gebhart/patrepeval huggingface dataset:
Therapeutic applications: natural killer cells in the clinic (2013)

Natural killer (NK) cells recognize targets stressed by malignant transformation or infection (particularly CMV). We now know that NK cells can be long-lived and remember past exposures. They become educated by interaction with MHC class I molecules to gain potent function to kill targets and produce cytokines. In the clinical setting, haploidentical NK cells can be transferred adoptively to treat cancer. Persistence and in vivo expansion of NK cells depends on lymphodepleting chemotherapy to make space for the release of endogenous IL-15. In vivo expansion is also enhanced by cytokine administration. IL-2 has been used at low doses to stimulate NK cells in vivo, but has the down side of stimulating CD25hi regulatory T cells. IL-15 is now being tested and has the advantage of avoiding inhibitory regulatory T cell stimulation. In refractory acute myeloid leukemia, leukemia clearance is correlated with the persistence and in vivo expansion of NK cells after adoptive transfer. Limitations to NK cell therapy include poor in vivo survival and lack of specificity. Monoclonal antibodies and bispecific or trispecific killer engagers to target CD16 on NK cells to enhance recognition of various tumor antigens and ADAM17 inhibition to prevent CD16 shedding after NK cell activation should promote enhanced killing of cancer with specificity. Future strategies to exploit favorable donor immunogenetics or to expand NK cells ex vivo from blood, progenitors, or pluripotent progenitors may overcome immune barriers of adoptive transfer and comparative clinical trials will be needed to test these approaches.
Ceph: a scalable, high-performance distributed file system (2006)

We have developed Ceph, a distributed file system that provides excellent performance, reliability, and scalability. Ceph maximizes the separation between data and metadata management by replacing allocation tables with a pseudo-random data distribution function (CRUSH) designed for heterogeneous and dynamic clusters of unreliable object storage devices (OSDs). We leverage device intelligence by distributing data replication, failure detection and recovery to semi-autonomous OSDs running a specialized local object file system. A dynamic distributed metadata cluster provides extremely efficient metadata management and seamlessly adapts to a wide range of general purpose and scientific computing file system workloads. Performance measurements under a variety of workloads show that Ceph has excellent I/O performance and scalable metadata management, supporting more than 250,000 metadata operations per second.
Differential Tropism and Chemokine Receptor Expression of Human Immunodeficiency Virus Type 1 in Neonatal Monocytes, Monocyte-Derived Macrophages, and Placental Macrophages (1998)

Laboratory-adapted (LA) macrophage-tropic (M-tropic) human immunodeficiency virus type 1 (HIV-1) isolates (e.g., HIV-1(Ba-L)) and low-passage primary (PR) isolates differed markedly in tropism for syngeneic neonatal monocytes, monocyte-derived macrophages (MDMs), and placental macrophages (PMs). Newly adherent neonatal monocytes and cultured PMs were highly refractory to infection with PR HIV-1 isolates yet were permissive for LA M-tropic isolates. Day 4 MDMs were also permissive for LA M-tropic isolates and additionally, were permissive for over half the PR isolates tested. Qualitative differences in PR HIV-1 infection of monocytes/MDMs could not be correlated with CD4 levels alone, and in all three cell types the block to PR HIV-1 strain replication preceded reverse transcription. Neonatal monocyte susceptibility to PR HIV-1 strains correlated with increasing CCR-5 expression during maturation. CCR-5 could not be detected on newly adherent (day 1) neonatal monocytes, in contrast to adult monocytes (H. Naif et al., J. Virol. 72:830-836, 1998), but was readily detectable after 4 to 7 days of culture. However, moderate CCR-5 mRNA levels were present in day 1 neonatal monocytes and remained constant during monocyte maturation. CCR-5 was not detectable on the surface of PMs, yet the receptor was present within permeabilized cells. Notably, two brain-derived PR HIV-1 isolates from a single patient, differing in their V3 loops, were discordant in their abilities to infect neonatal monocytes/MDMs and PMs, yet both isolates could infect newly adherent adult monocytes. Together these data strongly suggest that LA HIV-1 isolates are able to infect neonatal monocytes at earlier stages of maturation and lower-level expression of CCR-5 than PR isolates. The differences between neonatal and adult monocytes in susceptibility to PR isolates may also be related to the level of CCR-5 expression.
Transcriptional activation of the estrogen receptor (1993)

