gebhart/patrepeval huggingface dataset:
A high throughput screen to identify secreted and transmembrane proteins involved in Drosophila embryogenesis (1998)

Secreted and transmembrane proteins play an essential role in intercellular communication during the development of multicellular organisms. Because only a small number of these genes have been characterized, we developed a screen for genes encoding extracellular proteins that are differentially expressed during Drosophila embryogenesis. Our approach utilizes a new method for screening large numbers of cDNAs by whole-embryo in situ hybridization. The cDNA library for the screen was prepared from rough endoplasmic reticulum-bound mRNA and is therefore enriched in clones encoding membrane and secreted proteins. To increase the prevalence of rare cDNAs in the library, the library was normalized using a method based on cDNA hybridization to genomic DNA-coated beads. In total, 2,518 individual cDNAs from the normalized library were screened by in situ hybridization, and 917 of these cDNAs represent genes differentially expressed during embryonic development. Sequence analysis of 1,001 cDNAs indicated that 811 represent genes not previously described in Drosophila. Expression pattern photographs and partial DNA sequences have been assembled in a database publicly available at the Berkeley Drosophila Genome Project website (). The identification of a large number of genes encoding proteins involved in cell-cell contact and signaling will advance our knowledge of the mechanisms by which multicellular organisms and their specialized organs develop.
The culture of dermal papilla cells from human hair follicles (1984)

Dermal papillae were isolated from human hair follicles and primary cell cultures were established from the papilla explants. The cultured papilla cells spread slowly, initially as a monolayer, and eventually formed multi-layered parallel arrays of fibroblast-like cells. At the edges of expanding colonies the cells were large and flattened and showed a tendency to form clumps. The behaviour of human dermal papilla cells in culture is very similar to that reported in cultures of papilla cells from rat vibrissa follicles.
Phospholipids in Meibomian Gland Secretion (1996)

The bulk of the lipid layer overlying the aqueous portion of the precorneal tear film is composed of polar and nonpolar components. The nonpolar lipids have been the subject of numerous studies; however, the polar lipids have remained relatively uncharacterized. The polar lipids are thought to contain surfactant phospholipids that are critical to the spreading of a lipid film over the aqueous layer, by providing an interface between this layer and the nonpolar lipids. The purpose of the present study is to identify and quantitate the phospholipid complement of meibomian gland secretion which provides the tear film with phospholipids. Meibomian gland secretion was collected from rabbits and phospholipids identified and quantitated by 31P nuclear magnetic resonance spectroscopy. Ten phospholipids were detected from meibomian gland secretion: diphosphatidylglycerol, dihydrosphingomyelin, ethanolamine plasmalogen, phosphatidylethanolamine (PE), phosphatidylserine, sphingomyelin, lysophosphatidylcholine, phosphatidylinositol, alkylacylphosphatidylcholine, and phosphatidylcholine (PC). The two major phospholipids were PC and PE, together comprising nearly 60% of the total phospholipid profile. The nature and relative concentrations of the meibomian gland secretion phospholipids are congruous with a surfactant role at the aqueous-lipid interface and, considering the physical chemistry of the tear film, suggest that the phospholipids should be organized in a very flat or planar configuration.
Bipolar disorder. (1999)

Bipolar disorder's unique combination of three characteristics - clear genetic diathesis, distinctive clinical features, early availability of an effective treatment (lithium) - explains its special place in the history of psychiatry and its contribution to the current explosive growth of neuroscience. This article looks at the state of the art in bipolar disorder from the vantage point of: (i) genetics (possible linkages on chromosomes 18 and 21q, polygenic hypothesis, research into genetic markers); (ii) diagnosis (new focus on the subjective aspects of bipolar disorder to offset the current trend of underdiagnosis due to overreliance on standardized interviews and rating scales); (iii) outcome (increase in treatment-resistant forms signaling a change in the natural history of bipolar disorder); (iv) pathophysiology (research into circadian biological rhythms and the kindling hypothesis to explain recurrence); (v) treatment (emergence of the anticonvulsants, suggested role of chronic antidepressant treatment in the development of treatment resistance); (vi) neurobiology (evaluation of regulatory function in relation to affective disturbances, role of postsynaptic second-messenger mechanisms, advances in functional neuroimaging); and (vii) psychosocial research (shedding overly dualistic theories of the past to understand the mind and brain as an entity, thus emphasizing the importance of balancing the psychopharmacological and psychotherapeutic approaches). Future progress in the understanding and treatment of bipolar disorder will rely on successful integration of the biological and psychosocial lines of investigation.
IL-10 inhibits cytokine production by activated macrophages (1991)

