gebhart/patrepeval huggingface dataset:
Metastatic progression and gene expression between breast cancer cell lines from African American and Caucasian women (2007)

African American (AA) women have a lower overall incidence of breast cancer than do Caucasian (CAU) women, but a higher overall mortality. Little is known as to why the incidence of breast cancer is lower yet mortality is higher in AA women. Many studies speculate that this is only a socio-economical problem. This investigation suggests the possibility that molecular mechanisms contribute to the increased mortality of AA women with breast cancer. This study investigates the expression of 14 genes which have been shown to play a role in cancer metastasis. Cell lines derived from AA and CAU patients were analyzed to demonstrate alterations in the transcription of genes known to be involved in cancer and the metastatic process. Total RNA was isolated from cell lines and analyzed by RT-PCR analysis. Differential expression of the 14 targeted genes between a spectrum model (6 breast cancer cell lines and 2 non-cancer breast cell lines) and a metastasis model (12 metastatic breast cancer cell lines) were demonstrated. Additionally, an in vitro comparison of the expression established differences in 5 of the 14 biomarker genes between African American and Caucasian breast cell lines. Results from this study indicates that altered expression of the genes Atp1b1, CARD 10, KLF4, Spint2, and Acly may play a role in the aggressive phenotype seen in breast cancer in African American women.
Renal stress response and acute renal failure. (1997)

When kidneys are injured in vivo, the reaction of the renal epithelial is heterogeneous. Some cells, especially those of the proximal tubule, undergo necrosis, other cells undergo apoptosis, and still others survive the injury apparently intact. In addition, injured tubules are relined with new cells actively engaged in DNA synthesis. Nephrotoxic and ischemic renal damage also is accompanied by a typical immediate early gene (IEG) response, which does not always occur in cells that undergo DNA synthesis, suggesting that the role of the IEG response is not necessarily proliferative in this setting. The activation of parts of this pathway is mediated by the stress-activated protein kinases (SAPKs), which may induce cell-cycle arrest and apoptosis. Downregulation of the SAPKs improve renal function and improve long-term outcome during ischemic renal failure. It is thus possible that manipulation of this pathway could ameliorate acute renal failure. Clues to the pertinent pathways and genes to target therapy to alter the course of renal failure will come from continued understanding of the transduction pathways activated by renal cell stress and the identification of factors that promote survival of renal cells.
Modal gain and T/sub 0/ value improvements in quantum dot lasers using dots-in-a-well (DWELL) structure (2000)

The issues necessary to achieve high ground state modal gain and high T/sub 0/ value are addressed. It is found that the modal gain and the T/sub 0/ value can be increased simultaneously. Three different ways to improve the modal gain and T/sub 0/ value are discussed. Additionally, it is pointed out that the low threshold current density of QD lasers, is due primarily to "physical scaling" rather than any quantum effect. The performance tradeoffs occur between the threshold current density and the ground state modal gain and T/sub 0/ value. QD lasers with InAs/In/sub x/Ga/sub 1-x/As dots-in-a-well (DWELL) structure are used.
Migration, Nomadism, Networks: A Biography (2011)

Abstract This chapter summarizes Vilém Flusser’s biography through a description of essays that reflect Flusser’s identity as an immigrant, expellee, and intellectual nomad during his stay in Prague, London, São Paulo, and Robion. It begins by discussing events of Flusser’s life in Prague, from his birth to his forced exile in 1939, followed by a description of Flusser’s one-year residence in London during the start of the First World War. After London, Flusser moved to São Paulo where he married Edith Barth and fathered their first child, Dinah. The chapter concludes with Flusser’s time in Robion, France, where he wrote essays that often implied the concept of nomad life.
Management of sepsis in neutropenic patients: 2014 updated guidelines from the Infectious Diseases Working Party of the German Society of Hematology and Medical Oncology (AGIHO) (2014)

Sepsis is a major cause of mortality during the neutropenic phase after intensive cytotoxic therapies for malignancies. Improved management of sepsis during neutropenia may reduce the mortality of cancer therapies. Clinical guidelines on sepsis treatment have been published by others. However, optimal management may differ between neutropenic and non-neutropenic patients. Our aim is to give evidence-based recommendations for haematologist, oncologists and intensive care physicians on how to manage adult patients with neutropenia and sepsis.
A direct comparison of PET activation and electrocortical stimulation mapping for language localization (1997)

