gebhart/patrepeval huggingface dataset:
Hydrogels as artificial matrices for human embryonic stem cell self‐renewal (2006)

Human embryonic stem cells (hESCs) have the potential to differentiate into all cell types in the body and hold great promise for regenerative medicine; however, large-scale expansion of undifferentiated hESCs remains a major challenge. Self-renewal of hESCs requires culturing these cells on either mouse or human fibroblast cells (i.e., a feeder layer of cells), or on artificial extracellular matrices (ECMs) while supplementing the media with soluble growth factors. Here we report a completely synthetic ECM system composed of a semi-interpenetrating polymer network (sIPN), a polymer hydrogel, which was designed to allow the independent manipulation of cell adhesion ligand presentation and matrix stiffness. In the short term, hESCs that were cultured on the sIPN adhered to the surface, remained viable, maintained the morphology, and expressed the markers of undifferentiated hESCs. This was the first demonstration that a completely synthetic ECM can support short-term self-renewal of hESCs.
Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Potentiator VX-770 (Ivacaftor) Opens the Defective Channel Gate of Mutant CFTR in a Phosphorylation-dependent but ATP-independent Manner (2012)

The cystic fibrosis transmembrane conductance regulator (CFTR) acts as a channel on the apical membrane of epithelia. Disease-causing mutations in the cystic fibrosis gene can lead to CFTR protein misfolding as in the case of the F508del mutation and/or channel dysfunction. Recently, a small molecule, VX-770 (ivacaftor), has shown efficacy in restoring lung function in patients bearing the G551D mutation, and this has been linked to repair of its channel gating defect. However, these studies did not reveal the mechanism of action of VX-770 in detail. Normally, CFTR channel activity is regulated by phosphorylation, ATP binding, and hydrolysis. Hence, it has been hypothesized that VX-770 modifies one or more of these metabolic events. In this study, we examined VX-770 activity using a reconstitution system for purified CFTR protein, a system that enables control of known regulatory factors. We studied the consequences of VX-770 interaction with CFTR incorporated in planar lipid bilayers and in proteoliposomes, using a novel flux-based assay. We found that purified and phosphorylated CFTR was potentiated in the presence of Mg-ATP, suggesting that VX-770 bound directly to the CFTR protein, rather than associated kinases or phosphatases. Interestingly, we also found that VX-770 enhanced the channel activity of purified and mutant CFTR in the nominal absence of Mg-ATP. These findings suggest that VX-770 can cause CFTR channel opening through a nonconventional ATP-independent mechanism. This work sets the stage for future studies of the structural properties that mediate CFTR gating using VX-770 as a probe.
Sortase, a universal target for therapeutic agents against Gram-positive bacteria? (2000)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
An Inquiry into the Nature and Causes of the Wealth of Internet Miscreants (2007)

This paper studies an active underground economy which specializes in the commoditization of activities such as credit car d fraud, identity theft, spamming, phishing, online credential the ft, and the sale of compromised hosts. Using a seven month trace of logs collected from an active underground market operating on public Internet chat networks, we measure how the shift from “hacking for fun” to “hacking for profit” has given birth to a societal subs trate mature enough to steal wealth into the millions of dollars in less than one year.
Assessing the validity of blood‐based gene expression profiles for the classification of schizophrenia and bipolar disorder: A preliminary report (2005)

Recent advances have facilitated the use of blood-derived RNA to conduct genomic analyses of human diseases. This emerging technology represents a rigorous and convenient alternative to traditional tissue biopsy-derived RNA, as it allows for larger sample sizes, better standardization of technical procedures, and the ability to non-invasively profile human subjects. In the present pilot study, we have collected RNA from blood of patients diagnosed with schizophrenia or bipolar disorder (BPD), as well as normal control subjects. Using microarray analysis, we found that each disease state exhibited a unique expressed genome signature, allowing us to discriminate between the schizophrenia, BPD, and control groups. In addition, we validated changes in several potential biomarker genes for schizophrenia and BPD by RT-PCR, and some of these were found to code to chromosomal loci previously linked to schizophrenia. Linear and non-linear combinations of eight putative biomarker genes (APOBEC3B, ADSS, ATM, CLC, CTBP1, DATF1, CXCL1, and S100A9) were able to discriminate between schizophrenia, BPD, and control samples, with an overall accuracy of 95%-97% as indicated by receiver operating characteristic (ROC) curve analysis. We therefore propose that blood cell-derived RNA may have significant value for performing diagnostic functions and identifying disease biomarkers in schizophrenia and BPD.
Large scale multi-fingered end-effector teleoperation (2009)

