temperature area of E. Asia. China is the distribution center of the genus with 117 species. The species of Athyrium in Taiwan are particularly close to the species in mainland. Therefore, it is a representative example for revealing the phytogeographical relationship between the two banks of the strait. There are 32 species of Athyrium sensu lato in Taiwan, including 27 species of Athyrium sensu strict, 2 species of Dryoathyrium , 1 species of Lunathyrium , 1 species of Athyriopsis and 1 species of Pseudocystopteris . If ignoring 4 species of Athyrium sensu strict with doubt, there are 28 species in Taiwan at least. Among them, 21 species are in common with mainland, the common percentage is 75%. Moreover, although the other 7 species have not been found in mainland, they are very similar to some species in mainland morphologically. Whether there are the same species, subspecies or sibling species or not? Which is still waiting for the further studies. Among the 16 common species of Athyrium sensu strict between Taiwan and mainland, 7 species are disjunct distribution between Taiwan and Southwest China. Which not only shows Athyrium species in Taiwan have close relationship with mainland species may be with common origin, but also shows the flora of the highland of Taiwan has most close relationship with the flora of the highland in the Southwest mainland. Further investigating and examining of genetic relationship (such as genetic identity) of the common or related species of two banks of the strait with biosystematic or molecular systematic methods, and further understanding and quantitative studies on the historical and geographical relationships between the florae of Taiwan and mainland are necessary.
Clinical evaluation of a new polymerase chain reaction assay for detection of Chlamydia trachomatis in endocervical specimens (1993)

A clinical evaluation of the Amplicor polymerase chain reaction (PCR) assay for the detection of Chlamydia trachomatis in endocervical swabs (Roche Molecular Systems, Branchburg, N.J.) is described. This new clinical system used one-step sample preparation, amplification with biotinylated cryptic plasmid primer pairs (CP24-CP27), uracil-N-glycosylase (AmpErase), and a microtiter format for amplicon capture and detection. Culture with McCoy cells in duplicate 1-dram (3.697-ml) vials with fluorescent immunostaining was the reference system. Endocervical swab samples from 945 women provided 74 culture-positive specimens, of which PCR detected 71. The initial PCR result was positive for 12 additional specimens. Arbitration of the PCR-positive, culture-negative samples by PCR with major outer membrane protein primers, duplicate culture, elementary body direct fluorescent-antibody staining, and DNA extraction PCR showed that all 12 samples were positive for chlamydia, raising the number of truly positive samples from 74 to 86. After arbitration the true sensitivities of PCR and culture were 96.5 and 86%, respectively (P = 0.02). Specificities for both were 100%. For PCR, the positive and negative predictive values were 100 and 99.7%, respectively. Total test efficiency was 99.7%. A high-test-volume (121 samples) timing study with all items included in the College of American Pathologists work load method indicated that this PCR format took approximately 3 min per sample. Because of the high sensitivity, specificity, and improved ease of handling, we found PCR to be a good alternative to culture for detection of C. trachomatis.
Novel strategies for improved cancer vaccines (2009)

Therapeutic vaccination against cancer is an important modality complementing current standard therapies and may lead to long-term control of cancer. Numerous strategies are in development in an attempt to achieve better effectiveness but, except for the recent advent of vaccines against human papillomavirus, the long effort to produce a cancer vaccine has not succeeded. Nevertheless, a number of novel approaches can be pursued that, in our view, include optimized antigen design, in vivo-targeted dendritic cell vaccination and cancer vaccines used in combination with chemotherapy, monoclonal antibodies, adoptive T-cell transfer or stem cell transplantation. This article summarizes the rationale and development of these approaches for improved cancer vaccines.
NanoDrop Microvolume Quantitation of Nucleic Acids (2010)

Biomolecular assays are continually being developed that use progressively smaller amounts of material, often precluding the use of conventional cuvette-based instruments for nucleic acid quantitation for those that can perform microvolume quantitation. The NanoDrop microvolume sample retention system (Thermo Scientific NanoDrop Products) functions by combining fiber optic technology and natural surface tension properties to capture and retain minute amounts of sample independent of traditional containment apparatus such as cuvettes or capillaries. Furthermore, the system employs shorter path lengths, which result in a broad range of nucleic acid concentration measurements, essentially eliminating the need to perform dilutions. Reducing the volume of sample required for spectroscopic analysis also facilitates the inclusion of additional quality control steps throughout many molecular workflows, increasing efficiency and ultimately leading to greater confidence in downstream results. The need for high-sensitivity fluorescent analysis of limited mass has also emerged with recent experimental advances. Using the same microvolume sample retention technology, fluorescent measurements may be performed with 2 μL of material, allowing fluorescent assays volume requirements to be significantly reduced. Such microreactions of 10 μL or less are now possible using a dedicated microvolume fluorospectrometer. Two microvolume nucleic acid quantitation protocols will be demonstrated that use integrated sample retention systems as practical alternatives to traditional cuvette-based protocols. First, a direct A260 absorbance method using a microvolume spectrophotometer is described. This is followed by a demonstration of a fluorescence-based method that enables reduced-volume fluorescence reactions with a microvolume fluorospectrometer. These novel techniques enable the assessment of nucleic acid concentrations ranging from 1 pg/ μL to 15,000 ng/ μL with minimal consumption of sample.
Automated Genotyping Using the DNA MassArray™ Technology (2003)