Almost all breast cancer tumors progress to a hormone-resistant state. Evidence is presented that the existence of mutant estrogen receptors may explain some hormone-resistant phenotypes. Breast tumor cells bearing a mutant receptor that is constitutively active and does not bind hormone would have unregulated cell growth and thus appear to be hormone-independent. Alternatively, breast cancer cells may contain estrogen receptors that are transcriptionally inactive but when co-expressed with wild-type receptors render normal estrogen receptors inactive. These cells would be considered estrogen receptor-positive but would be hormone-resistant. The hormone-resistant phenotype could be further complicated by the finding that other nonreceptor proteins may also modulate the transcriptional activity of estrogen receptors. These findings, if substantiated in vivo, could add to the complexity of the hormone-resistant phenotype. Different strategies of treatment will need to be developed to effectively treat the various subtypes of hormone-resistant breast tumors.
Localization of magnetic pills (2011)

Numerous therapeutics demonstrate optimal absorption or activity at specific sites in the gastrointestinal (GI) tract. Yet, safe, effective pill retention within a desired region of the GI remains an elusive goal. We report a safe, effective method for localizing magnetic pills. To ensure safety and efficacy, we monitor and regulate attractive forces between a magnetic pill and an external magnet, while visualizing internal dose motion in real time using biplanar videofluoroscopy. Real-time monitoring yields direct visual confirmation of localization completely noninvasively, providing a platform for investigating the therapeutic benefits imparted by localized oral delivery of new and existing drugs. Additionally, we report the in vitro measurements and calculations that enabled prediction of successful magnetic localization in the rat small intestines for 12 h. The designed system for predicting and achieving successful magnetic localization can readily be applied to any area of the GI tract within any species, including humans. The described system represents a significant step forward in the ability to localize magnetic pills safely and effectively anywhere within the GI tract. What our magnetic pill localization strategy adds to the state of the art, if used as an oral drug delivery system, is the ability to monitor the force exerted by the pill on the tissue and to locate the magnetic pill within the test subject all in real time. This advance ensures both safety and efficacy of magnetic localization during the potential oral administration of any magnetic pill-based delivery system.
Abstract 2839: Specific mutant tumor DNA can be detected in ovarian cystic fluid of an unknown ovarian tumor cyst (2015)

Abstract Can we detect rare mutations in ovarian cystic fluid of unknown severity in order to develop a molecular genetic test for epithelial ovarian cancer? Background: Benign and malignant ovarian cysts are difficult to distinguish. Early diagnose is life saving, however 75% of ovarian adenocarcinomas is found in late stage. Approx. one operated ovarian cyst in 7-10 are found to be cancer and potentially life-threatening, subjecting the woman to unnecessary oophorectomy and morbidity. A genetic test of fine needle aspirated cystic fluid has to be very accurate to be able to substitute the histopathologic examination following surgery. Methods: DNA was purified from 78 ovarian cystic fluids (collected at the time of operation) from serous adenomas/adenocarcinomas and corresponding tumor tissues and subjected to state-of-the-art genetic analysis. We evaluated ∼10,000 bp for subtle mutations (single base substitutions, small insertions, small deletions). Under the conditions used, mutations present in &amp;gt;0.1% of template molecules could be detected. The analyses were carried out in a completely blind fashion. We then evaluated the DNA of the primary tumor. Results: We detected zero, one, or two mutations per cyst. The same mutations were identified in the corresponding tumor tissue, and no others. This dramatically confirms the specificity of the approach. 91% of the malignant cysts (n = 32) had at least one mutation and 62% of these were in TP53; 17% in low (n = 12) and 90% in high (n = 20) grade serous adenocarcinoma regardless of stage. In low-grade tumors mutations in KRAS dominated over PIK3C and PTEN. 65% of the borderline type (LMP n = 20) tumors had a BRAF V600E mutation. The mutant allelic fraction was much higher in malignant than benign tumors; the DNA concentration was relatively low in 20 benign cysts and no mutations were identified in this group consisting of 10 serous adenoma and 10 simple cysts (healthy controls). Results will be correlated to survival. Conclusion: Data proofs that we can detect mutant tumor DNA corresponding to the primary ovarian tumor in the ovarian cystic fluid. Data suggest that gene-testing of ovarian cystic fluid could aid in diagnostics and further guide its management. Citation Format: Karin Sundfeldt, Björg Kristjansdottir, Bert Vogelstein. Specific mutant tumor DNA can be detected in ovarian cystic fluid of an unknown ovarian tumor cyst. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2839. doi:10.1158/1538-7445.AM2015-2839
Cryptic α‐toxin gene in toxic shock syndrome and septicaemia strains of Staphylococcus aureus (1990)

