gebhart/patrepeval huggingface dataset:
American Society of Clinical Oncology/College of American Pathologists Guideline Recommendations for Immunohistochemical Testing of Estrogen and Progesterone Receptors in Breast Cancer (2010)

The Panel recommends that ER and PgR status be determined on all invasive breast cancers and breast cancer recurrences. A testing algorithm that relies on accurate, reproducible assay performance is proposed. Elements to reliably reduce assay variation are specified. It is recommended that ER and PgR assays be considered positive if there are at least 1% positive tumor nuclei in the sample on testing in the presence of expected reactivity of internal (normal epithelial elements) and external controls. The absence of benefit from endocrine therapy for women with ER-negative invasive breast cancers has been confirmed in large overviews of randomized clinical trials.
Functional screening identifies CRLF2 in precursor B-cell acute lymphoblastic leukemia (2009)

The prognosis for adults with precursor B-cell acute lymphoblastic leukemia (B-ALL) remains poor, in part from a lack of therapeutic targets. We identified the type I cytokine receptor subunit CRLF2 in a functional screen for B-ALL-derived mRNA transcripts that can substitute for IL3 signaling. We demonstrate that CRLF2 is overexpressed in approximately 15% of adult and high-risk pediatric B-ALL that lack MLL, TCF3, TEL, and BCR/ABL rearrangements, but not in B-ALL with these rearrangements or other lymphoid malignancies. CRLF2 overexpression can result from translocation with the IGH locus or intrachromosomal deletion and is associated with poor outcome. CRLF2 overexpressing B-ALLs share a transcriptional signature that significantly overlaps with a BCR/ABL signature, and is enriched for genes involved in cytokine receptor and JAK-STAT signaling. In a subset of cases, CRLF2 harbors a Phe232Cys gain-of-function mutation that promotes constitutive dimerization and cytokine independent growth. A mutually exclusive subset harbors activating mutations in JAK2. In fact, all 22 B-ALLs with mutant JAK2 that we analyzed overexpress CRLF2, distinguishing CRLF2 as the key scaffold for mutant JAK2 signaling in B-ALL. Expression of WT CRLF2 with mutant JAK2 also promotes cytokine independent growth that, unlike CRLF2 Phe232Cys or ligand-induced signaling by WT CRLF2, is accompanied by JAK2 phosphorylation. Finally, cells dependent on CRLF2 signaling are sensitive to small molecule inhibitors of either JAKs or protein kinase C family kinases. Together, these findings implicate CRLF2 as an important factor in B-ALL with diagnostic, prognostic, and therapeutic implications.
Functional analysis of avian class I (BFIV) glycoproteins by epitope tagging and mutagenesis in vitro (1995)

Similarities between the physical structures of avian and mammalian major histocompatibility complex (MHC) class I glycoproteins have been proposed based on comparative alignment of their amino acid sequences. To investigate the physical structure of the chicken class I glycoprotein, we cloned the cDNA representing the BFIV locus of the B21 haplotype. A unique, chimeric class I glycoprotein was constructed by incorporating an epitope tag (FLAG) at the N terminus. Monoclonal antibodies to the FLAG epitope served to monitor cell-surface expression for functional analysis of the BFIV21 class I glycoprotein. The chimeric class I glycoprotein was expressed in target cells using an avian leukosis virus (ALV)-derived retrovirus vector (RCASBP). The presence of the FLAG epitope did not interfere with either alloantibody recognition or cytotoxic T lymphocyte interaction. Functional analysis employing site-directed mutagenesis identified BF amino acid residues forming serologic epitopes as well as residues important in antigen presentation to ALV-induced cytotoxic T lymphocytes. BF residues 78 and 81, corresponding to HLA 79 and 82, form an antibody epitope with a slight effect on ALV antigen presentation, consistent with their predicted orientation based on the HLA-A2 crystal structure. Alignment of the BFIV21 sequence with previously published BFIV sequences revealed polymorphisms at position 34 (HLA 34), a monomorphic residues in HLA and H-2. Residue 34 is located in pocket B and is predicted to contact the main-chain carbon of peptides bound in HLA-A2. A site-directed substitution in BFIV residue 34 dramatically alters ALV antigen presentation by the BFIV21 class I glycoprotein. These data indicate that the physical molecular structure of the chicken MHC class I glycoprotein is similar to HLA.
A Method for Obtaining Digital Signatures and Public-Key Cryptosystems (1978)