The ongoing progress in establishing a reference sequence as part of the Human Genome Project (1) has revealed a new challenge: the large-scale identification and detection of intraspecies sequence variations, either between individuals or populations. The information drawn from those studies will lead to a detailed understanding of genetic and environmental contributions to the etiology of complex diseases.
Platelets Induce Apoptosis during Sepsis in a Contact-Dependent Manner That Is Inhibited by GPIIb/IIIa Blockade (2012)

In sepsis, platelet granzyme B-mediated apoptosis occurs in spleen and lung, and absence of granzyme B slows sepsis progression. This process proceeds in a contact-dependent manner that is inhibited ex vivo and in vivo by the platelet GPIIb/IIIa receptor inhibitor eptifibatide. The GPIIb/IIIa inhibitors and other classes of anti-platelet drugs may be protective in sepsis.
Advances in the production of human monoclonal antibodies (2011)

Abstract: Since the development of hybridoma technology over three decades ago, numerous monoclonal antibodies have been produced and the use of monoclonal antibodies has become one of the major breakthroughs in medicine. Significant progress has been made on new technologies for generating human monoclonal antibodies. This review serves as an introduction to the immortalization of antigen-specific human B cell and hybridoma technologies, phage display platform, the use of transgenic mice, and the generation of monoclonal antibodies from single B cells. Keywords: human monoclonal antibody, B cells, hybridoma, phage display, transgenic mice, immunoglobulin gene cloning
Isolation and Characterization of the Sheep Erythrocyte Receptor in Man (1975)

Properties of the sheep erythrocyte receptor on human lymphocytes were examined from two different aspects: inhibition of E-rosette formation by antisera, and extraction of T and non-T cells with 3 M KCl. Antisera to several T cell populations produced significant inhibition of E-rosette formation by human peripheral blood lymphocytes, whereas anti-B cell, anti-beta2-microglobulin, anti-I, and anit-i were ineffective. Sera with activity to HL-A subgroups on the HPBL tested produced complete rosette inhibition, although nonspecific anti-HL-A produced no inhibition. T cell preparations extracted by a 3M KCl technique contained activity that could be bound to SRBC and produce inhibition of rosette formation by HPBL. This inhibitory component could be quickly eluted from the SRBC and retain its inhibitory activity. No inhibitory activity could be demonstrated in extracts of B cells and non-lymphoid cells. These results suggest that 1) T cell-specific and HL-A specific antisera inhibit E-rosette formation; 2) beta2-M is not involved in the SRBC receptor as an active component; and 3) the receptor may be isolated by 3 M KCl extraction, and partially purified by the use of SRBC as a specific immunoadsorbent, without loss of biologic activity.
Recombinant Bombyx mori Nucleopolyhedrovirus Harboring Green Fluorescent Protein (1998)

The gene encoding the green fluorescent protein (gfp) under the control of the highly expressed Autographa californica nucleopolyhedrovirus (AcMNPV)-polyhedrin promoter has been introduced into the polyhedrin (polh) locus of Bombyx mori nucleopolyhedrovirus (BmNPV) by homologous recombination. The insect host larvae and the cultured cells infected with this recombinant virus (vBmGFP) showed high levels of expression of gfp. The larval tissues permissive to virus multiplication could be readily visualized using the tagged recombinant virus, thus providing a direct approach to study the progress of virus infection or its control in the animal host. The highly expressed recombinant protein, GFP, could be easily solubilized from fat bodies. Thus, the caterpillar-based expression could serve as an economic alternative method for the large-scale production of recombinant proteins, even when they are nonsecretory in nature. Further, if the recombinant vBmGFP is used as a parent in generating other recombinants, conversion of the fluorescent plaques to colorless plaques serves as an easy means for screening recombinants. Such a method is especially helpful for BmNPV-recombinant selections in the absence of the other simplified techniques as are available for the prototype baculovirus AcMNPV system.