gebhart/patrepeval huggingface dataset:
Mitogen-activated protein kinase is required for bryostatin 1-induced differentiation of the human acute lymphoblastic leukemia cell line Reh. (2001)

Bryostatin 1 (bryo 1) is known to induce the differentiation and cell cycle arrest of human lymphoid leukemia cells in vitro. The extracellular signal-regulated kinase (ERK), originally identified as a participant in mitogenic signaling, has recently been implicated in the signaling of cellular differentiation. To examine the role of the ERK/mitogen-activated protein (MAP) kinase pathway in B-lymphoid cell differentiation of the Reh Acute Lymphoblastic Leukemia cell line, the effects of bryo 1 on ERK activation were determined. On bryo 1 treatment, the activity of ERK2 (p42) rapidly increased, with ERK1 (p44) protein levels remaining constant. p44/42 immunoprecipitates from lysates of bryo 1-treated cells had increased their ability to phosphorylate the transcription factor Elk-1. Constitutive AP-1 activity was shown to be potentiated after bryo 1 treatment using electrophoretic mobility shift assays. The protein composition of the AP-1 transcription factor complex activated by bryo 1 was analyzed using supershift analysis with specific antibodies against c-Fos, Fos B, c-Jun, Jun B, and Jun D proteins. Supershift analysis revealed that the bryo 1-induced AP-1 complex was composed predominantly of Fos B and Jun D. Therefore, we evaluated the effects of inhibiting MAP/ERK kinase (MEK) on both DNA binding and cellular differentiation. Treatment of Reh cells with 20 microM PD98059, a specific inhibitor of MEK, inhibited bryo 1-induced ERK activity and DNA binding. Furthermore, PD98059 blocked the bryo 1-induced differentiation of Reh cells, as assessed by a number of features associated with lymphoid differentiation, including changes in morphology, cell growth arrest, attachment, and increased expression of the leukocyte integrin CD11c. Moreover, transient transfection of Reh cells with antisense MAP kinase oligonucleotides blocked bryo 1-induced expression of CD11c. Our analysis also shows that CD11c's gene promoter activity is augmented by bryo 1. Therefore, we conclude that activation of the MEK/ERK signaling pathway is necessary for bryo 1-induced differentiation of the pre-B Acute Lymphoblastic Leukemia cell line Reh.
Pathologic Anatomy of the Pancreas in Juvenile Diabetes Mellitus (1965)

1. Quantitative study of insular tissue has revealed that the number of B cells is greatly diminished in Patients with acute juvenile diabetes from the time of clinical onset of the disease. The number of these cells is as a rule less than 10 per cent of normal. Such B cells as are still present show the cytological signs of marked activity. 2. The normal or supranormal insular activity that is usually found in juvenile diabetics in this stage of the disease cannot therefore be due to the presence of a normal insular tissue, but is produced by a small number of hyperactive B cells. 3. On the basis of histological findings (presence of islets of large size, signs of new islet formation), it may be assumed that during the preclinical phase of juvenile diabetes, an extrapancreatic factor has exerted a strong stimulant action on the insular tissue. In the long run this must lead to exhaustion of the islet-forming capacity on the pancreatic parenchyma and to a decrease in the number of the B cells. By the time the disease becomes clinically manifest only the latter stage of this process can be observed and the majority of islets consist of A cells or of atrophic tissue devoid of B cells. 4. Peri- and intra-insular inflaminatory infiltrates have been found in 68 per cent of those patients with juvenile diabetes who died soon after the clinical onset of their disease. In other words, and contrary to the generally held view, this lesion is not uncommon. It is specific for diabetes and has never been observed in the chronic cases 5. In patients with chronic juvenile diabetes, the B cells are completely absent, except in occasional cases. The islets consist of small, atrophic cells. 6. A valid assessment of the functional capacity of insular tissue can only be achieved if as much use as pos sible is made of quantitative technics and of cytological examination
Powerful tools for genetic analysis come of age (1999)

Microscopic arrays of oligonucleotides or cDNA containing up to several hundred thousand different sequences are starting to influence methodologies and paths to discovery in genomics. Gene polymorphisms and mutations can be found and gene expression measured with unprecedented speed and parallelism. The principles of this modern technology and some of the problems awaiting further study are discussed.
The Free Hormone Hypothesis: A Physiologically Based Mathematical Model* (1989)