An encryption method is presented with the novel property that publicly revealing an encryption key does not thereby reveal the corresponding decryption key.This has two important consequences:1. Couriers or other secure means are not needed to transmit keys, since a message can be enciphered using an encryption key publicly revealed by the intended recipient.Only he can decipher the message, since only he knows the corresponding decryption key.2. A message can be "signed" using a privately held decryption key.Anyone can verify this signature using the corresponding publicly revealed encryption key.Signatures cannot be forged, and a signer cannot later deny the validity of his signature.This has obvious applications in "electronic mail" and "electronic funds transfer" systems.A message is encrypted by representing it as a number M, raising M to a publicly specified power e, and then taking the remainder when the result is divided by the publicly specified product, n, of two large secret prime numbers p and q.Decryption is similar; only a different, secret, power d is used, where e • d ≡ 1 (mod (p -1) • (q -1)).The security of the system rests in part on the difficulty of factoring the published divisor, n.
High accuracy dispersion measurements of chirpedfibre gratings (1995)

A wavelength scanning interferometric technique has been used to provide phase dispersion and time delay measurements of photorefractive fibre gratings with sub-picosecond time delay and 3 pm wavelength resolutions for the first time. Chirped fibre grating filters for dispersion compensation in long fibre telecommunications links have been fully characterised.
Gene therapy in the adult primate brain: intraparenchymal grafts of cells genetically modified to produce nerve growth factor prevent cholinergic neuronal degeneration. (1996)

Gene therapy may be a useful means of delivering substances to the brain that are capable of preventing neuronal degeneration. In the present experiment, we determined whether intraparenchymal transplants of primary autologous cells genetically modified to produce nerve growth factor (NGF) would prevent injury-induced degeneration of cholinergic neurons. Cultured primary monkey fibroblasts were genetically modified to produce human NGF, and secreted 13.2 ng NGF/10(6) cells/h in vitro. Adult monkeys then underwent fornix transections to induce degeneration of basal forebrain cholinergic neurons, and received autologous grafts of either NGF-producing or control, beta-galactosidase-producing fibroblasts directly into the basal forebrain region. One month later, 61.7 +/- 8.9% of cholinergic neurons remained indentifiable in NGF-graft recipients compared to 26.2 +/- 5.0% in control graft recipients (P < 0.02). Neuronal protection correlated with the accuracy of graft placement: up to 92% protection from neuronal degeneration occurred when NGF-secreting grafts were accurately placed immediately adjacent to injured neurons. Thus, intraparenchymal NGF delivery to the adult primate brain by gene transfer can prevent the degeneration of basal forebrain cholinergic neurons. Gene therapy can target intraparenchymal brain sites for regionally specific neurotrophin delivery, thereby avoiding limitations imposed by diffusion of substances across the blood-brain barrier and through CNS parenchyma, while avoiding adverse effects of neurotrophic factors delivered in a non-directed manner to the central nervous system. The delivery of NGF by gene transfer to the brain merits further study as a means of preventing cholinergic neuronal degeneration in human disorders such as Alzheimer's disease.
Complete eradication of human B-cell lymphoma xenografts using rituximab in combination with the immunocytokine L19-IL2 (2008)

The antibody-mediated delivery of therapeutic agents to sites of angiogenesis is an attractive strategy for anticancer therapy, but is largely unexplored in hematologic malignancies. In the present study, we show that the extra domain B (EDB) of fibronectin, a marker of angiogenesis, is expressed in B-cell non-Hodgkin lymphoma (NHL) and that the human monoclonal anti-EDB antibody L19 can selectively localize to the lymphoma-associated subendothelial extracellular matrix. In vivo, the preferential accumulation of the antibody at the tumor site was confirmed by quantitative biodistribution analyses with radioiodinated antibody preparations. The fusion protein L19-IL2, which mediates the delivery of interleukin-2 (IL-2) to the neovasculature, displayed a superior antilymphoma activity compared with unconjugated IL-2 in localized and systemic xenograft models of NHL. When coadministered with rituximab, L19-IL2 induced complete remissions of established localized lymphomas and provided long-lasting protection from disseminated lymphoma. The combined use of rituximab and L19-IL2, which dramatically increases the infiltration of immune effector cells in lymphomas, may deserve clinical investigations, facilitated by the fact that L19-IL2 is currently being studied in phase II clinical trials in patients with solid tumors.
Drug Release from a pH-Sensitive Multiblock Co-Polymer Thermogel (2012)