Mapping eloquent language cortex in presurgical patients typically is accomplished using highly invasive direct cortical stimulation techniques. Functional imaging during language activation using positron emission tomography (PET) is a promising, noninvasive alternative that requires validation. In seven patients undergoing surgical evaluation for intractable epilepsy, we performed both direct cortical stimulation and PET activation mapping of language cortex using identical tasks. MRI, PET, and CT scans were coregistered to directly compare the location of language centers determined by cortical stimulation versus activation PET. We found that cortical regions that showed increased cerebral blood flow during both visual and auditory naming tasks were located in the same regions as subdural electrodes which disrupted language during electrical stimulation. Cortical regions underlying electrodes that did not disrupt language also showed no consistent changes in regional cerebral blood flow during PET activation. Used cautiously, PET activation produces language maps similar to those obtained with direct cortical stimulation, with more complete brain coverage and considerably less invasion.
A nanoscale Ti/GaAs metal-semiconductor hybrid sensor for room temperature light detection (2010)

We report an individually addressable Ti∕GaAs metal-semiconductor hybrid optical nanosensor with positive photoresistance and a sensitivity that increases as the device dimensions shrink. The underlying physics relates to the crossover from ballistic to diffusive transport of the photoinduced carriers and the geometric enhancement of the effect associated with a Schottky-barrier-coupled parallel metal shunt layer. For a 250 nm device under 633 nm illumination we observe a specific detectivity of D(*)=5.06×10(11) cm √Hz∕W with a dynamic response of 40 dB.
P38 Mapk Mediates Fibrogenic Signal Through Smad3 Phosphorylation in Rat Myofibroblasts (2003)

Hepatic stellate cells (HSCs) spontaneously transdifferentiate into myofibroblast (MFB)-phenotype on plastic dishes. This response recapitulates the features of activation in vivo. Transforming growth factor beta (TGF-beta) plays a prominent role in stimulating liver fibrogenesis by MFBs. In quiescent HSCs, TGF-beta signaling involves TGF-beta type I receptor (TbetaRI)-mediated phosphorylation of serine residues within the conserved SSXS motif at the C-terminus of Smad2 and Smad3. The middle linker regions of Smad2 and Smad3 also are phosphorylated by mitogen-activated protein kinase (MAPK). This study elucidates the change of Smad3-mediated signals during the transdifferentiation process. By using antibodies highly specific to the phosphorylated C-terminal region and the phosphorylated linker region of Smad3, we found that TGF-beta-dependent Smad3 phosphorylation at the C-terminal region decreased, but that the phosphorylation at the linker region increased in the process of transdifferentiation. TGF-beta activated the p38 MAPK pathway, further leading to Smad3 phosphorylation at the linker region in the cultured MFBs, irrespective of Smad2. The phosphorylation promoted hetero-complex formation and nuclear translocation of Smad3 and Smad4. Once combined with TbetaRI-phosphorylated Smad2, the Smad3 and Smad4 complex bound to plasminogen activator inhibitor-type I promoter could enhance the transcription. In addition, Smad3 phosphorylation mediated by the activated TbetaRI was impaired severely in MFBs during chronic liver injury, whereas Smad3 phosphorylation at the linker region was remarkably induced by p38 MAPK pathway. In conclusion, p38 MAPK-dependent Smad3 phosphorylation promoted extracellular matrix production in MFBs both in vitro and in vivo.
Cross‐Coupling Reactions Of Organoboranes: An Easy Way To Construct CC Bonds (Nobel Lecture) (2011)

Tools for chemists: The Nobel Prize in Chemie 2010 was awarded for research on palladium-catalyzed cross-coupling in organic synthesis. Two of the Laureates, A. Suzuki and E. Negishi, report here first hand on the historical development and the current status of this research.
Recent Applications of α‐Metalated Isocyanides in Organic Synthesis (1977)