Large multi-fingered end-effectors have promise to provide the added dexterity needed for manipulation while decreasing the amount of special fixturing required for tooling and object manipulation common to remote handling operations in hazardous and unstructured environments such as those in the nuclear domain. This paper presents the integration of a heavy-duty three-fingered articulated hand with a Schilling Titan hydraulic manipulator that is part of a comprehensive telerobotics test bed. Experiments demonstrated that a multi-fingered end effector approach has distinct benefits and advantages.
Human Herpesvirus 8 Interleukin-6 (vIL-6) Signals through gp130 but Has Structural and Receptor-Binding Properties Distinct from Those of Human IL-6 (1999)

Human herpesvirus 8 (HHV-8) has been associated with classical, endemic (African), and AIDS-related Kaposi's sarcoma (KS), body cavity-based primary effusion lymphomas, and multicentric Castleman's disease (MCD). HHV-8 encodes a functional homologue of interleukin-6 (IL-6), a cytokine that promotes the growth of KS and myeloma cells and is found at elevated levels in MCD lesions and patient sera. We have previously reported that the viral IL-6 (vIL-6) gene product can support the growth of the IL-6-dependent murine hybridoma cell line, B9, and that the gp80 (IL-6 receptor [IL-6R]) component of the IL-6 receptor-signal transducer (gp180) complex plays a role in mediating this activity. However, it has been shown by others that vIL-6 can function in human cells independently of IL-6R. Here we have extended our functional studies of vIL-6 by identifying transcription factors and pathways used in human Hep3B cells, investigating the utilization of gp130 and IL-6R by vIL-6, and undertaking mutational analyses of vIL-6 and gp130. The data presented here establish that vIL-6, in common with its endogenous counterparts, can mediate signal transduction through gp130 and activate multiple transcription factors, map residues within the vIL-6 protein that are and are not important for vIL-6 signalling, and identify a gp130 mutant that is nonfunctional with respect to vIL-6 signalling in the absence of IL-6R but that retains the ability to mediate vIL-6 and human IL-6 (hIL-6) signal transduction when IL-6R is coexpressed. The data presented demonstrate functional and mechanistic similarities between vIL-6 and endogenous IL-6 proteins but also highlight differences in the structural and receptor-binding properties of vIL-6 relative to its human counterpart.
Docosahexaenoic acid potentiates interleukin‐1β induction of nitric oxide synthase through mechanism involving p44/42 MAPK activation in rat vascular smooth muscle cells (2002)

The effect of docosahexaenoic acid (DHA) on nitric oxide (NO) production and inducible NO synthase (iNOS) expression induced by interleukin (IL)-1beta, and whether the effect of DHA is related to its effect on mitogen-activated protein kinase (MAPK) activation were investigated in cultured rat vascular smooth muscle cells (VSMCs). DHA and eicosapentaenoic acid (EPA), although less potent, increased the NO production induced by IL-1beta (3 ng ml(-1)) in a concentration-dependent manner (3 - 30 microM) Arachidonic acid had no significant effect. The stimulatory effect of DHA (30 microM) on the NO production was more obvious at lower concentrations of IL-1beta. IL-1beta induced iNOS protein and mRNA expressions, which were significantly potentiated by DHA. EPA (30 microM) had a tendency to increase the iNOS protein and mRNA expressions, but arachidonic acid had no effect. IL-1beta-induced iNOS protein expression was significantly inhibited by PD 98059 (10 microM), a selective inhibitor of p44/42 MAPK kinase, both in the absence and the presence of DHA. SB 203580 (10 microM), a selective inhibitor of p38 MAPK activity, had no significant effect, although had a tendency to inhibit slightly. IL-1beta increased the phosphorylation of p44/42 MAPK, while it did not apparently increase the phosphorylation of p38 MAPK. DHA significantly potentiated the IL-1beta-induced phosphorylation of p44/42 MAPK, while it had no significant effect on the phosphorylation of p38 MAPK. These results suggest that DHA increases NO production by potentiating iNOS expression induced by IL-1beta through mechanism involving p44/42 MAPK signalling cascade in rat VSMCs. The present study may contribute to the understanding of basic mechanisms underlying the beneficial effects of DHA on various cardiovascular disorders.
Strategies for the Expression of SUMO-Modified Target Proteins in Escherichia coli (2008)

