gebhart/patrepeval huggingface dataset:
Hippocampal Radial Glial Subtypes and Their Neurogenic Potential in Human Fetuses and Healthy and Alzheimer’s Disease Adults (2018)

Neuropathological conditions might affect adult granulogenesis in the adult human dentate gyrus. However, radial glial cells (RGCs) have not been well characterized during human development and aging. We have previously described progenitor and neuronal layer establishment in the hippocampal pyramidal layer and dentate gyrus from embryonic life until mid-gestation. Here, we describe RGC subtypes in the hippocampus from 13 gestational weeks (GW) to mid-gestation and characterize their evolution and the dynamics of neurogenesis from mid-gestation to adulthood in normal and Alzheimer's disease (AD) subjects. In the pyramidal ventricular zone (VZ), RGC density declined with neurogenesis from mid-gestation until the perinatal period. In the dentate area, morphologic and antigenic differences among RGCs were observed from early ages of development to adulthood. Density and proliferative capacity of dentate RGCs as well as neurogenesis were strongly reduced during childhood until 5 years, few DCX+ cells are seen in adults. The dentate gyrus of both control and AD individuals showed Nestin+ and/or GFAPδ+ cells displaying different morphologies. In conclusion, pools of morphologically, antigenically, and topographically diverse neural progenitor cells are present in the human hippocampus from early developmental stages until adulthood, including in AD patients, while their neurogenic potential seems negligible in the adult.
beta-catenin mutations are absent in hepatocellular carcinomas of SV40 T-antigen transgenic mice. (2000)

beta-catenin mutations have been found not only in melanoma and prostatic carcinoma but also in hepatocellular carcinomas in human, c-myc, H-ras genes transgenic mice and chemically-induced models. We investigated beta-catenin mutations in human hepatocellular carcinomas (HCCs), Hep G2 cell line and HCCs in SV40 T-antigen transgenic mice, in order to examine whether beta-catenin mutations are frequently observed in HCC in general. We found a point mutation of beta-catenin in one of nine HCCs in human and a deletion of it in Hep G2 cell line. However, we found no mutation in HCC in SV40 TG mice liver.
Formatting antibody fragments to mediate specific therapeutic functions (2002)

Monoclonal antibodies are increasingly being used as therapeutic agents in a wide range of indications, including oncology, inflammation and infectious disease. In most cases the basis of the therapeutic function is the high degree of specificity and affinity the antibody-based drug has for its target antigen. However, the mechanism of action (MOA), the way the drug takes advantage of this specificity to mediate a therapeutic effect, varies considerably from drug to drug. Three basic potential categories of MOAs exist: antagonists, agonists and specific delivery mechanisms to target an active function to a particular cell type. The latter functions include selective cell killing, based on Fc-mediated events, recruitment of effector cells, and drug or radioisotope delivery. The majority of these mechanisms are not necessarily optimally mediated by an IgG structure; clearly, in the case of antibody-dependent cellular cytotoxicity or complement-mediated lysis, Fc is required. However, Fab fragments (the fragment comprising one antigen-binding arm of the Y-shaped IgG molecule) can be formatted to mediate most mechanisms and have the advantage that valency and half-life can be controlled to simplify the drug and address only the mechanism required. Moreover, Fab fragments can be produced in microbial expression systems which address manufacturing issues such as scale of supply and cost of goods.
Removal of breast cancer cells by soybean agglutinin in an experimental model for purging human marrow. (1988)

Soybean agglutinin (SBA) was used as a differential reagent to achieve selective elimination of human breast cancer cells (T-47D cell line) from human marrow contaminated with tumor cells. Two successive cycles of direct agglutination by soluble SBA resulted in depletion of 3.5 logs of tumor cells as determined by radiolabeling, whereas removal of more than 4 logs of tumor cells was demonstrated by a clonogenic bioassay. A more convenient procedure for tumor purge involved the use of SBA bound to either polyglutaraldehyde magnetic beads or to commercial polystyrene magnetic beads. After one cycle of magnetic separation, 2 to 3.5 logs of tumor cells were removed. A second separation cycle using fresh magnetic beads improved depletion to more than 4 logs. Neither of these purging procedures affected the hematopoietic potential of granuloid-macrophage colony-forming unit cells. We suggest the use of SBA bound to magnetic beads as a convenient tool for effective ex vivo purging of marrow aspirates contaminated with metastatic breast cancer cells in patients with advanced disease. A similar procedure is applicable for all SBA-positive neoplasms.
Study of the Th1/Th2 balance, including IL‐10 production,in cultures of peripheral blood mononuclear cells frombirch‐pollen‐allergic patients (2000)

