gebhart/patrepeval huggingface dataset:
Prospective examination of pain-related and psychological predictors of CRPS-like phenomena following total knee arthroplasty: a preliminary study (2003)

We hypothesized that preoperative emotional distress and pain intensity would predict the occurrence of signs and symptoms of complex regional pain syndrome (CRPS) following total knee arthroplasty (TKA). Depression (Beck Depression Inventory, BDI), anxiety (State Trait Anxiety Inventory, STAI), pain (McGill Pain Questionnaire-Short Form, MPQ), and signs/symptoms meeting IASP criteria for CRPS were assessed preoperatively, and at 1-, 3-, and 6-months postoperatively in 77 patients undergoing TKA. The prevalence of subjects fulfilling CRPS criteria was 21.0% at 1 month, 13.0% at 3 months, and 12.7% at 6 months postoperative. Higher preoperative scores on the STAI predicted positive CRPS status at 1-month follow-up (P<0.05), with a similar non-significant trend for preoperative BDI scores (P<0.10). Diagnostic sensitivity for the STAI was good (0.73), with moderate specificity (0.56). Neither measure predicted CRPS at later follow-up (P>0.10). Greater preoperative pain intensity predicted positive CRPS status at 3-month (MPQ-Sensory and MPQ-Affective; P<0.01) and 6-month (MPQ-Sensory) follow-up (P<0.01), but not at 1-month (P>0.10). Diagnostic sensitivity was high (0.83-1.00), with moderate specificity (0.53-0.60). Post-TKA patients with CRPS were more depressed at 1-month follow-up (P<0.05) and more anxious at 6-month follow-up (P<0.05) than patients with ongoing non-CRPS pain (all other comparisons non-significant, P>0.10). Overall, results indicate that CRPS-like phenomena occur in a significant number of patients early post-TKA; however, it is not associated with significantly greater complaints of postoperative pain. There appears to be a modest utility for preoperative distress and pain in predicting CRPS signs and symptoms following TKA, although false positive rates are relatively high.
Characteristics of a microbial assay for the detection of halogenated hydrocarbons using cells of an actinomycete‐like organism as a biological component (1997)

Abstract Cells of an Actinomycete‐like bacterium, strain GJ70, with the ability to degrade several haloalkanes were used as a biological component in a discontinuous microbial bioassay for the detection of 1,3‐dichloropropene and 1,2‐dibromoethane in water. The cells were entrapped in different matrices such as calcium alginate, carrageenan, chitosan, polyacrylamide‐hydrazide and chitosan‐carboxy‐methyl cellulose; the specific dehalogenating activity of the immobilized cells to a stirred sample solution and by the use of an ion selective electrode (ISE) for the quantification of enzymatically released halogen ions, the concentration of halogenated hydrocarbons could be estimated by determining the change of electrode potential within a period of 5 min. The detection limits for 1,3‐dichloropropene and 1,2‐dibromoethane were below 100 μg/l and 25 μg/l, respectively; the relative standard deviation was &lt; 10%. In addition, several chlorinated and brominated hgydrocarbons were converted by the bacterial cells at a reduced rate e.g. 1, 2‐dibromopropane, 1‐bromoethane, 1,5‐dichloropentane, etc. Moreover, temperatures of between 20 and 40%C did not affect the enzymatic activity of the cells, and a pH of between at 5 and 9 had little influence. Several organic substances and non‐metabolizable compounds did not affect the conversion, whereas some heavy metal ions acted as inhibitors.
β-Amyloid Induces Paired Helical Filament-like Tau Filaments in Tissue Culture (2003)

Paired helical filaments (PHF) are the principal pathologic components of neurofibrillary tangles in Alzheimer's disease (AD). To reproduce the formation of PHF in tissue culture, we stably expressed human tau with and without pathogenic mutations in human SH-SY5Y cells and exposed them for 5 days to aggregated synthetic beta-amyloid peptide (A beta 42). This caused a decreased solubility of tau along with the generation of PHF-like tau-containing filaments. These were 20 nm wide and had periodicities of 130-140 nm in the presence of P301L mutant tau or 150-160 nm in the presence of wild-type tau. Mutagenesis of the phosphoepitope serine 422 of tau prevented both the A beta 42-mediated decrease in solubility and the generation of PHF-like filaments, suggesting a role of serine 422 or its phosphorylation in tau filament formation. Together, our data underscore a role of A beta 42 in the formation of PHF-like filaments. Our culture system will be useful to map phosphoepitopes of tau involved in PHF formation and to identify and characterize modifiers of the tau pathology. Further adaptation of the system may allow the screening and validation of compounds designed to prevent PHF formation.
Nifedipine or hydralazine as a first‐line agent to control hypertension in severe preeclampsia (2002)