A Pluronic(®)-based pH-sensitive multiblock co-polymer thermogel has been proposed for sustained release of therapeutic agents. Hydrophobic small-molecule drugs (paclitaxel and camptothecin) and model hy-drophilic macromolecules (fluorescein-labeled dextrans of molecular mass 10, 20, 40, 150 and 250 kDa) were successfully loaded into and released from the thermogels. Drug-loaded polymer solutions were characterized for gelation behavior and micelle size. Drug loading increased the size of the multiblock co-polymer micelles from 20 to 100 nm. The co-polymer improved paclitaxel and camptothecin loading in an aqueous solution by 6900- and 1050-fold, respectively, compared to their solubility in water. The ther-mogels released loaded drugs in a pH-dependent fashion, regardless of their properties. At pH 5.0 and 6.5, paclitaxel and camptothecin completely released in 4 and 15 days, respectively, by a combined mechanism of diffusion and erosion. At neutral pH, diffusion predominated gel erosion to sustain the drug release up to 40 days. Fluorescein-labeled dextran release from the thermogels showed a similar pH-dependent trend as the hydrophobic small molecule drugs. However, dextran release at neutral pH was entirely dependent on the molecular mass of the dextran. Low-molecular-mass (10 and 20 kDa) dextrans were completely released in 12 and 21 days, respectively, while high-molecular-mass (⩾40 kDa) dextrans being continuously released over 36 days, indicating that the threshold of molecular weight necessary for sustained release of a hydrophilic macromolecule from this thermogel (e.g., enzymes, monoclonal antibodies and immunotoxins) is 40 kDa. Taken together, the MBCP thermogel showed potential as a controlled drug-delivery system that showed sustained release of both hydrophilic and lipophilic molecules.
Modern Processor Design: Fundamentals of Superscalar Processors (2002)

Modern Processor Design: Fundamentals of Superscalar Processors is an exciting new first edition from John Shen of Carnegie Mellon University & Intel and Mikko Lipasti of the University of Wisconsin-Madison. This book brings together the numerous microarchitectural techniques for harvesting more instruction-level parallelism (ILP) to achieve better processor performance that have been proposed and implemented in real machines. These techniques, as well as the foundational principles behind them, are organized and presented within a clear framework that allows for ease of comprehension. This text is intended for an advanced computer architecture course or a course in superscalar processor design. It is written at a level appropriate for senior or first year graduate level students.
Ethanol production from xylose by enzymic isomerization and yeast fermentation (1981)

Repetitive enzymic isomerization of xylose followed by yeast fermentation of xylulose, and simultaneous enzymic isomerization and yeast fermentation were proven to be methods capable of converting xylose to ethanol. The fermentation product, ethanol, xylitol, or glycerol, has little inhibitory or deactivation effect on the activity of isomerase. In a comparison of the ability of yeasts to ferment xylulose to ethanol, Schizosaccharomyces pombe was found to be superior to industrial bakers' yeast. Under optimal conditions (pH 6, temperature 30/sup 0/C), a final ethanol concentration of 6.3 wt.% was obtained from simulated hemicellulose hydrolysate using a simultaneous fermentation process. The ethanol yield was over 80% of the theoretical value.
Development Of Clinical Disease In Cats Experimentally Infected With Feline Immunodeficiency Virus (1994)