BPE stimulation induces a Th2-like cytokine response by PBMC isolated during the pollen season from birch-pollen-allergic patients, indicating a Th2-type immune response to birch pollen in vivo.
Characterization of Gel-Filled Membranes for Plasma Protein Fractionation (2004)

Protein fractionation (i.e. protein-protein separation) is a challenging application for ultrafiltration (UF). However, the advantages over competing separation technologies (high product throughput and ease of scale-up) make UF an attractive process for such applications. This study examines the use of Gel-filled (GF) membranes for the separation of human plasma proteins human serum albumin (HSA) and human immunoglobulin G (HIgG). GF membranes consist of microporous/macroporous supports filled with cross-linked, charged, water swollen polyelectrolyte gels. Stirred cell UF experiments were conducted to characterize the GF membranes in terms of their permeate flux and plasma protein rejection properties. These membranes could be operated at significantly higher permeate fluxes than commercially available UF membranes while achieving equivalent protein-protein separation efficiencies. Thus the product throughputs obtained were significantly higher.
Mechanisms that direct ordered assembly of T cell receptor β locus V, D, and J gene segments (2000)

T cell receptor (TCR) beta variable region genes are assembled in progenitor T cells from germ-line Vbeta, Dbeta, and Jbeta segments via an ordered two-step process in which Dbeta to Jbeta rearrangements occur on both alleles before appendage of a Vbeta to a preexisting DJbeta complex. Direct joining of Vbeta segments to nonrearranged Dbeta or Jbeta segments, while compatible with known restrictions on the V(D)J recombination mechanism, are infrequent within the endogenous TCRbeta locus. We have analyzed mechanisms that mediate ordered Vbeta, Dbeta, and Jbeta assembly via an approach in which TCRbeta minilocus recombination substrates were introduced into embryonic stem cells and then analyzed for rearrangement in normal thymocytes by recombinase-activating gene 2-deficient blastocyst complementation. These analyses demonstrated that Vbeta segments are preferentially targeted for rearrangement to Dbeta as opposed to Jbeta segments. In addition, we further demonstrated that Vbeta segments can be appended to nonrearranged endogenous Dbeta segments in which we have eliminated the ability of Dbeta segments to join to Jbeta segments. Our findings are discussed in the context of the mechanisms that regulate the ordered assembly and utilization of V, D, and J segments.
Metabolism and turnover of cell surface-associated heparan sulfate proteoglycan and chondroitin sulfate proteoglycan in normal and cholesterol-enriched macrophages. (1991)

Analysis of sulfur-35-labeled proteoglycans indicated that cholesterol-enriched pigeon peritoneal macrophages synthesized 42% more 35S-labeled proteoglycan when compared with control macrophages during a 24-hour incubation. Proteoglycan turnover was subsequently studied in radiolabeled macrophage cultures after a 1-, 3-, 6-, 12-, or 24-hour chase with fresh media. During the chase, intracellular proteoglycan disappeared rapidly, whereas there was a small accumulation of 35S-labeled proteoglycan in the media that plateaued at about 6 hours and remained relatively constant thereafter. Pericellular heparan sulfate proteoglycan and chondroitin sulfate proteoglycan disappeared throughout the chase and did not appear to accumulate in the media or in the intracellular compartment. The rapid disappearance of intracellular proteoglycans along with the relative lack in metabolism of media proteoglycans indicated that the majority of pericellular proteoglycans were metabolized via an intracellular degradative pathway. Kinetic analysis of pericellular proteoglycans revealed the presence of a single pool of heparan sulfate proteoglycan (half-life [t1/2] = 6.9 hours) and a single pool of chondroitin sulfate proteoglycan (t1/2 = 11.5 hours) in control macrophage cultures. Cholesterol-enriched macrophage cultures also contained a single pool of pericellular heparan sulfate proteoglycan (t1/2 = 7.3 hours) but contained two pools of chondroitin sulfate proteoglycan (t1/2 = 0.8 hour and 25.9 hours).
Chemokine receptor trafficking and viral replication (1999)