Nifedipine is safe and more effective than hydralazine in controlling blood pressure in severe pre-eclampsia. It has the added advantage of being cheaper and more widely available than the latter and is easily administered.
Point-of-Care Diagnostics for Global Health (2008)

Biomedical engineers have traditionally developed technologies in response to the needs of the developed world's medical community. As a result, the diagnostic systems on which they have worked have met the requirements of well-funded laboratories in highly regulated and quality-assessed environments. However, such approaches do not address the needs of the majority of the world's people afflicted with infectious diseases, who have, at best, access to poorly resourced health care facilities with almost no supporting clinical laboratory infrastructure. A major challenge for the biomedical engineering community is to develop diagnostic tests to meet the needs of these people, the majority of whom are in the developing world. We here review the context in which the diagnostics must operate, some of the appropriate diagnostic technologies already in distribution, and some emerging technologies that promise to address this challenge. However, there is much room for innovation, adaptation, and cost reduction before these technologies can impact health care in the developing world.
Rapid prototyping of 3D DNA-origami shapes with caDNAno (2009)

DNA nanotechnology exploits the programmable specificity afforded by base-pairing to produce self-assembling macromolecular objects of custom shape. For building megadalton-scale DNA nanostructures, a long 'scaffold' strand can be employed to template the assembly of hundreds of oligonucleotide 'staple' strands into a planar antiparallel array of cross-linked helices. We recently adapted this 'scaffolded DNA origami' method to producing 3D shapes formed as pleated layers of double helices constrained to a honeycomb lattice. However, completing the required design steps can be cumbersome and time-consuming. Here we present caDNAno, an open-source software package with a graphical user interface that aids in the design of DNA sequences for folding 3D honeycomb-pleated shapes A series of rectangular-block motifs were designed, assembled, and analyzed to identify a well-behaved motif that could serve as a building block for future studies. The use of caDNAno significantly reduces the effort required to design 3D DNA-origami structures. The software is available at http://cadnano.org/, along with example designs and video tutorials demonstrating their construction. The source code is released under the MIT license.
Pharmacological profile of mangostin and its derivatives. (1979)

Mangostin (M), a naturally occurring xanthone in the rinds of the fruits of Garcinia mangostana Linn. (Guttiferae) and its derivatives such as 3-0-methyl mangostin (MM), 3,6-di-O-methyl mangostin (DM), 1-isomangostin (IM), mangostin triacetate (MT), mangostin 3,6-di-O-(tetra acetyl) glucoside (MTG) and mangostin-6,6-di-O-glucoside (MOG) were screened for various pharmacological effects in experimental animals. With the exception of DM all the test compounds produced CNS depression characterised by ptosis, sedation, decreased motor activity, potentiation of pentobarbital sleeping time and ether anaesthesia in mice and rats. None of the compounds exhibited analgesic, antipyretic and anticonvulsant effects. With the exception of MOG, none of the test compounds produced significant effects on the cardiovascular system of frogs and dogs. MOG produced myocardial stimulation and a rise in blood pressure which was partially blocked by propranolol. M, IM and MT produced pronounced antiinflammatory activity both by intraperitoneal and oral routes in rats as tested by carrageenininduced hind paw oedema, cotton pellet implantation and granuloma pouch techniques. Antiinflammatory activity for M, IM and MT was observed even in bilaterally adrenalectomised rats. M, IM and MT did not produce any mast cell membrane stabilising effect and the degranulation effect of polymyxin B, diazoxide and Triton X-100 on rat peritoneal mast cells in vitro was not prevented. M, IM and MT did not alter the prothrombin time of albino rats. M alone produced significant antiulcer activity in rats.
Induction of carcinoembryonic antigen (cea)-specific cytotoxic t-lymphocyte responsesIn vitro using autologous dendritic cells loaded with cea peptide or cea rna in patients with metastatic malignancies expressing cea (1999)