Abstract Being both nucleophilic and electrophilic, α‐metalated isocyanides can add to polar double bonds, forming heterocycles. They are also synthons for α‐metalated primary amines. This article describes recent or improved procedures for their use in organic synthesis: (1) In heterocyclic syntheses to give 2‐oxazolines, 2‐imidazolines, 2‐thiazolines, oxazoles and oligooxazoles, thiazoles, triazoles, imidazolinones, pyrroles, 5,6‐dihydro‐1,3‐oxazines and ‐thiazines, and ( via cycloaddition with nitrones) 2‐imidazolidinones. (2) In the field of formylaminomethylenation, for example transformation of estrone methyl ether and a keto sugar into the corresponding α‐formylaminoacrylic esters, and the conversion of aldehydes and ketones by 3‐ and 4‐pyridyl‐methyl isocyanides into N ‐(1‐pyridyl‐1‐alkenyl)formamides and their hydrolysis to 3‐ and 4‐acylpyridines. (3) In connection with the use of α‐metalated isocyanides as synthons for α‐metalated primary amines, the author demonstrates how they may be used for preparation of 1,2‐ and 1,3‐amino alcohols, 1,2‐diamines, 2,3‐diaminoalkanoic acids and for synthesis of higher amino acids starting from simple amino acids.
Inability of outer-surface protein C (OspC)-primed mice to elicit a protective anamnestic immune response to a tick-transmitted challenge of Borrelia burgdorferi (2003)

A one-inoculation regimen of recombinant outer-surface protein C (OspC), which has been demonstrated to elicit protective immunity against a tick-borne challenge of Borrelia burgdorferi, was administered to outbred mice. Following seroconversion, the serum antibody titre against OspC was allowed to wane with time until there was little or no detection of anti-OspC antibodies by immunoblot. The mice were then challenged with an infectious dose of B. burgdorferi by tick transmission. Eleven of 12 OspC-primed mice subsequently became infected by B. burgdorferi, demonstrating that a protective anamnestic response was not generated in these mice following the introduction of infectious OspC-expressing spirochaetes.
IL-33, the IL-1-like cytokine ligand for ST2 receptor, is a chromatin-associated nuclear factorin vivo (2006)

Recent studies indicate that IL-1alpha functions intracellularly in pathways independent of its cell surface receptors by translocating to the nucleus and regulating transcription. Similarly, the chromatin-associated protein HMGB1 acts as both a nuclear factor and a secreted proinflammatory cytokine. Here, we show that IL-33, an IL-1-like cytokine that signals via the IL-1 receptor-related protein ST2 and induces T helper type 2-associated cytokines, is an endothelium-derived, chromatin-associated nuclear factor with transcriptional repressor properties. We found that IL-33 is identical to NF-HEV, a nuclear factor preferentially expressed in high endothelial venules (HEV), that we previously characterized. Accordingly, in situ hybridization demonstrated that endothelial cells constitute a major source of IL-33 mRNA in chronically inflamed tissues from patients with rheumatoid arthritis and Crohn's disease. Immunostaining with three distinct antisera, directed against the N-terminal part and IL-1-like C-terminal domain, revealed that IL-33 is a heterochromatin-associated nuclear factor in HEV endothelial cells in vivo. Association of IL-33 with heterochromatin was also observed in human and mouse cells under living conditions. In addition, colocalization of IL-33 with mitotic chromatin was noted. Nuclear localization, heterochromatin-association, and targeting to mitotic chromosomes were all found to be mediated by an evolutionarily conserved homeodomain-like helix-turn-helix motif within the IL-33 N-terminal part. Finally, IL-33 was found to possess transcriptional repressor properties, associated with the homeodomain-like helix-turn-helix motif. Together, these data suggest that, similarly to IL1alpha and HMGB1, IL-33 is a dual function protein that may function as both a proinflammatory cytokine and an intracellular nuclear factor with transcriptional regulatory properties.
Distribution of nerve growth factor following direct delivery to brain interstitium (1995)