IL-10 inhibits the ability of macrophage but not B cell APC to stimulate cytokine synthesis by Th1 T cell clones. In this study we have examined the direct effects of IL-10 on both macrophage cell lines and normal peritoneal macrophages. LPS (or LPS and IFN-gamma)-induced production of IL-1, IL-6, and TNF-alpha proteins was significantly inhibited by IL-10 in two macrophage cell lines. Furthermore, IL-10 appears to be a more potent inhibitor of monokine synthesis than IL-4 when added at similar concentrations. LPS or LPS- and IFN-gamma-induced expression of IL-1 alpha, IL-6, or TNF-alpha mRNA was also inhibited by IL-10 as shown by semiquantitative polymerase chain reaction or Northern blot analysis. Inhibition of LPS-induced IL-6 secretion by IL-10 was less marked in FACS-purified peritoneal macrophages than in the macrophage cell lines. However, IL-6 production by peritoneal macrophages was enhanced by addition of anti-IL-10 antibodies, implying the presence in these cultures of endogenous IL-10, which results in an intrinsic reduction of monokine synthesis after LPS activation. Consistent with this proposal, LPS-stimulated peritoneal macrophages were shown to directly produce IL-10 detectable by ELISA. Furthermore, IFN-gamma was found to enhance IL-6 production by LPS-stimulated peritoneal macrophages, and this could be explained by its suppression of IL-10 production by this same population of cells. In addition to its effects on monokine synthesis, IL-10 also induces a significant change in morphology in IFN-gamma-stimulated peritoneal macrophages. The potent action of IL-10 on the macrophage, particularly at the level of monokine production, supports an important role for this cytokine not only in the regulation of T cell responses but also in acute inflammatory responses.
Ensemble Learning for Confidence Measures in Stereo Vision (2013)

With the aim to improve accuracy of stereo confidence measures, we apply the random decision forest framework to a large set of diverse stereo confidence measures. Learning and testing sets were drawn from the recently introduced KITTI dataset, which currently poses higher challenges to stereo solvers than other benchmarks with ground truth for stereo evaluation. We experiment with semi global matching stereo (SGM) and a census data term, which is the best performing real-time capable stereo method known to date. On KITTI images, SGM still produces a significant amount of error. We obtain consistently improved area under curve values of sparsification measures in comparison to best performing single stereo confidence measures where numbers of stereo errors are large. More specifically, our method performs best in all but one out of 194 frames of the KITTI dataset.
Eosinophils and human cancer. (1997)

Eosinophils are rare granulocytes that are normally associated with allergic diseases or responses to various parasitic infections. Many types of human cancer, however, are also associated with extensive eosinophilia, either within the tumor itself, or in the peripheral blood, or in both locations. Special techniques such as autoflourescence or immunohistochemistry are sometimes needed to detect the presence of intact and degranulating eosinophils within the tumors. With the help of these techniques, extensive eosinophilia is most often seen in hematologic tumors such as Hodgkin's disease and certain lymphomas; however, many other types of cancer such as colon, cervix, lung, breast, and ovary also contain eosinophilia if diligently sought. Although the presence or absence of eosinophilia within these tumors does not appear to have a major influence on the prognosis of the patient, eosinophils may play an important role in the host interaction with the tumor, perhaps by promoting angiogenesis and connective tissue formation adjacent to the cancer. In addition, tumor-related eosinophilia provides some interesting clues into tumor biology, particularly with regard to production of cytokines by the tumor cells.
Pre-targeted immunoscintigraphy of murine tumors with indium-111-labeled bifunctional haptens. (1988)

