gebhart/patrepeval huggingface dataset:
Effects of Plasmid DNA Injection on Cyclophosphamide-Accelerated Diabetes in NOD Mice (2001)

Type 1 diabetes results in most cases from the destruction of insulin-secreting beta cells by the immune system. Several immunization methods based on administration of autoantigenic polypeptides such as insulin and glutamic acid decarboxylase (GAD) have been used to prevent autoimmune diabetes in the non-obese diabetic (NOD) mouse. In the work presented here, a gene-based approach was taken for a similar purpose. A plasmid carrying different cDNAs was used to investigate the effects of injecting naked DNA on cyclophosphamide-accelerated diabetes in female NOD mice. Four-week-old animals received intramuscular injections of plasmid DNA encoding either intracellular GAD, a secreted form of GAD, or a secreted form of a soft coral luciferase. Monitoring of glycosuria and hyperglycemia indicated that injection of plasmid DNA encoding secreted GAD and secreted luciferase could prevent and delay diabetes, respectively. In contrast, injection of DNA encoding intracellular GAD did not suppress the disease significantly. Analysis of anti-GAD IgG(1) antibody titers in animal sera indicated that diabetes prevention after injection of GAD-encoding DNA was possibly associated with increased Th2-type activity. These results suggest that cellular localization of GAD is a factor to consider in the design of GAD-based genetic vaccines for the prevention of autoimmune diabetes.
Molecular Phylogenetic Analyses Indicate a Wide and Ancient Radiation of African Hepatitis Delta Virus, Suggesting a Deltavirus Genus of at Least Seven Major Clades (2004)

Hepatitis D virus (HDV) is a satellite of hepatitis B virus (HBV) for transmission and propagation and infects nearly 20 million people worldwide. The HDV genome is a compact circular single-stranded RNA genome with extensive intramolecular complementarity. Despite its different epidemiological and pathological patterns, the variability and geographical distribution of HDV are limited to three genotypes and two subtypes that have been characterized to date. Phylogenetic reconstructions based on the delta antigen gene and full-length genome sequence data show an extensive and probably ancient radiation of African lineages, suggesting that the genetic variability of HDV is much more complex than was previously thought, with evidence of additional clades. These results relate the geographic distribution of HDV more closely to the genetic variability of its helper HBV.
Randomized study of antibodies to IFN-g and TNF-a in secondary progressive multiple sclerosis (2001)

Studies of cytokines in multiple sclerosis (MS) have shown that immune mechanisms connected with disturbance of the synthesis of cytokines probably play critical roles in the initiation and prolongation of MS. In a double-blind, placebo-controlled trial, 45 patients with active secondary progressive MS were randomized to three groups of 15 patients, each receiving a short course of antibodies to IFN-gamma, to tumor necrosis factor (TNF)-alpha, or a placebo. After 12 months with analysis of disability (Expanded Disability Status Scale scores), accompanied by interval determinations of lymphocyte subpopulations, cytokine production levels, MRI, and evoked potentials, it was found that only patients who received antibodies to IFN-gamma showed statistically significant improvement compared to the placebo group--a significant increase in the number of patients without confirmed disability progression. This was supported by MRI data (a decrease in the number of active lesions) and systemic changes in cytokine status (a decrease in IL-1beta, TNF-alpha, and IFN-gamma concentrations in supernatants of actvated blood cells of these MS patients and an increase in TGF-beta production). Neutralization of IFN-gamma could be a new approach to treating secondary progressive MS. Long-term administration of humanized monoclonal antibodies to IFN-gamma and simultaneous use of antibodies to IFN-gamma together with IFN-beta products are planned.
Quanto: tracking energy in networked embedded systems (1961)

We present Quanto, a network-wide time and energy profiler for embedded network devices. By combining well-defined interfaces for hardware power states, fast high-resolution energy metering, and causal tracking of programmer-defined activities, Quanto can map how energy and time are spent on nodes and across a network. Implementing Quanto on the TinyOS operating system required modifying under 350 lines of code and adding 1275 new lines. We show that being able to take fine-grained energy consumption measurements as fast as reading a counter allows developers to precisely quantify the effects of low-level system implementation decisions, such as using DMA versus direct bus operations, or the effect of external interference on the power draw of a low duty-cycle radio. Finally, Quanto is lightweight enough that it has a minimal effect on system behavior: each sample takes 100 CPU cycles and 12 bytes of RAM.
Experimental Investigation of Water Discharge Capability According to Shape of Sluice for Tidal Power Generation - I. Physical Experiment (2008)