Chemokines and chemokine receptors have emerged as crucial factors controlling the development and function of leukocytes. Recent studies have indicated that, in addition to these essential roles, both chemokines and chemokine receptors play critical roles in viral infection and replication. Not only are chemokine receptors key components of the receptor/fusion complexes of primate immunodeficiency viruses, but chemokines can also influence virus entry and infection. Many viruses, in particular herpesviruses, encode chemokines and chemokine receptors that influence the replication of both the parent virus and other unrelated viruses. The cell surface expression of the chemokine receptors is regulated through their interaction with membrane trafficking pathways. Ligands induce receptor internalization and downmodulation through endocytosis, and recycling is regulated within endosomes. Part of the mechanism through which chemokines protect cells from HIV infection is through ligand-induced internalization of the specific chemokine receptor co-receptors. In addition, mechanisms may exist to regulate the trafficking of newly synthesized receptors to the cell surface. Here we discuss aspects of the mechanisms through which chemokine receptors interact with membrane-trafficking pathways and the influence of these interactions on viral replication.
Expression of reverse transcriptase activity of human T-lymphotropic virus type III (HTLV-III/LAV) in Escherichia coli (1986)

The pol gene from a biologically active clone of the human T-cell lymphotropic virus type III provirus was inserted into a bacterial expression vector. The resulting gene fusion induced the formation of active reverse transcriptase that could be readily detected in extracts of bacterial cells. The activity exhibited the template and divalent cation requirements of the authentic enzyme. These constructs will be useful for safe and rapid analysis of potential inhibitors of this important enzyme.
An improved illumination model for shaded display (2005)

To accurately render a two-dimensional image of a three-dimensional scene, global illumination information that affects the intensity of each pixel of the image must be known at the time the intensity is calculated. In a simplified form, this information is stored in a tree of "rays" extending from the viewer to the first surface encountered and from there to other surfaces and to the light sources. A visible surface algorithm creates this tree for each pixel of the display and passes it to the shader. The shader then traverses the tree to determine the intensity of the light received by the viewer. Consideration of all of these factors allows the shader to accurately simulate true reflection, shadows, and refraction, as well as the effects simulated by conventional shaders. Anti-aliasing is included as an integral part of the visibility calculations. Surfaces displayed include curved as well as polygonal surfaces.
Marginal zone B cells exacerbate endotoxic shock via interleukin-6 secretion induced by Fcα/μR-coupled TLR4 signalling (2016)

Marginal zone (MZ) B cells produce a first wave of antibodies for protection from blood-borne pathogens. However, the role of MZ B cells in inflammatory responses has not been elucidated. Here we show that MZ B cells produce pro-inflammatory cytokines, such as interleukin-6 (IL-6), and exacerbate systemic inflammatory responses to lipopolysaccharide (LPS). After intravenous injection of LPS or E. coli, mice deficient in MZ B cells or IL-6 only in MZ B cells have attenuated systemic inflammatory responses and prolonged survival compared with wild-type mice. LPS directly stimulates MZ B cells via Toll-like receptor 4 (TLR4) and MyD88 pathways for IL-6 production. Furthermore, TLR4 requires physical and functional association with Fcα/μR (CD351) for its oligomer formation, NF-κB signalling and IL-6 production from MZ B cells; this association is responsible for systemic inflammatory responses and endotoxic shock. These results reveal a pro-inflammatory role of MZ B cells in endotoxic shock.
Characterization of human placental insulin-like growth factor-I/insulin hybrid receptors by protein microsequencing and purification (1993)