The majority of clinical isolates of Staphylococcus aureus that produce toxic shock syndrome toxin-1 (TSST-1) fail to express alpha-toxin, despite having a copy of the hla gene in the chromosome. The hla gene was cloned from an Hla- TSST-1+ strain, Todd 555, which had been isolated from a case of toxic shock syndrome in the USA. Of the 630 bases of the Todd 555 gene sequenced, 46 differed from the hla gene sequence of strain Wood 46. The defect in alpha-toxin expression was shown to be due to a nonsense mutation which converted a CAG glutamine codon in the equivalent position in the functional Wood 46 sequence to a TAG stop codon. The same mutation was present in the hla gene cloned from a human septicaemia strain (V37) isolated in Dublin. The nonsense mutation of Todd 555 was suppressed by the supE44 mutation in Escherichia coli resulting in haemolytic activity in cell lysates. Hybrid hla genes were formed by splicing fragments of hla from Todd 555 and Wood 46. Expression of one such chimaeric hla gene in S. aureus demonstrated that the Todd 555 hla gene has a functional agr-regulated promoter. The silent hla gene may be a cryptic gene in S. aureus.
An epiilluminator/detector unit permitting arc lamp illumination for fluorescence activated cell sorters (1982)

The application of arc lamps to flow cytometers is discussed and epiillumination for jet-in-air cell sorters is introduced. An epiilluminator/detector unit equipped with a mercury arc lamp constructed for a commercially available cell sorter is described. Experiments in which laser and mercury arc lamp illumination were compared show that the signal-to-noise ratio for the arc lamp illumination is predominantly limited by shot noise from constant light backgrounds due to reflected excitation light and ambient light. Arc lamp illumination can be used for the sorting of highly fluorescent objects such as cells stained for DNA by for example: ethidium bromide, propidium iodide, or the Hoechst dyes. The simultaneous employment of mercury arc and laser light sources as an inexpensive dual wavelength system is discussed.
Enzyme replacement improves nervous system pathology and function in a mouse model for metachromatic leukodystrophy (2005)