An hydraulic experiment was carried out in an open channel flume in order to improve the technique of designing shape of the sluice used for tidal power generation, which greatly affects the economical efficiency of the construction of a tidal power plant. To predict the influence of change in the major design parameters relating to the sluice shape on the water discharge capability of the sluice, it was necessary to perform a precise experiment that is discriminated to previous feasibility studies or design projects. For this purpose, by installing various flow straighteners and rectifying structures inside the water supply system and the rectifying tank, the flow in the flume was stabilized as tranquil as possible. In addition, the measuring instruments and the location of installing them were carefully determined so as to minimize the errors intervened during the measurement of water discharge and water level. The method of estimating head difference between upstream and downstream of the sluice was also developed by taking account of the head loss due to the friction at the bottom and side walls in the flume.
Antisuppressor mutations and sulfur-carrying nucleosides in transfer RNAs of Schizosaccharomyces pombe. (1986)

Antisuppressor mutations reduce the efficiency of nonsense suppressors. A mutation in the gene sin4 of Schizosaccharomyces pombe leads to loss of 5-(methoxycarbonylmethyl) thiouridine (mcm5s2U) from the first anticodon position of tRNAs. This resembles the phenotype of sin3 (Heyer, W. D., Thuriaux, P., Kohli, J., Ebert, P., Kersten, H., Gehrke, C., Kuo, K. C., and Agris, P. F. (1984) J. Biol. Chem. 259, 2856-2862), but the mutations reside in different genes. In vivo 35S-labeled tRNA from the parental suppressor strain sup3, the antisuppressor strains sin3 and sin4, and the double mutant sin3 sin4 has been digested to nucleosides and analyzed with high performance liquid chromatography methods. The major sulfur-carrying nucleoside in wild-type S. pombe tRNA is mcm5s2U. It is reduced in the mutant strains. Two other thiolated nucleosides are also present: 2-thiouridine and a nucleoside of unknown structure. Neither was affected by the antisuppressor mutations. Thiocytidine has not been found. Independent from their effect on suppressors, the two mutations sin3 and sin4 reduce the growth rate of cells, and sin3 also increases cell length. In vivo decoding of the serine codon UCG by the UCA reading serine tRNA is not promoted by the two antisuppressor mutations.
Basic Neurophysiology of Primate Locomotion (1996)

To initiate and terminate bipedal and quadrupedal locomotor movements, a smooth transition to and from standing is necessary. For this, integration of postural and locomotor control systems is required. Recent studies in nonhuman primates and other quadrupedal animals such as cats have clearly shown that there exist significant analogies between the primate species investigated (Macaca mulatta, Macaca fascicularis, and marmosets) and the cats regarding the spinal stepping generator or central pattern generator (CPG), supraspinal descending pathways which activate CPG, and the midbrain and brain stem postural and locomotor control structures. Further studies aimed at elucidating the differences and similarities in the manner of locomotor control among different animal species will help us in understanding the control mechanisms involved in both bipedal and quadrupedal locomotor movements in nonhuman primates.
Pathophysiological Interactions of Ventilation, Arousals, and Blood Pressure Oscillations during Cheyne–Stokes Respiration in Patients with Heart Failure (2000)