The application of dendritic cells (DC) to the active immunotherapy of cancer currently relies on the generation of potent DC capable of presenting tumor antigens such as carcinoembryonic antigen (CEA). It is unknown whether the T cells of patients with advanced malignancies can be reliably stimulated against tumor antigens by their autologous DC. In this study, starting with the peripheral blood mononuclear cells (PBMC) of patients with metastatic malignancies expressing CEA, autologous DCs were generated in vitro in serum-free media supplemented with GM-CSF and IL-4. The DCs from HLA A2 positive patients were loaded with the CEA peptide CAP-1 and the DCs from HLA A2 negative patients were depleted of bystander lymphocytes and loaded with mRNA encoding CEA. The DC preparations were tested to determine their phenotype and were used to stimulate autologous PBMC twice, separated by 10-14 days. The stimulated cells were then tested for their ability to lyse CEA-expressing target cells. We successfully generated an adequate number of DC for a clinical trial from all patients. The harvested DC preparations contained 49% DC and 87% DC if depleted of bystander lymphocytes. Phenotypic analysis showed the typical pattern of CD11c+ CD40+ CD86+ HLA-DR+ CD80(low) CD83(low) CD14(low). All preparations but one were able to stimulate CEA-specific cytotoxic T-lymphocyte (CTL) activity, suggesting that the majority of patients are not anergic to CEA and possess functional DC. The CTL activity was similar for the CEA peptide and CEA RNA-loaded DC.
Characteristics of Extracts from Interferon-treated HeLa Cells: Presence of a Protein Kinase and Endoribonuclease Activated by Double-stranded RNA and of an Inhibitor of mRNA Methylation (1977)

SUMMARY Extracts from mouse interferon-treated mouse cells (Ehrlich ascites tumour and L929) were reported earlier to differ in several characteristics from extracts of untreated cells. We report now that the effect of treatment with human interferon of cells of a human line (HeLa S3) is similarly manifested in the cell extract. A comparison of extracts from interferon-treated HeLa S3 cells (S30 int ) with that from untreated cells (S30c) revealed: (a) an impairment in S30 int of the methylation of (unmethylated) reovirus mRNAs by the cellular and virus enzymes; (b) a faster degradation of reovirus mRNAs in S30 int but only in reaction mixtures supplemented with double-stranded RNA and ATP; (c) an increased phosphorylation by ATP of one (or two) proteins in S30 int but only in reaction mixtures supplemented with double-stranded RNA and (d) a more pronounced inhibition of translation by double-stranded RNA in S30 int . No such effects were observed in extracts prepared from HeLa cells treated with mouse interferon.
The role of packet-dropping mechanisms in QoS differentiation (2002)

Many research teams are developing technologies to turn the Internet into a QoS-capable network, which is one of the biggest challenges that this communication system currently faces. Naturally, at the core of such a challenge are IP routers and the technology they use. It is a well known fact that the common packet scheduling discipline that is used in routers (first come first served) makes them useless when QoS is needed. Thus, a different type of packet scheduling must be used. One of the most referred solutions for QoS-capable systems is the weighted fair queuing (WFQ) discipline. For FreeBSD-based routers, the ALTQ implementation of the WFQ discipline is, of course, an eligible and natural choice. Given this, it is important to fully understand the characteristics and operational behaviour of such an implementation. This paper presents several tests that guide the reader to a detailed knowledge about the WFQ/ALTQ operation-its behaviour, weaknesses, and flaws-with the purpose of showing how relevant can the influence of the dropper mechanism be on the effectiveness of IP routers.
Noninvasive fetal genome sequencing: a primer (2013)

We recently demonstrated whole genome sequencing of a human fetus using only parental DNA samples and plasma from the pregnant mother. This proof-of-concept study demonstrated how samples obtained noninvasively in the first or second trimester can be analyzed to yield a highly accurate and substantially complete genetic profile of the fetus, including both inherited and de novo variation. Here, we revisit our original study from a clinical standpoint, provide an overview of the scientific approach, and describe opportunities and challenges along the path toward clinical adoption of noninvasive fetal whole genome sequencing.
Unsupervised Semantic Intent Discovery from Call Log Acoustics (2006)