Protein microsequencing of human placental IGF-I receptors purified by immunoaffinity chromatography using IGF-I receptor specific monoclonal antibody revealed amino acid sequences of both IGF-I and insulin receptors. Since this finding indicated the presence of IGF-I/insulin receptor hybrids, hybrid receptors were further purified by immunoaffinity chromatography using insulin receptor specific monoclonal antibody. The molecular size of the nonreduced hybrid receptor was approximately 350K, indicating that the IGF-I and insulin receptor alpha beta halves were disulfide-linked. The ratio of IGF/insulin binding activity of purified hybrid receptors was approximately 25 when measured using tracer amounts of radioactive ligands. 125I-IGF binding to these receptors was inhibited by IGF-I and insulin with IC50s of approximately 2 and approximately 1000 nM, respectively. 125I-Insulin binding to these receptors was similarly inhibited by IGF-I and insulin with IC50 of approximately 3 nM. Autophosphorylation and kinase activities of the hybrid receptor were stimulated by IGF-I more effectively than insulin in a dose-dependent manner. Thus, the present studies indicate that hybrid receptors purified from human placenta have the functional properties of an IGF-I receptor.
ISAAC: A Convolutional Neural Network Accelerator with In-Situ Analog Arithmetic in Crossbars (2016)

A number of recent efforts have attempted to design accelerators for popular machine learning algorithms, such as those involving convolutional and deep neural networks (CNNs and DNNs). These algorithms typically involve a large number of multiply-accumulate (dot-product) operations. A recent project, DaDianNao, adopts a near data processing approach, where a specialized neural functional unit performs all the digital arithmetic operations and receives input weights from adjacent eDRAM banks. This work explores an in-situ processing approach, where memristor crossbar arrays not only store input weights, but are also used to perform dot-product operations in an analog manner. While the use of crossbar memory as an analog dot-product engine is well known, no prior work has designed or characterized a full-fledged accelerator based on crossbars. In particular, our work makes the following contributions: (i) We design a pipelined architecture, with some crossbars dedicated for each neural network layer, and eDRAM buffers that aggregate data between pipeline stages. (ii) We define new data encoding techniques that are amenable to analog computations and that can reduce the high overheads of analog-to-digital conversion (ADC). (iii) We define the many supporting digital components required in an analog CNN accelerator and carry out a design space exploration to identify the best balance of memristor storage/compute, ADCs, and eDRAM storage on a chip. On a suite of CNN and DNN workloads, the proposed ISAAC architecture yields improvements of 14.8×, 5.5×, and 7.5× in throughput, energy, and computational density (respectively), relative to the state-of-the-art DaDianNao architecture.
Human diadenosine 5′,5′′′-P1,P4-tetraphosphate pyrophosphohydrolase is a member of the MutT family of nucleotide pyrophosphatases (1995)

The cDNA and derived amino acid sequence of human diadenosine 5',5"'-P1,P4-tetraphosphate pyrophosphohydrolase have been determined with the aid of the GenBank Expressed Sequence Tag database. This enzyme possesses a modification of the MutT sequence motif found in certain nucleotide pyrophosphatases. It is unrelated to the enzymes of diadenosine tetraphosphate catabolism found in prokaryotes and fungi.
Highly Efficient Genome Modifications Mediated by CRISPR/Cas9 in Drosophila (2013)

We report that Cas9/gRNA mediates efficient genetic modifications in Drosophila. Through targeting seven loci, we achieved a germline efficiency of up to 100%. Genes in both heterochromatin and euchromatin can be modified efficiently. Thus the Cas9/gRNA system is an attractive tool for rapid disruption of essentially any gene in Drosophila.
Early Pulmonary Inflammation in Infants with Cystic Fibrosis (1995)

The mechanisms underlying the initiation of lung disease and early respiratory morbidity in cystic fibrosis (CF) are poorly understood. By identifying infants with CF through a statewide neonatal screening program, we investigated whether airway inflammation was present in these infants, with the goal of furthering our understanding of the early events in this lung disease. Bronchoalveolar lavage fluid (BALF) from 16 infants with CF (mean age, 6 mo) and 11 disease control infants (mean age, 12 mo) was examined for the following inflammatory parameters: (1) neutrophil count; (2) activity of free neutrophil elastase; (3) elastase/alpha 1-antiprotease inhibitor complexes; and (4) the level of interleukin-8 (IL-8). We also quantified the spontaneous level of expression of IL-8 mRNA transcripts by airway macrophages. Each index of airway inflammation was increased in the BALF of infants with CF as compared with control infants. In addition, both the number of neutrophils and IL-8 levels were increased in infants with CF who had negative cultures (n = 7) for common bacterial CF-related pathogens, as well as for common respiratory viruses and fungi at the time of bronchoalveolar lavage (BAL). These findings suggest that airway inflammation is already present in infants with CF who are as young as 4 wks. Furthermore, although many different cell types (e.g., epithelial cells) may express IL-8, airway macrophages appear to be a source of this chemokine, and may thus play a prominent role in early neutrophil influx into the lung.
Insulin-Like Growth Factor I Activates c-Jun N-Terminal Kinase in MCF-7 Breast Cancer Cells (2000)