The free hormone hypothesis states that the biological activity of a given hormone is affected by its unbound (free) rather than protein-bound concentration in the plasma. The fundamental mathematical and physiological principles relating to this hypothesis are reviewed, along with experimental data that shed light on its validity. It is shown that whether or not this hypothesis is likely to be valid for any given hormone will depend largely on which step in the tissue uptake process (plasma flow, dissociation from plasma binding proteins, influx, or intracellular elimination) is rate-limiting to the net tissue uptake of that hormone. It is further shown that the free hormone hypothesis could hold even if tissue uptake of hormone occurred by a mechanism that acted directly on one or more circulating protein-bound pools of hormone. Indeed, many of the data previously interpreted as being inconsistent with the free hormone hypothesis are in fact readily consistent with it when its predictions are fully understood. Nevertheless, the free hormone hypothesis is not likely to be valid for all hormones with respect to all tissues. It is likely to be valid with respect to all tissues for the thyroid hormones, for cortisol, and for the hydroxylated metabolites of vitamin D. For many of the other steroid hormones, however, it is likely to be valid with respect to some tissues, but not with respect to others (in particular, the liver). And for some of the steroid hormones (in particular, progesterone) it may not hold at all.
Thermal Stability as a Determinant of AAV Serotype Identity (2017)

Currently, there are over 150 ongoing clinical trials utilizing adeno-associated viruses (AAVs) to target various genetic diseases, including hemophilia (AAV2 and AAV8), congenital heart failure (AAV1 and AAV6), cystic fibrosis (AAV2), rheumatoid arthritis (AAV2), and Batten disease (AAVrh.10). Prior to patient administration, AAV vectors must have their serotype, concentration, purity, and stability confirmed. Here, we report the application of differential scanning fluorimetry (DSF) as a good manufacturing practice (GMP) capable of determining the melting temperature (T<sub>m</sub>) for AAV serotype identification. This is a simple, rapid, cost effective, and robust method utilizing small amounts of purified AAV capsids (∼25 μL of ∼10<sup>11</sup> particles). AAV1-9 and AAVrh.10 exhibit specific T<sub>m</sub>s in buffer formulations commonly used in clinical trials. Notably, AAV2 and AAV3, which are the least stable, have varied T<sub>m</sub>s, whereas AAV5, the most stable, has a narrow T<sub>m</sub> range in the different buffers, respectively. Vector stability was dictated by VP3 only, specifically, the ratio of basic/acidic amino acids, and was independent of VP1 and VP2 content or the genome packaged. Furthermore, stability of recombinant AAVs differing by a single basic or acidic amino acid residue are distinguishable. Hence, AAV DSF profiles can serve as a robust method for serotype identification of clinical vectors.
Digital speckle photography: visualization of mesoflow through clustered fiber networks (2002)

Digital speckle photography (DSP) is used for velocity field measurements inside a fiber network. The width of the channels in which the flow is measured is typically less than 1 mm. Therefore a microscope is used to image the fiber network. When we sample 30 images/s and separate the moving parts of the images from the stationary parts, the velocity field can be deduced with DSP.
Persistent infection of rhesus macaques with a molecular clone of human immunodeficiency virus type 2: evidence of minimal genetic drift and low pathogenetic effects (1990)

In an attempt to generate a suitable animal model to study the infectivity and possible pathogenicity of human immunodeficiency viruses, we intravenously inoculated juvenile rhesus macaques and African green monkeys with a molecularly cloned virus, human immunodeficiency virus type 2 HIV-2sbl/isy, as well as with the uncloned HIV-2nih-z virus. Infection was monitored by virus recovery from the peripheral blood cells and by seroconversion against HIV-2 antigens measured by Western immunoblot, radioimmunoprecipitation, and enzyme-linked immunosorbent assay. We successfully infected two out of two macaques with the molecularly cloned virus and one macaque out of two with the HIV-2nih-z. No evidence of infection was seen in the African green monkeys with either virus. We followed the infected animals for 2 years. The animals remained healthy, although we observed intermittent lymphadenopathy and a transient decrease in the absolute number of circulating CD4+ T lymphocytes in both animals infected with the molecularly cloned virus. Virus isolation from the peripheral blood cells of the infected animals was successful only within the first few months after inoculation. Evidence of persistent infection was provided by the detection of proviral DNA by polymerase chain reaction analysis of the blood cells of the inoculated animals and by the stability of antiviral antibody titers. To evaluate the genetic drift of the proviral DNA, we molecularly cloned viruses which were reisolated 1 and 5 months postinoculation from one of these animals. Comparison of the DNA sequences of the envelope genes of both these isolates indicated that a low degree of variation (0.2%) in the envelope protein had occurred in vivo during the 5-month period. These data suggest that the use of HIV-2sbl/isy in rhesus macaques may represent a good animal model system to study prevention of viral infection. In particular, molecularly cloned virus can be manipulated for functional studies of viral genes in the pathogenesis of acquired immune deficiency syndrome and provides a reproducible source of virus for vaccine studies.
Severe Community-acquired Pneumonia: Etiology, Prognosis, and Treatment (1990)