A method of tumor imaging utilizing the nonspecific accumulation of antibody through leaky capillaries is described, in which the antibody and the radiolabel are administered separately. Nonradioactive antibody is given first (pre-targeted), and allowed adequate time to reach maximum tumor concentration. Depending on the antibody, this may take several days. At the time of maximum tumor concentration of nonradioactive antibody, the blood is quickly cleared of excess circulating nonradioactive antibody using a special i.v. "chase". The radiolabel then is given and imaging done in 1 to 3 hr. The use of short lived tracers (hours) to image antibodies that localize slowly (days) in-vivo is made possible by this method.
The 1990 Elections in Côte d’Ivoire (1991)

Paraphrasing Felix Houphouet-Boigny, Ivoirian politician Camille Aliali once said, “Democracy is a system of government for virtuous people. It seldom works even in mature countries. We must be realistic. Our people are ignorant of the problems we face. They cannot be left to choose the solutions,....” In 1990, the president and his close associates changed their minds. On May 3, 1990, the president of Cote d’Ivoire announced the legalization of opposition parties and the intent to hold multi-party elections. On October 28, Ivoirians voted in their first multi-candidate presidential election, which pitted the eighty-five year old Houphouet against long-standing critic and candidate of the “democratic left” coalition, Laurent Gbagbo.
Whole-Genome Microarray and Gene Deletion Studies Reveal Regulation of the Polyhydroxyalkanoate Production Cycle by the Stringent Response in Ralstonia eutropha H16 (2012)

Poly(3-hydroxybutyrate) (PHB) production and mobilization in Ralstonia eutropha are well studied, but in only a few instances has PHB production been explored in relation to other cellular processes. We examined the global gene expression of wild-type R. eutropha throughout the PHB cycle: growth on fructose, PHB production using fructose following ammonium depletion, and PHB utilization in the absence of exogenous carbon after ammonium was resupplied. Our results confirm or lend support to previously reported results regarding the expression of PHB-related genes and enzymes. Additionally, genes for many different cellular processes, such as DNA replication, cell division, and translation, are selectively repressed during PHB production. In contrast, the expression levels of genes under the control of the alternative sigma factor σ(54) increase sharply during PHB production and are repressed again during PHB utilization. Global gene regulation during PHB production is strongly reminiscent of the gene expression pattern observed during the stringent response in other species. Furthermore, a ppGpp synthase deletion mutant did not show an accumulation of PHB, and the chemical induction of the stringent response with DL-norvaline caused an increased accumulation of PHB in the presence of ammonium. These results indicate that the stringent response is required for PHB accumulation in R. eutropha, helping to elucidate a thus-far-unknown physiological basis for this process.
Increased intratumoral androgens in human breast carcinoma following aromatase inhibitor exemestane treatment (2010)

Sex steroids play important roles in the development of many human breast carcinomas, and aromatase inhibitors are used for the anti-estrogen therapy. Recent studies have demonstrated that aromatase suppressed 5alpha-dihydrotestosterone (DHT) synthesis in breast carcinoma cells, but intratumoral concentration of androgens and its significance have not been reported in the breast carcinoma patients treated with aromatase inhibitors. Therefore, we examined androgen concentrations in breast carcinoma tissues treated with exemestane, and further performed in vitro studies to characterize the significance of androgen actions. Intratumoral DHT concentration was significantly higher in breast carcinoma tissues following exemestane treatment (n=9) than those without the therapy (n=7), and 17beta-hydroxysteroid dehydrogenase type 2 (17betaHSD2) status was significantly altered to be positive after the treatment. Following in vitro studies showed that 17betaHSD2 expression was dose dependently induced by both DHT and exemestane in T-47D breast carcinoma cells, but these inductions were not additive. DHT-mediated induction of 17betaHSD2 expression was markedly suppressed by estradiol (E(2)) in T-47D cells. E(2)-mediated cell proliferation was significantly inhibited by DHT in T-47D cells, associated with an increment of 17betaHSD2 expression level. These findings suggest that intratumoral androgen actions are increased during exemestane treatment. 17betaHSD2 is a potent DHT-induced gene in human breast carcinoma, and may not only be involved in anti-proliferative effects of DHT on breast carcinoma cells but also serve as a potential marker for response to aromatase inhibitor in the breast carcinoma patients.
Replacement of Lysine by Arginine, Phenylalanine and Tryptophan in the Reactive Site of the Bovine Trypsin‐Kallikrein Inhibitor (Kunitz) and Change of the Inhibitory Properties (1976)