We previously described the establishment of a binary vector system that allows co-expression of SUMO conjugation enzymes and a target protein of interest, leading to efficient SUMO modification and the production of a large amount of recombinant SUMO-modified proteins in Escherichia coli. The advantages of this E. coli expression/modification approach include scalability of experiments, low cost, fast growth, and a lack of proteases that cleave the isopeptide linkage between SUMO and the target protein. Thus, this E. coli method provides a useful alternative to authentic SUMO modification assays, such as in vitro SUMO conjugation and in vivo SUMO modification using baculovirus or mammalian cell culture, that are usually complicated, time-consuming and expensive.
Long‐term efficacy of miglustat in paediatric patients with Niemann‐Pick disease type C (2012)

Niemann-Pick disease type C (NP-C) is a rare inherited neurovisceral disease characterized by progressive neurological manifestations. Oral miglustat was first approved for the treatment of children and adults with NP-C in Europe in 2009. There are still relatively few published data on the long-term efficacy and safety of miglustat in patients with NP-C in clinical practice. We report the effects of up to 6 years of treatment with miglustat 100 mg t.i.d. in five children. Overall, 3/5 patients displayed progressive dysphagia before starting miglustat, and 4/5 showed marked cognitive and/or motor impairment. The mean age at treatment start was 11.6 years, and the median (range) duration of therapy so far is 4 (4.1 to 6.1) years. No treatment dose alterations were required, but therapy was interrupted for 1-3 months at least once in all patients due to supply issues. Swallowing function was stabilised during miglustat therapy, with no significant increase in Han dysphagia scale or aspiration-penetration index scores among four evaluable patients (p > 0.05). Scores on the mini-mental state examination indicated an improvement in cognitive function during the first 3-6 months of miglustat therapy, followed by stabilisation up to 5 years. Ambulatory function remained stable for at least the first 2 years of treatment in most patients, but there was a trend towards deterioration thereafter, possibly related to treatment interruptions. The safety/tolerability profile of miglustat was similar to previous clinical studies, although reports of gastrointestinal disturbances were rare. Overall, miglustat appeared to stabilise key parameters of neurological disease progression.
Question classification for E-learning by artificial neural network (2004)

Text categorization is the classification of unstructured text documents with respect to a set of one or more predefined categories. This paper describes our work in exploring automatic question classification tests which can be used in e-learning system. Such tests can take the form of multiple-choice tests, as well as fill-in-the-blank and short-answer tests. We acquired 20 texts used for high school students and each text is followed by several multiple choice questions from e-learning Webpage. We propose a text categorization model using an artificial neural network trained by the backpropagation learning algorithm as the text classifier. Our test results show that the system achieved the performance in terms of F/sub 1/ value of nearly 78%.
Evidence of recurrent type I diabetes following HLA-mismatched pancreas transplantation. (2000)