The frequency of community-acquired pneumonia coupled with its mortality rate of 10 to 25% is of growing concern to clinicians. A prospective study of 67 patients with severe community-acquired pneumonia was carried out to determine the causative agents, the impact fore-knowledge of the etiology has on the outcome, the value of clinical and radiologic criteria in predicting the evolution, and the efficacy of empirical therapy. The study group included 45 men and 22 women (mean age: 56.8 +/- 16.6 yr), and 46.2% suffered from a concurrent debilitating disease. The cause of pneumonia was diagnosed in 32 cases, and the most common pathogens were Streptococcus pneumoniae (37.5%), Legionella pneumophila (21.8%), and gram-negative bacilli (25.0%). The fact that fungal infections were present in three patients and Pneumocystis carinii in one are worthy of note. The overall death rate was 20.8%. A fatal outcome was related to the age of the patient (p less than 0.05), the presence of debilitating disease (p = 0.026), and septic shock (p = 0.0009). Diagnosis of the causative agents did not aid in increasing the survival rate, but it did allow for better patient management. Most of the patients (85.1%) initiated on treatment with erythromycin plus tobramycin recovered, but only 68.4% of the subjects commenced on treatment with other therapeutics survived. Furthermore, it was necessary to modify the therapy of a greater percentage of the latter group (p less than 0.025). Gram-negative bacillary pneumonia was a frequent finding among the patients who did not recover, making empirical treatment with erythromycin plus third generation cephalosporins most advisable for severe cases of community-acquired pneumonia.
Transcription factor EB: from master coordinator of lysosomal pathways to candidate therapeutic target in degenerative storage diseases (2016)

The lysosome is the main catabolic hub of the cell. Owing to its role in fundamental processes such as autophagy, plasma membrane repair, mTOR signaling, and maintenance of cellular homeostasis, the lysosome has a profound influence on cellular metabolism and human health. Indeed, inefficient or impaired lysosomal function has been implicated in the pathogenesis of a number of degenerative diseases affecting various organs and tissues, most notably the brain, liver, and muscle. The discovery of the coordinated lysosomal expression and regulation (CLEAR) genetic program and its master controller, transcription factor EB (TFEB), has provided an unprecedented tool to study and manipulate lysosomal function. Most lysosome-based processes-including macromolecule degradation, autophagy, lysosomal exocytosis, and proteostasis-are under the transcriptional control of TFEB. Interestingly, impaired TFEB signaling has been suggested to be a contributing factor in the pathogenesis of several degenerative storage diseases. Preclinical studies based on TFEB exogenous expression to reinstate TFEB activity or promote CLEAR network-based lysosomal enhancement have highlighted TFEB as a candidate therapeutic target for the treatment of various degenerative storage diseases.
S-Nitrosoglutathione is a substrate for rat alcohol dehydrogenase class III isoenzyme (1998)