Arousals from sleep can be associated with increases in blood pressure (BP). However, it is uncertain whether this is due to a direct effect of arousals on BP, or is secondary to respiratory stimuli present at the time of the arousal. Cheyne-Stokes respiration (CSR) in patients with congestive heart failure (CHF) provides unique conditions that may allow these two possibilities to be distinguished. In CSR, the apnea-hyperpnea cycle can be dissociated from arousals because when CSR occurs during wakefulness, it does so in the absence of arousals, and when it occurs during sleep, arousals occur either at the termination of apnea (early arousals) or several breaths after the onset of hyperpnea (late arousals). We therefore measured BP during wakefulness and non-rapid eye movement (NREM) sleep in eight patients with CHF and CSR. During wakefulness, CSR was associated with wide fluctuations in systolic BP (mean +/- SD, 11.3 +/- 6.0 mm Hg) synchronous with the apnea-hyperpnea cycle, in the absence of arousals. Similar fluctuations in BP were observed during CSR with early arousals (13. 7 +/- 7.0 mm Hg) in NREM sleep. However, late arousals during CSR were associated with a small, but significant additional effect on systolic BP (14.2 +/- 7.1 mm Hg, p < 0.05). Furthermore, the degree of BP increase following arousals was directly related to the associated increase in ventilation (r = 0.70, p < 0.05). We conclude that BP fluctuations during CSR in patients with CHF are primarily related to oscillations in ventilation during the CSR cycle and can occur in the absence of arousals. Arousals augment these BP oscillations, but only when they occur late in hyperpnea.
Multicenter study of banked third-party virus-specific T cells to treat severe viral infections after hematopoietic stem cell transplantation (2013)

Virus-specific T cell (VST) lines could provide useful antiviral prophylaxis and treatment of immune-deficient patients if it were possible to avoid the necessity of generating a separate line for each patient, often on an emergency basis. We prepared a bank of 32 virus-specific lines from individuals with common HLA polymorphisms who were immune to Epstein-Barr virus (EBV), cytomegalovirus, or adenovirus. A total of 18 lines were administered to 50 patients with severe, refractory illness because of infection with one of these viruses after hematopoietic stem cell transplant. The cumulative rates of complete or partial responses at 6 weeks postinfusion were 74.0% (95% CI, 58.5%-89.5%) for the entire group (n = 50), 73.9% (95% CI, 51.2% -96.6%) for cytomegalovirus (n = 23), 77.8% for adenovirus (n = 18), and 66.7% (95% CI, 36.9%-96.5%) for EBV (n = 9). Only 4 responders had a recurrence or progression. There were no immediate infusion-related adverse events, and de novo graft-versus-host disease developed in only 2 patients. Despite the disparity between the lines and their recipients, the mean frequency of VSTs increased significantly postinfusion, coincident with striking decreases in viral DNA and resolution of clinical symptoms. The use of banked third-party VSTs is a feasible and safe approach to rapidly treat severe or intractable viral infections after stem cell transplantation. This study is registered at www.clinicaltrials.gov as NCT00711035.
Myocardial Revascularization Experiments Using the Epicardium (1969)

Renewed interest in surgery for coronary artery disease has increased research efforts in this field.<sup>1-3</sup>New techniques are required to explore ideas which may result in simpler operations that will have wider clinical application. In the indirect surgical approach to coronary artery disease, the epicardium has been intentionally destroyed by acid<sup>4</sup>and abrasion<sup>5</sup>to permit the ingrowth of new blood vessels. Work with the direct approach has demonstrated that the epicardium is an extremely valuable tissue which makes it possible to explore a number of experimental ideas for myocardial vascularization. It has, for example, been shown that a vein can be sutured to the epicardium to enlarge the lumen of a coronary artery,<sup>6</sup>and it can be used to effectively tamponade a coronary arteriotomy.<sup>7</sup> It is the purpose of this paper to demonstrate the value of the epicardium, and to report findings with further attempts
[Typing of the apx toxin gene of Actinobacillus pleuropneumoniae using PCR]. (1996)

For the determination of the apx toxin genes in Actinobacillus pleuropneumoniae strains, five PCR reactions were developed which allow the detection of the activator and structural genes and the secretion genes of the toxins ApxI, ApxII and ApxIII. The oligonucleotide primers were chosen in order to amplify characteristic parts of the activator and structural genes apxICA, apxIICA and apxIIICA, and the secretion genes apxIBD and apxIIIBD. The annealing temperature of all five reaction was identical in order to allow the five reactions in a single PCR run. The differences in length between the individual amplified gene fragments allowed all product fragments to be separated in a single electrophoresis. This way, a typical toxin gene pattern could be obtained which is characteristic for the five toxin gene groups of A. pleuropneumoniae including serotypes 1, 5a, 5b, 9 and 11 (group 1), serotypes 2, 4, 6 and 8 (group 2), serotype 3 (group 3), serotypes 7 and 12 (group 4), and serotype 10 (group 5). The identification of the toxin genes, which have significance in virulence, enhance and facilitate differentiation of A. pleuropneumoniae and allow the detection of serotypes with an atypical toxin pattern.
Protein Expression Profiling of Breast Cancer Cells by Dissociable Antibody Microarray (DAMA) Staining (2007)