Cats naturally infected with feline immunodeficiency virus (FIV) develop an AIDS-like syndrome whereas experimentally infected cats do not. To investigate the role of cofactors in the development of this disease in cats, 7 specific pathogen-free (SPF) and 12 random-source (RS) cats were infected with FIV. Over 4 years, infected cats developed similar phenotypic and functional immune abnormalities characterized by early and chronic inversion of CD4+:CD8+ cell ratios and significantly decreased mitogen responses compared with controls. Beginning 18-24 months after infection, 10 RS cats developed chronic clinical disease typical of feline AIDS, including stomatitis and recurrent upper respiratory disease; 4 SPF cats also developed chronic clinical disease, 2 with neurologic disease and 2 with B cell lymphomas. Thus, immunologic background is important in the type of disease that develops in cats infected with FIV, and FIV represents a promising animal model for studying the immunopathogenesis of AIDS in humans.
5-Fluorouracil and Interleukin-2 Immunochemotherapy Enhances Immunogenicity of Non-Small Cell Lung Cancer A549 Cells through Upregulation of NKG2D Ligands (2014)

5-FU and IL-2 immunochemotherapy significantly inhibited tumor growth and activated NK cytotoxicity in vivo, and these effects were partly impaired after depleting NK cells in tumor-bearing mice. Combination treatment of 5-FU and IL-2 upregulated the expression and the promoter activity of MICA/MICB in A549 cells, which enhanced the recognition of A549 cells by NK cells. All of the data indicated that immunochemotherapy of 5-FU and IL-2 may provide a new treatment option for patients with lung cancer.
A Microarray-Matrix-assisted Laser Desorption/Ionization-Mass Spectrometry Approach for Site-specific Protein N-glycosylation Analysis, as Demonstrated for Human Serum Immunoglobulin M (IgM)* (2015)

We demonstrate a new approach for the site-specific identification and characterization of protein N-glycosylation. It is based on a nano-liquid chromatography microarray-matrix assisted laser desorption/ionization-MS platform, which employs droplet microfluidics for on-plate nanoliter reactions. A chromatographic separation of a proteolytic digest is deposited at a high frequency on the microarray. In this way, a short separation run is archived into thousands of nanoliter reaction cavities, and chromatographic peaks are spread over multiple array spots. After fractionation, each other spot is treated with PNGaseF to generate two correlated traces within one run, one with treated spots where glycans are enzymatically released from the peptides, and one containing the intact glycopeptides. Mining for distinct glycosites is performed by searching for the predicted deglycosylated peptides in the treated trace. An identified peptide then leads directly to the position of the "intact" glycopeptide clusters, which are located in the adjacent spots. Furthermore, the deglycosylated peptide can be sequenced efficiently in a simple collision-induced dissociation-MS experiment. We applied the microarray approach to a detailed site-specific glycosylation analysis of human serum IgM. By scanning the treated spots with low-resolution matrix assisted laser desorption/ionization-time-of-flight-MS, we observed all five deglycosylated peptides, including the one originating from the secretory chain. A detailed glycopeptide characterization was then accomplished on the adjacent, untreated spots with high mass resolution and high mass accuracy using a matrix assisted laser desorption ionization-Fourier transform-MS. We present the first detailed and comprehensive mass spectrometric analysis on the glycopeptide level for human polyclonal IgM with high mass accuracy. Besides complex type glycans on Asn 395, 332, 171, and on the J chain, we observed oligomannosidic glycans on Asn 563, Asn 402 and minor amounts of oligomannosidic glycans on the glycosite Asn 171. Furthermore, hybrid type glycans were found on Asn 402, Asn 171 and in traces Asn 332.
[Adequacy of the pharmacologic treatment to the recommendations of a performance protocol in hypercholesterolemia in primary care]. (1996)

Treatment was initiated when LDL-c figures were over the limit specified in the protocol. In most cases this was because of the accumulation of cardiovascular risk factors.
Pyrolysis of chlorogenic acid and rutin. (1982)

Chlorogenic acid and rutin, major polyphenols in tobacco, were pyrolysed with a furnace type pyrolyser connected directly to a gas chromatograph and 22 compounds (including catechol, benzoic acid, 4-vinylcatechol and quinic acid γ-lactone) from Chlorogenic acid and 24 compounds [including catechol, 5-methyl-2-furaldehyde, 4-methylcatechol and 1, 6-anhydroglucopyranose (levoglucosan)] from rutin have been identified as pyrolysis products. The gas chromatograph was also replaced by a capillary cold trap which allowed collection of the pyrolysis products prior to a quantitative determination using an internal standard. Comparison of the pyrolysis products produced from chlorogenic acid or rutin with those derived from tobacco and analysis of the pyrolysis products from a mixture of tobacco and chlorogenic acid or rutin indicated that fairly large proportions of catechol, 4-vinylcatechol and quinic acid γ-lactone produced by the pyrolysis of tobacco may originate from endogenous chlorogenic acid.
Digital Risk Management: Protecting Your Privacy, Improving Security, and Preparing for Emergencies (2006)