The reactive-site sequence of a proteinase inhibitor can be written as . . . -P3-P2-P1-P'1-P'2-P'3- . . . , where-P1-P'1-denotes the reactive site. Three semisynthetic homologues have been synthesized of the bovine trypsin-kallikrein inhibitor (Kunitz) with either arginine, phenylalanine or tryptophan in place of the reactive-site residue P1, lysine-15. These homologues correspond to gene products after mutation of the lysine 15 DNA codon to an arginine, phenylalanine or tryptophan DNA codon. Starting from native (virgin) inhibitor, reactive-site hydrolyzed, still active (modified) inhibitor was prepared by chemical and enzymic reactions. Modified inhibitor was then converted into inactive des-Lys15-inhibitor by reaction with carboxypeptidase B. Inactive des-Lys15-inhibitor was reactivated by enzymic replacement of the P1 residue according to Leary and Laskowski, Jr. The introduction of arginine was catalyzed by an inverse reaction with carboxypeptidase B, while phenylalanine or tryptophan were replaced by carboxypeptidase A. The reactivated semisynthetic inhibitors were trapped by complex formation with either trypsin or chymotrypsin. The enzyme - inhibitor complexes were subjected to kinetic-control dissociation, and the semisynthetic virgin inhibitors were isolated. The inhibitory properties of the semisynthetic inhibitors have been investigated against bovine trypsin and chymotrypsin and against porcine pancreatic kallikrein and plasmin. The homologues with either lysine or arginine in the P1 position are equally good inhibitors of trypsin, plasmin and kallikrein. The Arg-15-homologue is a slightly more effective kallikrein inhibitor than the Lys15-inhibitor. The semisynthetic phenylalanine and tryptophan homologues, however, are weak inhibitors of trypsin and still weaker inhibitors of kallikrein, but are excellent inhibitors of chymotrypsin. Their association constant with chymotrypsin is at least ten times higher than that of native Lys-15-inhibitor. A dramatic specificity change is observed with the phenylalanine and tryptophan homologues, which in contrast to the native inhibitor do not at all inhibit porcine plasmin. Thus, the nature of the P1 residue strongly influences the primary inhibitory specificity of the bovine inhibitor (Kunitz).
Modelling Access Propagation in Dynamic Systems (2013)

Access control is a critical feature of many systems, including networks of services, processes within a computer, and objects within a running process. The security consequences of a particular architecture or access control policy are often difficult to determine, especially where some components are not under our control, where components are created dynamically, or where access policies are updated dynamically. The SERSCIS Access Modeller (SAM) takes a model of a system and explores how access can propagate through it. It can both prove defined safety properties and discover unwanted properties. By defining expected behaviours, recording the results as a baseline, and then introducing untrusted actors, SAM can discover a wide variety of design flaws. SAM is designed to handle dynamic systems (i.e., at runtime, new objects are created and access policies modified) and systems where some objects are not trusted. It extends previous approaches such as Scollar and Authodox to provide a programmer-friendly syntax for specifying behaviour, and allows modelling of services with mutually suspicious clients. Taking the Confused Deputy example from Authodox we show that SAM detects the attack automatically; using a web-based backup service, we show how to model RBAC systems, detecting a missing validation check; and using a proxy certificate system, we show how to extend it to model new access mechanisms. On discovering that a library fails to follow an RFC precisely, we re-evaluate our existing models under the new assumption and discover that the proxy certificate design is not safe with this library.
Eradication of Helicobacter pylori in Patients with S-2 Stage Duodenal Ulcer Scar an Interim Report (2002)

Background/Aims: It is recommended that duodenal ulcer patients who are infected with H. pylori should be treated with eradication therapy, whether the ulcer is active or in remission. However, there has been no report on the effect of eradication treatment in patients with incidentally found S-2 stage duodenal ulcer scar. Methods: We prospectively enrolled 80 H. pylori-positive patients with S-2 stage duodenal ulcer scar who have no past history of ulcer treatment. Treatment group received triple therapy consisted of omeprazole, amoxicillin, and clarithromycin for 2 weeks, whereas control group received no treatment. The follow-up endoscopy was performed every 1 year and when the patients have symptoms of ulcer disease. Fifty-three patients were followed up for more than 1 year. Results: The eradication rate of the treatment group was 92.9%. During the follow-up period of 14.7 months, 20% (5/25) of patients in the control group (2 gastric ulcers and 3 duodenal ulcers) and 3.6% (1/2S) of patients in the treatment group (1 duodenal ulcer) developed active or healing stage peptic ulcers (p=0.089). Conclusions: Our results suggest that H. pylori eradication may be effective in preventing peptic ulcers in patients with S-2 stage duodenal ulcer scar.
Total syntheses of the structures assigned to salimine and jerusalemine, alkaloids from Colchicum decaisnei boiss. (Liliaceae) (1994)