Several studies suggest the potential of nerve growth factor (NGF) in the treatment of patients with Alzheimer's disease. To characterize NGF transport within the brain interstitium, we implanted controlled release polymers containing NGF and [125I]NGF into the brains of adult male rats and measured spatial distributions of NGF for up to one week. NGF concentration in the brain was quantified using ELISA, radiation counting, and autoradiography. At 2 days post-implantation, quantities of NGF in excess of 50 pg per section were detected within thick (1 mm) coronal slices of the hemisphere ipsilateral to the site of implantation up to 3 mm rostral and caudal to the edge of the polymer. Lower levels of radioactivity (> 5 pg but < 50 pg NGF per section) could be detected throughout the rest of the brain. Levels were highest in the tissue sections containing the polymer, reaching 9.5 ng per section. Autoradiography of thin (20 microns) coronal sections indicated that local NGF concentrations immediately adjacent to the polymer approached 40 micrograms/ml. Analysis of sequential sections on the autoradiograph confirmed that NGF was transported only 2-3 mm from the polymer in any direction. At one week post-implantation, the pattern of NGF distribution was similar to that seen at 2 days, and concentrations remained high near the site of the implant. Comparison of local NGF concentration profiles to simple models of diffusion with first-order elimination suggests that the NGF moved through the tissue by diffusion through the interstitial space with a half-life on the order of 0.5 h. The limited range of NGF transport in brain tissue indicates that: (i) protein drug agents such as NGF will probably need to be delivered almost directly to the site of action for efficacy; and (ii) toxicities associated with delivery of NGF and other protein agents to non-target cells, as often occurs with systemic delivery of drugs, may be reduced by local, interstitial delivery since therapy can be restricted to a small volume of the brain.
Particle separation by dielectrophoresis (2002)

The application of dielectrophoresis to particle discrimination, separation, and fractionation is reviewed, some advantages and disadvantages of currently available approaches are considered, and some caveats are noted.
Sequence Level Training with Recurrent Neural Networks (2015)

Many natural language processing applications use language models to generate text. These models are typically trained to predict the next word in a sequence, given the previous words and some context such as an image. However, at test time the model is expected to generate the entire sequence from scratch. This discrepancy makes generation brittle, as errors may accumulate along the way. We address this issue by proposing a novel sequence level training algorithm that directly optimizes the metric used at test time, such as BLEU or ROUGE. On three different tasks, our approach outperforms several strong baselines for greedy generation. The method is also competitive when these baselines employ beam search, while being several times faster.
American Airlines' "Sabre" electronic reservations system (1961)

The American Airlines Sabre System, a joint development of American Airlines and IBM, is a major step into the field of total data processing. This system is designed to solve the problems confronting the airlines in passenger sales, seat inventory control, and maintenance and retrieval of passenger records.
Molecular and immunological evidence of oral Treponema in the human brain and their association with Alzheimer's disease (2002)

The purpose of this investigation was to use molecular and immunological techniques to determine whether oral Treponema infected the human brain. Pieces of frontal lobe cortex from 34 subjects were analyzed with species-specific PCR and monoclonal antibodies. PCR detected Treponema in 14/16 Alzheimer's disease (AD) and 4/18 non-AD donors (P < 0.001), and AD specimens had more Treponema species than controls (P < 0.001). PCR also detected Treponema in trigeminal ganglia from three AD and two control donors. Cortex from 15/16 AD subjects and 6/18 controls contained Treponema pectinovorum and/or Treponema socranskii species-specific antigens (P < 0.01). T. pectinovorum and/or T. socranskii antigens were also found in trigeminal ganglia and pons from four embalmed cadavers, and 2/4 cadavers also had Treponema in the hippocampus. These findings suggest that oral Treponema may infect the brain via branches of the trigeminal nerve.
Microarray Analysis of the Nitrate Response in Arabidopsis Roots and Shoots Reveals over 1,000 Rapidly Responding Genes and New Linkages to Glucose, Trehalose-6-Phosphate, Iron, and Sulfate Metabolism (2003)