A deficiency of arylsulfatase A (ASA) causes the lysosomal storage disease metachromatic leukodystrophy, which is characterized by accumulation of the sphingolipid 3-O-sulfogalactosylceramide (sulfatide). Sphingolipid storage results in progressive demyelination and severe neurologic symptoms. The disease is lethal, and curative therapy is not available. To assess the therapeutic potential of enzyme replacement therapy (ERT), ASA knockout mice were treated by intravenous injection of recombinant human ASA. Plasma levels of ASA declined with a half-time of approximately 40 min, and enzyme was detectable in tissues within minutes after injection. The uptake of injected enzyme was high into liver, moderate into peripheral nervous system (PNS) and kidney and very low into brain. The apparent half-life of endocytosed enzyme was approximately 4 days. A single injection led to a time- and dose-dependent decline of the excess sulfatide in PNS and kidney by up to 70%, but no reduction was seen in brain. Four weekly injections with 20 mg/kg body weight not only reduced storage in peripheral tissues progressively, but also were surprisingly effective in reducing sulfatide storage in brain and spinal cord. The histopathology of kidney and central nervous system was ameliorated. Improved neuromotor coordination capabilities and normalized peripheral compound motor action potential demonstrate the benefits of ERT on the nervous system function. Enzyme replacement may therefore be a promising therapeutic option in this devastating disease.
Mucosal biomarkers in inflammatory bowel disease: Key pathogenic players or disease predictors? (2010)

Inflammatory bowel diseases (IBDs) are chronic inflammatory disorders of the bowel, including ulcerative colitis and Crohn's disease. A single etiology has not been identified, but rather the pathogenesis of IBD is very complex and involves several major and minor contributors, employing different inflammatory pathways which have different roles in different patients. Although new and powerful medical treatments are available, many are biological drugs or immunosuppressants, which are associated with significant side effects and elevated costs. As a result, the need for predicting disease course and response to therapy is essential. Major attempts have been made at identifying clinical characteristics, concurrent medical therapy, and serological and genetic markers as predictors of response to biological agents. Only few reports exist on how mucosal/tissue markers are able to predict clinical behavior of the disease or its response to therapy. The aim of this paper therefore is to review the little information available regarding tissue markers as predictors of response to therapy, and reevaluate the role of tissue factors associated with disease severity, which can eventually be ranked as "tissue factor predictors". Five main categories are assessed, including mucosal cytokines and chemokines, adhesion molecules and markers of activation, immune and non-immune cells, and other mucosal components. Improvement in the design and specificity of clinical studies are mandatory to be able to classify tissue markers as predictors of disease course and response to specific therapy, obtain the goal of achieving "personalized pathogenesis-oriented therapy" in IBD.
Direct thrombosis of aneurysms with cellulose acetate polymer (1992)

The authors report the treatment of seven intracranial aneurysms in six patients with direct infusion of cellulose acetate polymer solution, a new liquid thrombotic material. These aneurysms were considered inoperable because of their size or location, or because of the patient's neurological condition. This material avoids the difficulties associated with balloon occlusion, and completely fills even irregularly shaped aneurysms. Cellulose acetate polymer solution hardens in about 5 minutes and remains solid once inside the aneurysm. Because this technique is less invasive than surgery, it can be used for high-risk patients in the acute stage of subarachnoid hemorrhage. Transient motor aphasia occurred in one patient. A small residual neck, which caused rebleeding 3 months after the treatment, remained in another patient. This article describes the new material, the procedure for direct thrombosis, and preliminary clinical results.
ICOSAHEDRAL RNA VIRUS STRUCTURE (1989)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Kumada Arylation of Secondary Amides Enabled by Chromium Catalysis for Unsymmetric Ketone Synthesis under Mild Conditions (2018)

The synthesis of aromatic ketones by chromium-catalyzed Kumada arylation of secondary amides with organomagnesium reagents is described. This reaction was enabled by using low-cost chromium(III) salt as a precatalyst, combined with trimethylsilyl chloride as an additive, and presents a rare example of catalytic transformation of secondary amides to ketones at room temperature. It was shown that catalytically active low-valent chromium species might be responsible for the amide–ketone exchange by mechanism involving the activation of benzimidate intermediate.
Regulatory Architecture of the Iron-Regulated fepD-ybdA Bidirectional Promoter Region in Escherichia coli (2001)