Type 1 diabetes mellitus is considered as an autoimmune disease against beta cells. Diabetes recurrence after pancreas transplantation is well known in HLA-identical twins while it is rarely reported in recipients of cadaveric pancreatic grafts. In the present case report, diabetes recurrence occurred in a recipient who underwent cadaveric combined pancreas kidney transplantation. Seven years after transplantation the patient exhibited progressive hyperglycemia needing insulin therapy while the renal graft was well functioning. The diagnosis of recurrent disease was obtained on the histological features such as selective loss of beta cells without clear signs of insulitis and on the presence of markers (GAD 65 and IA-2) for humoral autoimmunity. It is intriguing that, at the time of recurrence of type 1 diabetes, the patient had stopped steroids and azathioprine, while only cyclosporine was maintained as immunosuppressive treatment. Our case report underlines the relevance of studying the humoral autoimmune response directed to islet autoantigens in cadaveric pancreas allograft recipients. Furthermore, it suggests that an efficient immunosuppressive treatment after transplantation may be able to reduce the autoimmune response against the pancreatic allograft.
Detection and analysis of nucleic acids using nanometer-scale pores (2010)

Advances in genomics and in its application to personalized medicine have increased the demand for faster and cheaper methods of nucleic acid analysis techniques. Nanopore-based single-molecule detection schemes are exceptionally good candidates for novel technologies to address this demand. This thesis presents the initial attempts and characterization of two implementations of the alpha-hemolysin (aHL) protein nanopore as a nanosensor for the detection and analysis of single nucleic acid molecules. The two detection schemes address shortcomings in present analysis techniques, and are distinguished by the mode of molecule capture and identification and by the proposed application. In the first method, single-stranded DNA fragments are captured from the bulk solution on the cis -side of the pore membrane, with the resulting rate of capture used as an electronic means of measuring local nucleic acid concentrations, obviating the need for optics or fluorescent molecular tags used during conventional DNA detection. Experimental results of single-stranded DNA fragment capture at high transmembrane potentials and an improved model of molecule capture from the bulk solution show that nanopore capture rates may be a viable method of estimating nucleic acid concentrations. In the second method, the aHL pore is used in conjunction with a synthetic probe molecule to capture individual single stranded DNA molecules on the trans -side of the membrane to perform single-molecule hybridization and force-dissociation experiments. Experimental results demonstrate that ensemble measurements can be used to measure the kinetics of hybridization and dissociation of single molecules of nucleic acids hybridizing to the probe molecule, with single-molecule sensitivity and single-nucleotide specificity. The detection of molecules across a membrane using force-dissociation techniques shows potential in use for the next generation of instrumentation for genomics and potentially for in vivo, real-time detection of biomolecules.
A close look at human IgG sialylation and subclass distribution after lectin fractionation (2009)

Polyspecific human IgG preparations are indicated for the treatment of primary immunodeficiency disorders associated with defects in humoral immunity. In addition, intraveneous IgG (IVIG) is used to treat patients with autoimmune and systemic inflammatory diseases. Lectin chromatography on Sambucus nigra agglutinin stood at the cradle of the hypothesis that the anti-inflammatory properties depend on sialylation of the N-glycans in the Fc region of IgG. A detailed analysis of fractions obtained by lectin chromatography revealed that binding of IVIG is essentially mediated by Fab glycosylation. Moreover, experiments with a monoclonal antibody from a human cell line and IVIG Fc fragments indicated that at least two sialic acids in the Fc region of an antibody are required for lectin binding. Such glycoforms contain either two monosialylated glycans or a disialylated glycan and constitute 1% or less of the total human IgG. Arguably this small proportion holds the entire anti-inflammatory potency. A new mass spectrometric quantification method of IgG subclass ratio revealed that the IVIG Fc preparation essentially consists of IgG1. This observation may be relevant when studying the effect of human Fc in murine models of inflammation because mouse IgG subclasses differ substantially in their interaction with receptors.
Characterization of the RNA Binding Properties of Ku Protein (1998)

Ku protein, a heterodimer of 70 and 83 kDa polypeptides, is the regulatory component of the DNA-dependent protein kinase (DNA-PK). Ku protein binds to DNA ends and is essential for DNA double-strand break repair and V(D)J recombination. Although there is some evidence that Ku protein also binds RNA, its RNA binding properties have not been systematically explored. In the present study, Ku-binding RNAs were identified using systematic evolution of ligands by exponential enrichment (SELEX) technology. These RNAs were assigned to three classes based on common sequence motifs. Most of the selected RNAs bound to Ku protein with a Kd < or = 2 nM, comparable to the affinity of DNA fragments for Ku protein under similar conditions. Many of the RNAs inhibited DNA-PK activity by competing with DNA for a common binding site in Ku protein. None of several RNAs that were tested activated DNA-PK in the absence of DNA. The identification of diverse RNAs that bind avidly to Ku protein is consistent with the idea that natural RNAs may serve as modulators of DNA-PK activity. Moreover, the RNAs identified in this study may have utility as tools for experimental manipulation of DNA double-strand break repair activity in cells and cell extracts.
Undistracted driving (2011)