As our information systems grow more complex and we rely more on the electronic storage and transfer of information, the risk of damage, loss, and fraud increases dramatically. What information needs to be protected, and how do we go about doing that? This paper defines a variety of data vulnerabilities, and presents some simple steps that you can take to protect yourself, your company, and your information
Revisiting Distributed Synchronous SGD (2017)

Distributed training of deep learning models on large-scale training data is typically conducted with asynchronous stochastic optimization to maximize the rate of updates, at the cost of additional noise introduced from asynchrony. In contrast, the synchronous approach is often thought to be impractical due to idle time wasted on waiting for straggling workers. We revisit these conventional beliefs in this paper, and examine the weaknesses of both approaches. We demonstrate that a third approach, synchronous optimization with backup workers, can avoid asynchronous noise while mitigating for the worst stragglers. Our approach is empirically validated and shown to converge faster and to better test accuracies.
Rapid Active Internal Core Cooling for Induction of Moderate Hypothermia in Head Injury by Use of an Extracorporeal Heat Exchanger (1998)

The results of this investigation suggest that the use of an extracorporeal heat exchanger to achieve active core cooling is suitable for fast and accurately controllable induction, maintenance, and reversal of moderate hypothermia in emergency situations with reliable control of temperature. In this small series of highly selected patients with severe head injuries, we did not note a beneficial effect of hypothermic therapy on outcome.
An adaptive fuzzy C-means algorithm for image segmentation in the presence of intensity inhomogeneities (1999)

We present a novel algorithm for obtaining fuzzy segmentations of images that are subject to multiplicative intensity inhomogeneities, such as magnetic resonance images. The algorithm is formulated by modifying the objective function in the fuzzy C-means algorithm to include a multiplier field, which allows the centroids for each class to vary across the image. First and second order regularization terms ensure that the multiplier field is both slowly varying and smooth. An iterative algorithm that minimizes the objective function is described, and its efficacy is demonstrated on several test images.
A novel pathway for vitamin A signaling mediated by RXR heterodimerization with NGFI-B and NURR1. (1995)

In addition to its role as a 9-cis retinoic acid receptor, RXR has an important role in the regulation of multiple hormonal pathways through heterodimerization with nuclear receptors. Here, we show that two orphan receptors, NGFI-B and NURR1, which have been shown previously to interact with DNA as monomers, also can heterodimerize with RXR. These heterodimers bind selectively to a class of retinoic acid response elements composed of direct repeats spaced by 5 nucleotides. In this respect they are similar to heterodimers formed between RXR and the receptor for all-trans retinoic acid, RAR. However, whereas RXR is inhibited in the RXR-RAR heterodimer, NGFI-B/NURR1 promote efficient activation in response to RXR ligands and therefore shift RXR from a silent to an active heterodimerization partner. These data show that NGFI-B and NURR1 can increase the potential of RXR to modulate gene expression in a ligand-dependent manner by allowing a distinct class of direct repeats to serve as specific RXR response elements. Because expression of both NGFI-B and NURR1 is rapidly induced by various growth factors, these findings also suggest a novel mechanism for convergence between vitamin A or retinoid and growth factor signaling pathways.
Gill Gymnastics (2011)

Mushrooms release astonishing numbers of spores. A large bracket fungus discharges 30 billion spores every day, which amounts to five trillion spores during its six months of activity each year. Spore release in mushrooms, which is a kind of jumping mechanism, is driven by the movement of microscopic droplets of fluid over the spore surface. This was studied by A. H. R. Buller, “the Einstein of mycology,” in the first half of the twentieth century. Many questions about the mechanism were solved very recently, with the aid of high-speed video cameras. Spore discharge in bracket fungi entails precise geotropic positioning of millions of tiny tubes beneath the fruit body. The mechanism has been adjusted in different species by adaptations in spore shape and size. Its success offers a beautiful illustration of the principles of Darwinian evolution.