Unforeseen user intents can account for a significant portion of unsuccessful calls in an automatic voice response system. Discovering these unforeseen semantic intents usually requires expensive manual transcriptions. We propose a method to cluster the acoustics from logged calls by their estimated semantic intents. This is achieved through training a mixture of language models in an unsupervised manner. Each cluster is presented to the application developer with a suggested language model to cover the semantic intent of the data in that cluster. The application developer validates the cluster and its suggested language model, and then updates the application. A quantitative evaluation on a corporate voice-dialer application shows that updating the application in this manner yields a relative 13.4% reduction in semantic error rate.
Dioxygenases Catalyze O-Demethylation and O,O-Demethylenation with Widespread Roles in Benzylisoquinoline Alkaloid Metabolism in Opium Poppy (2013)

In opium poppy, the antepenultimate and final steps in morphine biosynthesis are catalyzed by the 2-oxoglutarate/Fe(II)-dependent dioxygenases, thebaine 6-O-demethylase (T6ODM) and codeine O-demethylase (CODM). Further investigation into the biochemical functions of CODM and T6ODM revealed extensive and unexpected roles for such enzymes in the metabolism of protopine, benzo[c]phenanthridine, and rhoeadine alkaloids. When assayed with a wide range of benzylisoquinoline alkaloids, CODM, T6ODM, and the functionally unassigned paralog DIOX2, renamed protopine O-dealkylase, showed novel and efficient dealkylation activities, including regio- and substrate-specific O-demethylation and O,O-demethylenation. Enzymes catalyzing O,O-demethylenation, which cleave a methylenedioxy bridge leaving two hydroxyl groups, have previously not been reported in plants. Similar cleavage of methylenedioxy bridges on substituted amphetamines is catalyzed by heme-dependent cytochromes P450 in mammals. Preferred substrates for O,O-demethylenation by CODM and protopine O-dealkylase were protopine alkaloids that serve as intermediates in the biosynthesis of benzo[c]phenanthridine and rhoeadine derivatives. Virus-induced gene silencing used to suppress the abundance of CODM and/or T6ODM transcripts indicated a direct physiological role for these enzymes in the metabolism of protopine alkaloids, and they revealed their indirect involvement in the formation of the antimicrobial benzo[c]phenanthridine sanguinarine and certain rhoeadine alkaloids in opium poppy.
Killing of virulent Mycobacterium tuberculosis by reactive nitrogen intermediates produced by activated murine macrophages. (1992)

Tuberculosis remains one of the major infectious causes of morbidity and mortality in the world, yet the mechanisms by which macrophages defend against Mycobacterium tuberculosis have remained obscure. Results from this study show that murine macrophages, activated by interferon gamma, and lipopolysaccharide or tumor necrosis factor alpha, both growth inhibit and kill M. tuberculosis. This antimycobacterial effect, demonstrable both in murine macrophage cell lines and in peritoneal macrophages of BALB/c mice, is independent of the macrophage capacity to generate reactive oxygen intermediates (ROI). Both the ROI-deficient murine macrophage cell line D9, and its ROI-generating, parental line J774.16, expressed comparable antimycobacterial activity upon activation. In addition, the oxygen radical scavengers superoxide dismutase (SOD), catalase, mannitol, and diazabicyclooctane had no effect on the antimycobacterial activity of macrophages. These findings, together with the results showing the relative resistance of M. tuberculosis to enzymatically generated H2O2, suggest that ROI are unlikely to be significantly involved in killing M. tuberculosis. In contrast, the antimycobacterial activity of these macrophages strongly correlates with the induction of the L-arginine-dependent generation of reactive nitrogen intermediates (RNI). The effector molecule(s) that could participate in mediating this antimycobacterial function are toxic RNI, including NO, NO2, and HNO2, as demonstrated by the mycobacteriocidal effect of acidified NO2. The oxygen radical scavenger SOD adventitiously perturbs RNI production, and cannot be used to discriminate between cytocidal mechanisms involving ROI and RNI. Overall, our results provide support for the view that the L-arginine-dependent production of RNI is the principal effector mechanism in activated murine macrophages responsible for killing and growth inhibiting virulent M. tuberculosis.
Distributed scientific video movie making (1988)

A description is given of a versatile, low-cost, video movie-making system for generating and displaying scientific graphics from remote supercomputers. The system makes video movies by single-frame animation from the output of time-dependent, numerical simulations typically done on supercomputers. It uses extensive data compression to permit its use over wide area, as well as local area networks. The system demonstrates an easily used, elementary visualization capability for time-dependent data in a heterogeneous, distributed computing environment. >
Efficient Cell Infection by Moloney Murine Leukemia Virus-Derived Particles Requires Minimal Amounts of Envelope Glycoprotein (2000)