Dissociable antibody microarray (DAMA) staining is a technology that combines protein microarrays with traditional immunostaining techniques. It can simultaneously determine the expression and subcellular location of hundreds of proteins in cultured cells and tissue samples. We developed this technology and demonstrated its application in identifying potential biomarkers for breast cancer. We compared the expression profiles of 312 proteins among three normal breast cell lines and seven breast cancer cell lines and identified 10 differentially expressed proteins by the data analysis program DAMAPEP (DAMA protein expression profiling). Among those proteins, RAIDD, Rb p107, Rb p130, SRF, and Tyk2 were confirmed by Western blot and statistical analysis to have higher expression levels in breast cancer cells than in normal breast cells. These proteins could be potential biomarkers for the diagnosis of breast cancer.
Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR (2006)

We report here a systematic, quantitative population analysis of transcription factor expression within developmental progenitors, made possible by a microfluidic chip-based "digital RT-PCR" assay that can count template molecules in cDNA samples prepared from single cells. In a survey encompassing five classes of early hematopoietic precursor, we found markedly heterogeneous expression of the transcription factor PU.1 in hematopoietic stem cells and divergent patterns of PU.1 expression within flk2- and flk2+ common myeloid progenitors. The survey also revealed significant differences in the level of the housekeeping transcript GAPDH across the surveyed populations, which demonstrates caveats of normalizing expression data to endogenous controls and underscores the need to put gene measurement on an absolute, copy-per-cell basis.
Widespread Changes in Dendritic Spines in a Model of Alzheimer's Disease (2008)

The mechanism by which dementia occurs in patients with Alzheimer's disease (AD) is not known. We assessed changes in hippocampal dendritic spines of APP/PS1 transgenic mice that accumulate amyloid beta throughout the brain. Three-dimensional analysis of 21,507 dendritic spines in the dentate gyrus, a region crucial for learning and memory, revealed a substantial decrease in the frequency of large spines in plaque-free regions of APP/PS1 mice. Plaque-related dendrites also show striking alterations in spine density and morphology. However, plaques occupy only 3.9% of the molecular layer volume. Because large spines are considered to be the physical traces of long-term memory, widespread decrease in the frequency of large spines likely contributes to the cognitive impairments observed in this AD model.
The Non-Hodgkin's lymphomas (1990)

The non-Hodgkin's lymphomas - an introduction, Ian Magrath historical perspective - the origins of modern concepts of biology and management, Ian Magrath lymphocyte ontogeny - a conceptual basis for understanding neoplasia of the immune system, Ian Magrath histopathology and immunophenotyping, Paul J.Cohen and Elaine S.Jaffe cytogenetics, Jacqueline Whang-Peng and Elaine C.Lee the molecular genetics of non-Hodgkin's lymphomas, Frank G.Haluska et al molecular genetic markers in the diagnosis and classification of non-Hodgkin's lymphomas, Riccardo Dalla-Favera et al pathogenesis of non-Hodgkin's lymphomas - clues from geography, Denis H.Wright lymphoproliferative disorders associated with immunodeficiency, A.H. Filipovich et al lymphomas in HIV-positive individuals, Dharam V.Ablashi and S. Zaki Salahuddin clinical features and staging, Ian Magrath et al principles of chemotherapy, Wyndham Wilson and Ian Magrath radiation therapy in the non-Hodgkin's lymphomas, Jane Grayson and Eli Glatstein lymphoblastic lymphoma, John Sandlund and Ian Magrath small non-cleaved cell lymphomas, Ian Magrath complications in the management of non-Hodgkin's lymphoma, Francisco Barriga et al large cell lymphomas in childhood, Ian Magrath and Marshall Kadin follicular lymphomas, Dan L.Longo and Wyndham Wilson diffuse small cell lymphomas, Sandra J.Horning diffuse aggressive lymphomas in adults, Ellen R.Gaynor and Richard I.Fisher T-cell lymphoreticular malignancies in adults, Ray Lamb and Paul A.Bunn Jr primary intestinal lymphoma and alpha heavy chain disease, B.Ramot and G.Rechavi management of recurrent or refractory disease, Fernando Cabanillas et al bone marrow transplantation in non-Hodgkin's lymphomas, Augusto Pedrozzini et al immunological approaches to the therapy of lymphoid neoplasmas, Kenneth A.Foon et al future prospects for treatment, Ian Magrath.
A solvent having switchable hydrophilicity (2010)