The genomic response to low levels of nitrate was studied in Arabidopsis using the Affymetrix ATH1 chip containing more than 22,500 probe sets. Arabidopsis plants were grown hydroponically in sterile liquid culture on ammonium as the sole source of nitrogen for 10 d, then treated with 250 microm nitrate for 20 min. The response to nitrate was much stronger in roots (1,176 genes showing increased or decreased mRNA levels) than in shoots (183 responding genes). In addition to known nitrate-responsive genes (e.g. those encoding nitrate transporters, nitrate reductase, nitrite reductase, ferredoxin reductase, and enzymes in the pentose phosphate pathway), genes encoding novel metabolic and potential regulatory proteins were found. These genes encode enzymes in glycolysis (glucose-6-phosphate isomerase and phosphoglycerate mutase), in trehalose-6-P metabolism (trehalose-6-P synthase and trehalose-6-P phosphatase), in iron transport/metabolism (nicotianamine synthase), and in sulfate uptake/reduction. In many cases, only a few select genes out of several in small gene families were induced by nitrate. These results show that the effect of nitrate on gene expression is substantial (affecting almost 10% of the genes with detectable mRNA levels) yet selective and affects many genes involved in carbon and nutrient metabolism.
Plasmacytoid predendritic cells initiate psoriasis through interferon-α production (2005)

Psoriasis is one of the most common T cell-mediated autoimmune diseases in humans. Although a role for the innate immune system in driving the autoimmune T cell cascade has been proposed, its nature remains elusive. We show that plasmacytoid predendritic cells (PDCs), the natural interferon (IFN)-alpha-producing cells, infiltrate the skin of psoriatic patients and become activated to produce IFN-alpha early during disease formation. In a xenograft model of human psoriasis, we demonstrate that blocking IFN-alpha signaling or inhibiting the ability of PDCs to produce IFN-alpha prevented the T cell-dependent development of psoriasis. Furthermore, IFN-alpha reconstitution experiments demonstrated that PDC-derived IFN-alpha is essential to drive the development of psoriasis in vivo. These findings uncover a novel innate immune pathway for triggering a common human autoimmune disease and suggest that PDCs and PDC-derived IFN-alpha represent potential early targets for the treatment of psoriasis.
Randomized Trial of Human Milk Cream as a Supplement to Standard Fortification of an Exclusive Human Milk-Based Diet in Infants 750-1250 g Birth Weight (2014)

Premature infants who received HM-derived cream to fortified HM had improved weight and length velocity compared with the control group. HM-derived cream should be considered an adjunctive supplement to an exclusive HM-based diet to improve growth rates in premature infants.
Binding of ribosomes to the rough endoplasmic reticulum mediated by the Sec61p-complex. (1994)

The cotranslational translocation of proteins across the ER membrane involves the tight binding of translating ribosomes to the membrane, presumably to ribosome receptors. The identity of the latter has been controversial. One putative receptor candidate is Sec61 alpha, a multi-spanning membrane protein that is associated with two additional membrane proteins (Sec61 beta and gamma) to form the Sec61p-complex. Other receptors of 34 and 180 kD have also been proposed on the basis of their ability to bind at low salt concentration ribosomes lacking nascent chains. We now show that the Sec61p-complex has also binding activity but that, at low salt conditions, it accounts for only one third of the total binding sites in proteoliposomes reconstituted from a detergent extract of ER membranes. Under these conditions, the assay has also limited specificity with respect to ribosomes. However, if the ribosome-binding assay is performed at physiological salt concentration, most of the unspecific binding is lost; the Sec61p-complex then accounts for the majority of specific ribosome-binding sites in reconstituted ER membranes. To study the membrane interaction of ribosomes participating in protein translocation, native rough microsomes were treated with proteases. The amount of membrane-bound ribosomes is only slightly reduced by protease treatment, consistent with the protease-resistance of Sec61 alpha which is shielded by these ribosomes. In contrast, p34 and p180 can be readily degraded, indicating that they are not essential for the membrane anchoring of ribosomes in protease-treated microsomes. These data provide further evidence that the Sec61p-complex is responsible for the membrane-anchoring of ribosomes during translocation and make it unlikely that p34 or p180 are essential for this process.
Individual Responses to a Cholesterol-Lowering Diet in 50 Men With Moderate Hypercholesterolemia (1994)

The Step 1 Diet is effective in lowering LDL cholesterol levels for many hypercholesterolemic men, and with appropriate counseling, outpatients can achieve results predicted by inpatient metabolic diet studies. Nonetheless, the responsiveness for individuals is highly variable, and this variability is influenced by both compliance and biologic factors. Since many men achieved LDL cholesterol levels low enough to remove the need for drug therapy in primary prevention for coronary heart disease, dietary therapy should remain the initial approach to the treatment of hypercholesterolemia.