The overlapping and opposing promoter elements for the Escherichia coli fepDGC operon and the ybdA gene (encoding a 43-kDa cytoplasmic membrane protein) within the enterobactin gene cluster were investigated by measuring the effects of site-specific mutations on transcript levels and on expression of reporter genes in a bidirectional transcriptional fusion vector. Primary promoter structures for the opposing transcripts overlapped extensively such that their -10 sequences were almost directly opposed on the two strands of the DNA helix and their +1 transcription start sites were only 23 bp apart. Relative to the E. coli consensus sequence, both promoters were poorly conserved at the -35 position and mutations which strengthened the -35 element of either promoter significantly enhanced its transcription, decreased that of the opposing promoter, and dramatically altered iron-mediated regulation of expression. Both the fepD and ybdA primary promoters were shown to require a 5'-TGn-3' upstream extension of their -10 elements for optimal activities. Secondary promoters were identified for both fepD and ybdA, and their contributions to the overall expression levels were evaluated in these dual expression vector constructs. The data provided strong evidence that the architecture of the regulatory elements within the overlapping fepD and ybdA promoters is configured such that there is a direct competition for binding RNA polymerase and that the expression levels at these promoters are influenced not only by the activity of the opposing promoters but also by additional promoter sequence elements and perhaps accessory regulatory factors. Iron-mediated regulation of these promoters through the repressor protein Fur is a consequence of the relative promoter strengths and the position of an operator site that consists of two overlapping Fur-binding sequences in this compact regulatory region.
Upregulation of Interleukin-12 and -17 in Active Inflammatory Bowel Disease (2003)

The expression of both IL-12 and IL-17 mRNA is induced in active UC and CD and may thus be involved in sustaining the intestinal inflammation in IBD. Inhibition of IL-12 or IL-17 might be future therapeutic targets in IBD.
Structural determinants for EB1-mediated recruitment of APC and spectraplakins to the microtubule plus end (2005)

EB1 is a member of a conserved protein family that localizes to growing microtubule plus ends. EB1 proteins also recruit cell polarity and signaling molecules to microtubule tips. However, the mechanism by which EB1 recognizes cargo is unknown. Here, we have defined a repeat sequence in adenomatous polyposis coli (APC) that binds to EB1's COOH-terminal domain and identified a similar sequence in members of the microtubule actin cross-linking factor (MACF) family of spectraplakins. We show that MACFs directly bind EB1 and exhibit EB1-dependent plus end tracking in vivo. To understand how EB1 recognizes APC and MACFs, we solved the crystal structure of the EB1 COOH-terminal domain. The structure reveals a novel homodimeric fold comprised of a coiled coil and four-helix bundle motif. Mutational analysis reveals that the cargo binding site for MACFs maps to a cluster of conserved residues at the junction between the coiled coil and four-helix bundle. These results provide a structural understanding of how EB1 binds two regulators of microtubule-based cell polarity.
Nucleotide sequence of cloned rat serum albumin messenger RNA. (1981)

The nucleotide sequences of the recombinant DNA inserts of three bacterial plasmid clones containing nearly all of the rat serum albumin mRNA have been determined. A statistical analysis of the nucleotide sequence reveals a pattern of repeated internal homology that confirms the "intragenic triplication" model of albumin evolution.
Ultrafast Magnetization Reversal Dynamics Investigated by Time Domain Imaging (2001)

Spatiotemporal magnetization reversal dynamics in a Ni(80)Fe(20) microstructure is studied using ps time scale scanning Kerr microscopy. Time domain images reveal a striking change in the reversal associated with the reduction in switching time when a transverse bias field is applied. Magnetization oscillations subsequent to reversal are observed at two resonance frequencies, which sensitively depend on the bias field strength. The oscillation at f = 2 GHz is caused by the damped precession of M, while the lower frequency approximately 0.8 GHz mode is interpreted in terms of domain wall oscillation.
Target antigens of transmission-blocking immunity on gametes of plasmodium falciparum. (1983)

Three proteins of apparent molecular weights on reducing SDS-PAGE of 255, 59, and 53 kilodaltons have been identified as the targets on gametes of P. falciparum malaria of two monoclonal antibodies (MAbs) that act synergistically to block transmission of the parasites to mosquitoes.