An enzyme isolated from rat liver cytosol (native molecular mass 78. 3 kDa; polypeptide molecular mass 42.5 kDa) is capable of catalysing the NADH/NADPH-dependent degradation of S-nitrosoglutathione (GSNO). The activity utilizes 1 mol of coenzyme per mol of GSNO processed. The isolated enzyme has, as well, several characteristics that are unique to alcohol dehydrogenase (ADH) class III isoenzyme: it is capable of catalysing the NAD+-dependent oxidations of octanol (insensitive to inhibition by 4-methylpyrazole), methylcrotyl alcohol (stimulated by added pentanoate) and 12-hydroxydodecanoic acid, and also the NADH/NADPH-dependent reduction of octanal. Methanol and ethanol oxidation activity is minimal. The enzyme has formaldehyde dehydrogenase activity in that it is capable of catalysing the NAD+/NADP+-dependent oxidation of S-hydroxymethylglutathione. Treatment with the arginine-specific reagent phenylglyoxal prevents the pentanoate stimulation of methylcrotyl alcohol oxidation and markedly diminishes the enzymic activity towards octanol, 12-hydroxydodecanoic acid and S-hydroxymethylglutathione; the capacity to catalyse GSNO degradation is also checked. Additionally, limited peptide sequencing indicates 100% correspondence with known ADH class III isoenzyme sequences. Kinetic studies demonstrate that GSNO is an exceptionally active substrate for this enzyme. S-Nitroso-N-acetylpenicillamine and S-nitrosated human serum albumin are not substrates; the activity towards S-nitrosated glutathione mono- and di-ethyl esters is minimal. Product analysis suggests that glutathione sulphinamide is the major stable product of enzymic GSNO processing, with minor yields of GSSG and NH3; GSH, hydroxylamine, nitrite, nitrate and nitric oxide accumulations are minimal. Inclusion of GSH in the reaction mix decreases the yield of the supposed glutathione sulphinamide in favor of GSSG and hydroxylamine.
Integration of RFID and WSN technologies in a Smart Parking System (2014)

In this paper, a Smart Parking System (SPS) based on the integration of Ultra-High Frequency (UHF) Radio Frequency Identification (RFID) and IEEE 802.15.4 Wireless Sensor Network (WSN) technologies is presented. The system is able to collect information about the occupancy state of parking spaces, and to direct drivers to the nearest vacant parking spot by using a customized software application. Such application also leverages an NFC-based e-wallet system to allow users to pay for the parking fee. Furthermore, a software application based on RESTful Java and Google Cloud Messaging (GCM) technologies has been installed on a Central Server in order to manage alert events (e.g. improper use of a reserved space or expiration of the purchased time). In such a case, it promptly informs the traffic cops through an Android mobile app, which has been designed ad hoc for the considered scenario. A proof-of-concept has demonstrated that the proposed solution can meet the real requirements of a SPS.
Inhibition of Calcineurin Abrogates While Inhibition of mTOR Promotes Regulatory T Cell Expansion and Graft-Versus-Host Disease Protection by IL-2 in Allogeneic Bone Marrow Transplantation (2014)

Regulatory T cells (Treg)s attenuate excessive immune responses, making their expansion beneficial in immune-mediated diseases including allogeneic bone marrow transplantation (BMT)-associated graft-versus-host disease (GVHD). We have recently reported that Treg expansion does not require phospholipase Cγ activation when IL-2 is provided. As such, the combination of IL-2 and a calcineurin inhibitor (Cyclosporine A; CsA) expands Tregs while inhibiting Tconv proliferation and protects against a mouse model of multiple sclerosis. However, CsA inhibits Treg proliferation in the presence of a TCR stimulus, suggesting that CsA may negatively impact Treg proliferation when they receive strong allogeneic MHC-mediated TCR signals. In this study, we show that CsA inhibits Treg proliferation and inducible Treg generation in allogeneic but not in syngeneic BMT when IL-2 is provided. In contrast to CsA, the mTOR inhibitor (Rapamycin) almost completely suppressed IL-2-mediated Treg proliferation. However, CsA and Rapamycin inhibited Treg proliferation to a similar extent when TCR stimulation was provided. Furthermore, Rapamycin promoted Treg expansion and inducible Treg generation in allogeneic BMT recipients treated with IL-2. Consistent with these observations, CsA abrogated while Rapamycin promoted the protective effect of IL-2 on allogeneic BMT-induced GVHD. These results suggest that while CsA permits IL-2-induced Treg proliferation in the syngeneic setting (absence of strong TCR signals), CsA in combination with IL-2 may be detrimental for Treg proliferation in an allogeneic setting. Thus, in allogeneic settings, an mTOR inhibitor such as Rapamycin is a better choice for adjunct therapy with IL-2 in expansion of Tregs and protection against allogeneic BMT-induced GVHD.
Hypothermia in Focal Ischemia: Implications of Experiments and Experience (2009)