Distracted driving is a major problem that leads to unnecessary accidents and human casualties everywhere in the world. The ubiquity of mobile phones is one cause of distracted driving. In United States alone, operating mobile phones while driving has been cited as a factor in crashes that have led to 995 deaths and 24,000 injuries in 2009. To mitigate the problem of distracted driving caused by mobile phones, we propose using context-awareness to implement burden-shifting, time-shifting, and activity-based sharing. Although the first two concepts have been introduced before in the research literature and the latter two are novel, none of these concepts have yet been explored in the context of mobile phones and driving. We present our initial interaction designs for these concepts on the Android platform.
Selective activation of small motor axons by quasitrapezoidal current pulses (1991)

We have found a method to activate electrically smaller nerve fibers without activating larger fibers in the same nerve trunk. The method takes advantage of the fact that action potentials are blocked with less membrane hyperpolarization in larger fibers than in smaller fibers. In our nerve stimulation system, quasitrapezoidal-shaped current pulses were delivered through a tripolar cuff electrode to effect differential block by membrane hyperpolarization. The quasitrapezoidal-shaped pulses with a square leading edge, a 350 microsecond(s) plateau, and an exponential trailing phase ensured the block of propagating action potentials and prevented the occurrence of anodal break excitation. The tripolar cuff electrode design restricted current flow inside the cuff and thus eliminated the undesired nerve stimulation due to a "virtual cathode." Experiments were performed on 13 cats. The cuff electrode was placed on the medial gastrocnemius nerve. Both compound and single fiber action potentials were recorded from L7 ventral root filaments. The results demonstrated that larger alpha motor axons could be blocked at lower current levels than smaller alpha motor axons, and that all alpha fibers could be blocked at lower current levels than gamma fibers. A statistical analysis indicated that the blocking threshold was correlated with the axonal conduction velocity or fiber diameter. This method could be used in physiological experiments and neural prostheses to achieve a small-to-large recruitment order in motor or sensory systems.
Synthesis of Granulatimide Positional Analogues. (2003)

The Stille coupling reaction of the stannylindole 13 with the 5-iodoimidazole derivative 14 (or 27) in the presence of PdCl(2)(PPh(3))(2) gave the corresponding indole-imidazole coupling product 15 (or 28), thereby affording a synthetic approach to 10-methylgranulatimide (7), 15-methylgranulatimide (11), and 10, 15-dimethylgranulatimide (12), as well as 10-methylisogranulatimide B (5).
Biosynthesis and periplasmic segregation of human proinsulin in Escherichia coli. (1981)

A plasmid containing human preproinsulin cDNA inserted into the endonuclease Pst I site of the ampicillinase gene of plasmid pBR322 was modified by excision of large portions of the ampicillinase-coding region to produce a variety of gene fusion combinations, many of which generated proteins detectable with antisera to insulin or human C peptide. In one case a perfect hybrid of the NH2-terminal half of the leader sequence of ampicillinase (residues -23 to -12) with the human preproinsulin prepeptide beginning at residue -13 was formed; the result was the synthesis and secretion of human proinsulin into the periplasmic space. We have characterized this protein immunologically and also by labeling it biosynthetically or by iodination followed by immunoprecipitation and automated amino acid sequence analysis. It contains the A and B chain regions of insulin as well as specific human C peptide immunodeterminants and is convertible to an insulin-like component by tryptic digestion. These results demonstrate that human proinsulin can be produced by bacteria and that this biosynthetic approach should prove feasible for the production of adequate amounts of human proinsulin for a variety of clinical studies and human insulin for therapeutic purposes.