Insulin-like growth factor I (IGF-I) is an important mediator of breast cancer cell growth, although the signaling pathways important for IGF-I-mediated effects in breast cancer cells are still being elucidated. We had demonstrated previously that increased intracellular cAMP in MCF-7 breast cancer cells inhibited cell growth and IGF-I-induced gene expression, as determined using a reporter gene assay. This effect of cAMP on IGF-I signaling was independent of IGF-I-induced activation of the mitogen-activated protein kinases extracellular signal-regulated kinases 1 and 2 (ERK1 and -2). To determine whether this effect of cAMP may be mediated via another mitogen-activated protein kinase, the ability of IGF-I to activate the c-Jun N-terminal kinases (JNKs) was investigated. Treatment of MCF-7 cells with 100 ng/ml IGF-I increased the level of phosphorylated JNK, as determined by Western blot analysis. JNK phosphorylation was not evident until 15 min after treatment with IGF-I, and peak levels of phosphorylation were present at 30 -60 min. This was in contrast to ERK phosphorylation, which was present within 7.5 min of IGF-I treatment. Determination of JNK activity using an immune complex assay demonstrated a 3.3-and 3.5-fold increase in JNK1 and -2 activity, respectively, 30 min after treatment with 100 ng/ml IGF-I. The use of PD98059, which inhibits activation of ERK1 and -2, and LY 294002, an inhibitor of phosphatidylinositol 3-kinase, demonstrated that IGF-I-induced activation of JNK1 is independent of ERK and phosphatidylinositol 3-kinase activation. In contrast, increasing intracellular cAMP with forskolin resulted in abrogation of IGF-I-induced JNK activity. In summary, these data demonstrate that IGF-I activates the JNKs in MCF-7 breast cancer cells and, taken together with the results of our previous study, suggest that JNK may contribute to IGF-I-mediated gene expression and, possibly, cell growth in MCF-7 breast cancer cells.
Molecule by Molecule Direct and Quantitative Counting of Antibody−Protein Complexes in Solution (2004)

We have used two-color fluorescence coincidence detection to directly count individual protein-antibody complexes of protein G or herpes simplex virus labeled with one or more red- and blue-excited antibodies. This allowed quantitative measurement of the concentration of the protein-antibody complexes over 3 orders of magnitude down to the femtomolar level. Single molecule measurements in diluted serum are also possible. The sample preparation is simple, takes place in solution, and requires no separation. Both the antibody affinity and complex dissociation rate are important in determining the sensitivity of the method. At present, the sensitivity limit of 50 fM is determined by the encounter rate of the labeled analyte with the probe volume. This method can be used to detect and quantitate proteins and to measure the stoichiometry, equilibrium constant, and dissociation rate of protein-protein complexes at low concentrations.
Naked Fluoride Ion Sources:  Synthesis, Characterization, and Coupling Reaction of 1-Methylhexamethylenetetramine Fluoride (1997)

Anhydrous 1-methylhexamethylenetetramine (also referred to as N-methylurotropinium or methylhexaminium) fluoride was prepared by either halogen exchange between the corresponding iodide and AgF or by a single-step, one-pot, self-assembling synthesis from aqueous CH3NH2, HF, formaldehyde, and NH3. It was characterized by NMR and vibrational spectroscopy. Its hydrate undergoes at 70 °C a Sommelet-type ring opening and coupling reaction to form a potential cryptand system consisting of two bicyclic triazine groups that are connected through a methylene bridge and contain eight ternary nitrogen atoms. The compound was characterized by multinuclear NMR and vibrational spectroscopy, and its structure was determined from single-crystal X-ray diffraction data.