Total syntheses of the dibenzo[a,c]cycloheptylamines (±)-1 and (±)-2 have been developed; the spectroscopic properties of synthetic 2 match those reported for the alkaloid jerusalemine but compound 1 is different from the alkaloid salimine.
Estrogen regulation of the insulin-like growth factor I gene transcription involves an AP-1 enhancer. (1994)

As a step toward elucidating the physiological role of insulin-like growth factor-I (IGF-I) in mediating estrogen action, we sought to determine the molecular basis of the phenomenon. In HepG2 cells expressing exogenous estrogen receptors (ER), a reporter gene plasmid containing 600 base pairs of the chicken IGF-I promoter enhanced expression of luciferase 8.6-fold in response to 10(-6) M 17 beta-estradiol, indicating that the IGF-I promoter is a target of estrogen regulation. Although no conventional estrogen-responsive element was identified within the promoter fragment, the AP-1 motif located therein was shown to be essential; the estrogen-responsive enhancement of the Fos-Jun binding to the AP-1 motif, which takes place by means of post-translational modification, mediates the estrogen action. A direct or indirect interaction between the estrogen-ER complex and the Fos-Jun complex seems to facilitate the Fos-Jun binding to the target DNA. Although ER binding to the target DNA was not considered to be involved in the signaling pathway, the DNA binding domain-deficient ER did not mediate the phenomenon, providing support for the existence of a unique function of the DNA binding domain of ER in facilitating some protein-protein interaction. In conclusion, our present observations demonstrate that the chicken IGF-I gene promoter is controlled by estrogen through a unique pathway involving Fos, Jun, and the DNA binding domain of ER.
In situ hybridization and translocation breakpoint mapping (1985)

Using a combination of banding techniques, we examined two atypical 21;22 translocations, 46,XX or XY,t(21;22)(p11;q11). In situ chromosomal hybridization of a probe for the constant region of the lambda light chain locus demonstrated that the 22q11 breakpoints of both rearrangements were proximal to the C lambda gene cluster. These studies permitted us to distinguish the 22q11 breakpoints of these translocations from the breakpoint of the 22q--chromosome of chronic myelogenous leukemia.
Human cytomegalovirus infection induces transcription and secretion of transforming growth factor beta 1 (1994)

Human cytomegalovirus (CMV) infection can elicit a transitory, but profound, immunodepression in immunocompetent individuals. Cytopathogenic destruction of CMV-infected leukocytes alone does not seem sufficient to explain this phenomenon, which suggests that immune system mediators (cytokines) may play a role in amplifying local modifications wrought by CMV infection. We reported previously that transforming growth factor beta 1 (TGF-beta 1) stimulates CMV replication (J. Alcami, C. V. Paya, J. L. Virelizier, and S. Michelson, J. Gen. Virol. 74:269-274, 1993). Since TGF-beta 1 can have profound negative effects on cell growth and immune responses, we investigated the induction of TGF-beta 1 following CMV infection of permissive fibroblasts. TGF-beta 1 promoter was activated by immediate-early (IE) proteins in the absence of infection and transactivated at 5 and 9 h after infection. TGF-beta 1 mRNA increased during the early phase of infection, suggesting that this phenomenon is due to enhanced transcription of the TGF-beta 1 gene. A comparative study of the influence of CMV infection and IE protein expression on TGF-beta 1 promoter function in permissive cells pointed to a possible cooperative role between IE proteins and protein(s) expressed during the early phase of viral infection. Induction of TGF-beta 1 by CMV infection could modify infected cells individually, surrounding tissues, and systemic immune reactions to the advantage of virus replication by both upregulating CMV replication and downregulating host immune responses.