Beside aspirin administration and stroke unit care, thrombolysis is the only approved and effective therapy in acute ischemic stroke. Thrombolysis is essentially limited by the short therapeutic window and its potential side effects. Although there is a robust body of evidence on the neuroprotective characteristics of hypothermia in animal models of focal ischemia, the clinical data on hypothermia in stroke are inconclusive in terms of effectiveness. Previous trials suggest that hypothermia is safe and feasible in stroke, and may decrease intracranial pressure (ICP) in patients suffering from space-occupying infarcts. However, neuroprotection by hypothermia has never been shown previously in stroke patients. This lack of efficacy might be explained by the fact that hypothermia is not appropriately used in patients and animal data are not correctly interpreted. This review summarizes the major conclusions of animal studies and presents results of clinical stroke trials to date. Methods of delivery and maintenance of hypothermia are discussed, as well as a variety of open questions in the relevant animal and clinical research.
Accuracy of cytogenetic findings on Chorionic Villus Sampling (CVS)—diagnostic consequences of CVS Mosaicism and non-Mosaic Discrepancy in Centres contributing to EUCROMIC 1986–1992 (1997)

Of 62,865 karyotyped chorionic villus (CV) samples that were reported to EUCROMIC 1986-1992, 98.5 per cent showed either a normal karyotype (true negative result; 94.8 per cent of the total) or a non-mosaic chromosomal aberration (true positive non-mosaic result; 3.7 per cent). True fetal mosaicism was diagnosed in about 0.15 per cent of the 62,865 CV samples, while confined placental mosaicism (CPM) occurred in 1.0 per cent. False-positive non-mosaic aberrations were observed in 0.15 per cent and false-negative CVS (chorionic villus sampling) results in only 0.03 per cent. The remaining 0.15 per cent of the CVS results were unclassifiable. These figures determined a sensitivity of CVS for prenatal detection of chromosome aberrations of 98.9-99.6 per cent (95 per cent confidence intervals), a specificity of 98.5-98.8 per cent, a positive predictive value of 72.6-78.3 per cent, and a negative predictive value of 99.95-99.98 per cent. False-positive non-mosaic aberrations that could not from the outset be suspected of being confined to the placenta were very rare (0.07 per cent of CV samples). They most often involved non-mosaic monosomy X and trisomy 18 encountered after direct preparation alone. False-negative CVS results were extremely rare (0.03 per cent) and occurred, with only one exception, after direct preparation alone. Thirteen of the 19 false-negative CVS diagnoses were from pregnancies at a particularly high risk for fetal chromosomal aberration. Seventy-five per cent of the pregnancies with CVS mosaicism or non-mosaic discrepancy and known outcome continued to livebirth. When CVS mosaicism was encountered, the definitive prenatal cytogenetic diagnosis was most often obtained through subsequent amniocentesis. However, the use of amniocentesis and the frequency of pregnancy termination depended on the type of chromosomal aberration involved. We conclude that CVS is an accurate method for prenatal chromosome analysis. In pregnancies at high risk for fetal chromosomal abnormality, we recommend, however, not relying solely on a normal karyotype obtained after direct preparation alone.
Aspergillus niger lipase: Heterologous expression in Pichia pastoris, molecular modeling prediction and the importance of the hinge domains at both sides of the lid domain to interfacial activation (2009)

Aspergillus niger lipase (ANL) is an important biocatalyst in the food processing industry. However, there is no report of its detailed three-dimensional structure because of difficulties in crystallization. In this article, based on experimental data and bioinformational analysis results, the structural features of ANL were simulated. Firstly, two recombinant ANLs expressed in Pichia pastoris were purified to homogeneity and their corresponding secondary structure compositions were determined by circular dichroism spectra. Secondly, the primary structure, the secondary structure and the three-dimensional structure of ANL were modeled by comparison with homologous lipases with known three-dimensional structures using the BioEdit software, lipase engineering database (http://www.led.uni-stuttgart.de/), PSIPRED server and SwissModel server. The predicted molecular structure of ANL presented typical features of the alpha/beta hydrolase fold including positioning of the putative catalytic triad residues and the GXSXG signature motif. Comparison of the predicted three-dimensional structure of ANL with the X-ray three-dimensional structure of A. niger feruloyl esterase showed that the functional difference of interfacial activation between lipase and esterase was concerned with the difference in position of the lid. Our three-dimensional model of ANL helps to modify lipase structure by protein engineering, which will further expand the scope of application of ANL.