Retrovirus entry into cells is mediated by specific interactions between the retrovirally encoded Env envelope glycoprotein and a host cell surface receptor. Though a number of peptide motifs responsible for the structure as well as for the binding and fusion activities of Env have been identified, only a few quantitative data concerning the infection process are available. Using an inducible expression system, we have expressed various amounts of ecotropic and amphotropic Env at the surfaces of Moloney murine leukemia virus-derived vectors and assayed for the infectivity of viral particles. Contrary to the current view that numerous noncooperative Env-viral receptor interactions are required for cell infection, we report here that very small amounts of Env are sufficient for optimal infection. However, increasing Env density clearly accelerates the rate at which infectious attachment to cells occurs. Moreover, our data also show that a surprisingly small number of Env molecules are sufficient to drive infection, albeit at a reduced efficiency, and that, under conditions of low expression, Env molecules act cooperatively. These observations have important consequences for our understanding of natural retroviral infection as well as for the design of cell-targeted infection techniques involving retroviral vectors.
Transforming and c-fos promoter/enhancer-stimulating activities of a GDP/GTP exchange protein for small GTP-binding proteins. (1991)

There is a superfamily of ras p21/ras p21-like small GTP-binding proteins (G proteins). Small G proteins have GDP-bound inactive and GTP-bound active forms which are interconvertible by GDP/GTP exchange and GTPase reactions. The former and latter reactions are regulated by GDP/GTP exchange proteins (GEPs) and GTPase activating proteins (GAPs), respectively. We have isolated two types of GEP: one is a stimulatory type called GDP dissociation stimulator (GDS) and the other is an inhibitory type called GDP dissociation inhibitor (GDI). Among the GEPs thus far isolated, only smg GDS is active on Ki-ras p21. This GEP is also active on smg p21 and rho p21, but is inactive on Ha-ras p21. For the action of smg GDS, the post-translational processing of the C-terminal region of its substrate small G proteins is essential. Point-mutated Ki-ras p21 strongly transforms NIH/3T3 cells and markedly stimulates the c-fos promoter/enhancer in this cell line, whereas normal Ki-ras p21 is almost inactive in these activities. smg GDS induces the Ki-ras p21 activation which eventually leads to the transformation of NIH/3T3 cells and to the stimulation of the c-fos promoter/enhancer in this cell line. Thus, smg GDS plays an important role in regulating the activity of Ki-ras p21 as well as of other small G proteins.
Genotype/phenotype analyses of low frequency tumor cells using computerized image microscopy (1996)

Techniques to identify low frequency (i.e., 10−4–10−5) tumor cells in bone marrow and peripheral blood of cancer patients provide opportunities for early detection of disseminated disease and characterization of the properties of cells released from the tumor. Low frequency epithelial cells in marrow and blood can be detected using immunophenotypic markers directed against intracellular and/or cell surface antigens. However, nonspecific phenotypic labeling may compromise the ability to discriminate tumor from nontumor cells. We describe optimization of slide-based approaches that facilitate identification and subsequent molecular cytogenetic characterization of rare tumor cell populations in hematopoietic tissues. Colon tumor cells seeded in a hematopoietic background provided a model system to optimize methodologies that are applicable to detection and quantification of micrometastases in clinical specimens. Mixtures of cytogenetically aberrant epithelial cells and hematopoietic cells on slides were labeled with an anti-cytokeratin 20 (anti-CK20) antibody that recognizes >90% of colon adenocarcinomas. Computerized image analysis was used to record the location of the immunofluorescent cells on microscopic slides. Cells on slides were then hybridized using fluorescence in situ hybridization (FISH) with repeat-sequence DNA probes to detect aneusomies. Previously discriminated epithelial cells were relocated for molecular cytogenetic characterization. Tumor cells present at frequencies approximating 5 × 10−5 were discriminated on the basis of immunofluorescence and cell size. A low frequency (4 × 10−4) population of normal hematopoietic cells also labeled with anti-CK20 (data not shown). This strategy of sequential immunophenotyping and molecular cytogenetic analyses may be useful to discriminate tumor from nontumor cells in cancer patients with micrometastatic disease. © 1996 Wiley-Liss, Inc.