A new kind of switchable solvent, a switchable-hydrophilicity solvent, is hydrophobic and has very low miscibility with water when in air but is hydrophilic and has complete miscibility with water when under an atmosphere of CO2. We report here the first example of such a solvent, N,N,N′-tributylpentanamidine. Solvents such as these could be used for the extraction of low-polarity organic products, such as vegetable oils, followed by the removal of the solvent from the product by carbonated water. Carbonated water is able to extract the solvent from the product because the CO2 converts the solvent to its hydrophilic form. The solvent can then be separated from the carbonated water upon removal of the CO2, because this removal triggers the conversion of the solvent back to its hydrophobic, water-immiscible form. Importantly, distillation is not required for removal of the solvent from the product.
Characteristic performance evaluation of a photon counting Si strip detector for low dose spectral breast CT imaging (2014)

The prototype energy resolved photon counting Si strip detector can offer superior imaging performance for dedicated breast CT as compared to a conventional energy-integrating detector due to its high output count rate, high spatial and energy resolution, and low noise characteristics, which are essential characteristics for spectral breast CT imaging.
TNF -induced insulin resistance in adipocytes as a membrane microdomain disorder: involvement of ganglioside GM3 (2004)

Membrane microdomains (lipid rafts) are now recognized as critical for proper compartmentalization of insulin signaling, but their role in the pathogenesis of insulin resistance has not been investigated. Detergent-resistant membrane microdomains (DRMs), isolated in the low-density fractions, are highly enriched in cholesterol, glycosphingolipids and various signaling molecules. Tumor necrosis factor alpha (TNFalpha) induces insulin resistance in type 2 diabetes, but its mechanism of action is not fully understood. In other studies we have found a selective increase in the acidic glycosphingolipid ganglioside GM3 in 3T3-L1 adipocytes treated with TNFalpha, suggesting a specific function for GM3. In the DRMs from TNFalpha-treated 3T3-L1 adipocytes, GM3 levels were doubled compared with results in normal adipocytes. Additionally, insulin receptor (IR) accumulations in the DRMs were diminished, whereas caveolin and flotillin levels were unchanged. Furthermore, insulin-dependent IR internalization and intracellular movement of the IR substrate 1(IRS-1) were both greatly suppressed in the treated cells, leading to an uncoupling of IR-IRS-1 signaling. GM3 depletion was able to counteract the TNFalpha-induced inhibitions of IR internalization and accumulation into DRMs. Together, these findings provide compelling evidence that in insulin resistance the insulin metabolic signaling defect can be attributed to a loss of IRs in the microdomains due to an accumulation of GM3.
JLigand: a graphical tool for the CCP4 template-restraint library (2012)

Biological macromolecules are polymers and therefore the restraints for macromolecular refinement can be subdivided into two sets: restraints that are applied to atoms that all belong to the same monomer and restraints that are associated with the covalent bonds between monomers. The CCP4 template-restraint library contains three types of data entries defining template restraints: descriptions of monomers and their modifications, both used for intramonomer restraints, and descriptions of links for intermonomer restraints. The library provides generic descriptions of modifications and links for protein, DNA and RNA chains, and for some post-translational modifications including glycosylation. Structure-specific template restraints can be defined in a user's additional restraint library. Here, JLigand, a new CCP4 graphical interface to LibCheck and REFMAC that has been developed to manage the user's library and generate new monomer entries is described, as well as new entries for links and associated modifications.