gebhart/patrepeval huggingface dataset:
Electrically Addressable Biomolecular Functionalization of Carbon Nanotube and Carbon Nanofiber Electrodes (2004)

We demonstrate the electrically addressable biomolecular functionalization of single-walled carbon nanotube electrodes and vertically aligned carbon nanofiber electrodes. The method uses an electrochemical reaction in which nitro groups on specific nanostructures are reduced to amino groups and then used to covalently link DNA to only these nanostructures. We demonstrate fabrication of a four-element array of distinct DNA oligonucleotides on carbon nanotube electrodes and the addressable functionalization of submicron bundles of <100 nm diameter vertically aligned carbon nanofibers. DNA hybridization shows that the DNA-modified nanoscale structures have excellent biological selectivity.
Corticotropin-Releasing Hormone Receptor Type 1 (CRHR1) Genetic Variation and Stress Interact to Influence Reward Learning (2011)

Stress is a general risk factor for psychopathology, but the mechanisms underlying this relationship remain largely unknown. Animal studies and limited human research suggest that stress can induce anhedonic behavior. Moreover, emerging data indicate that genetic variation within the corticotropin-releasing hormone type 1 receptor gene (CRHR1) at rs12938031 may promote psychopathology, particularly in the context of stress. Using an intermediate phenotypic neurogenetics approach, we assessed how stress and CRHR1 genetic variation (rs12938031) influence reward learning, an important component of anhedonia. Psychiatrically healthy female participants (n = 75) completed a probabilistic reward learning task during stress and no-stress conditions while 128-channel event-related potentials were recorded. Fifty-six participants were also genotyped across CRHR1. Response bias, an individual's ability to modulate behavior as a function of reward, was the primary behavioral variable of interest. The feedback-related positivity (FRP) in response to reward feedback was used as a neural index of reward learning. Relative to the no-stress condition, acute stress was associated with blunted response bias as well as a smaller and delayed FRP (indicative of disrupted reward learning) and reduced anterior cingulate and orbitofrontal cortex activation to reward. Critically, rs12938031 interacted with stress to influence reward learning: both behaviorally and neurally, A homozygotes showed stress-induced reward learning abnormalities. These findings indicate that acute, uncontrollable stressors reduce participants' ability to modulate behavior as a function of reward, and that such effects are modulated by CRHR1 genotype. Homozygosity for the A allele at rs12938031 may increase risk for psychopathology via stress-induced reward learning deficits.
Detection of metastatic breast cancer by β-hCG polymerase chain reaction (1996)

Reverse transcriptase-polymerase chain reaction (RT-PCR) for detection of occult malignancies in breast cancer patients is evolving as a useful diagnostic tool. However, no reliable molecular mRNA markers are available. We developed an RT-PCR plus Southern blot assay using beta-hCG (beta-subunit of human chorionic gonadotropin) gene expression as a tumor marker for detection of breast malignancies metastatic to tumor-draining lymph nodes and blood. Breast carcinoma cell lines, primary breast malignancies and human placenta were used as positive controls for establishing the beta-hCG RT-PCR assay. Peripheral blood leukocytes (PBL) from normal volunteer donors, normal breast tissue and lymph nodes from cancer-free patients were used as negative controls. beta-hCG RT-PCR was used to assess tumor cell presence in PBL and tumor-draining axillary nodes from patients with AJCC stage I-IV breast cancer. The assay sensitivity and specificity were enhanced by restriction endonuclease digestion of an Sty I site of the RT-PCR cDNA product followed by Southern blot analysis. beta-hCG mRNA was expressed in all breast cancer cell lines and 80% of primary breast cancers; it was not expressed in negative controls. The assay reliably detected one cancer cell in > 10(7) PBL, with a sensitivity of 10(-5) microgram RNA. Eighty percent of PBL and 61% of tumor-draining axillary nodes from breast cancer patients expressed beta-hCG mRNA. The assay is a sensitive and specific method of identifying breast cancer cells in breast tissues, lymph nodes and blood.
Prevalence of patent foramen ovale and stroke in pulmonary embolism patients (2013)

Purpose: Patent foramen ovale (PFO) is associated with paradoxical embolism and mortality in pulmonary embolism (PE). The aim of this study was to assess the prevalence of PFO comparing trans-thoracic echocardiography (TTE) and trans-oesophageal echocardiography (TOE) and its association with ischaemic stroke (as assessed by magnetic resonance imaging (MRI)) in patients hospitalized for PE.

Methods and results: We prospectively enrolled 40 consecutive patients hospitalized in the cardiology department for intermediate early-mortality risk PE. Patients with recent history of stroke or contra-indication to TOE were excluded from this study. Local ethics approval was obtained for the study. Contrast TTE and TOE were performed within 5 days after admission. Mean time from admission to TOE was 3.4±1.2 days, whereas mean time to MRI was 14±5.8 days. On admission, mean systolic arterial pressure was 132±40 mmHg, mean troponine Ic was 0.4±1.7 ng/ml (normal reference value < 0.06 ng/ml) and mean BNP was 585±2200 pg/ml. PFO was found in 22.5% (n=9) and 52.5% (n=21) of our patients, respectively with TTE and TOE. Compared with TTE, TOE significantly improved the sensitivity of echocardiography in detecting PFO (p = 0.002). No significant difference on admission's characteristics was found between patients without PFO (PFO-; n=19) and patients with PFO (PFO+; n=21). On MRI evidence of recent ischaemic stroke was found in 7 PFO+ patients (33.3%), versus none in PFO- patients (p=0.004). In the sub-group of stroke patients (n=7), TOE was positive for PFO in all, whereas TTE failed to identify PFO in 3 of them (recognition of PFO, TOE vs TTE: 100 vs 57%, p=0.02). No complication of TOE occurred in our cohort (including GI-bleeding).

Conclusion: PFO is frequent in patients hospitalized for intermediate risk-PE, and occurred in 52.5% of our patients. In our study, PFO is strongly associated with ischaemic stroke on MRI and recognition of PFO in patients with PE could help identifying patients with high-risk of stroke and potential bleeding complications.
Rapid Identification of Staphylococci Isolated in Clinical Microbiology Laboratories by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (2007)

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) of intact bacteria yields a reproducible spectrum depending upon growth conditions, strain, or species. Using whole viable bacteria we describe here the application of MALDI-TOF-MS to the identification of coagulase-negative staphylococci (CoNS). Our aim was, once a bacterium has been recognized as Micrococcaceae, to identify peaks in the spectrum that can be used to identify the species or subspecies. MALDI-TOF-MS was performed using bacteria obtained from one isolated colony. One reference strain for each of the 23 clinically relevant species or subspecies of Micrococcaceae was selected. For each reference strain, the MALDI-TOF-MS profile of 10 colonies obtained from 10 different passages was analyzed. For each strain, only peaks that were conserved in the spectra of all 10 isolated colonies and with a relative intensity above 0.1 were retained, thus leading to a set of 3 to 14 selected peaks per strain. The MALDI-TOF-MS profile of 196 tested strains was then compared with that of the set of selected peaks of each of the 23 reference strains. In all cases the best hit was with the set of peaks of the reference strain belonging to the same species as that of the tested strain, thus demonstrating that the 23 sets of selected peaks can be used as a database for the rapid species identification of CoNS. Similar results were obtained using four different growth conditions. Extending this strategy to other groups of relevant pathogenic bacteria will allow rapid bacterial identification.
Recursive Partitioning Analysis of Prognostic Factors in Three Radiation Therapy Oncology Group Malignant Glioma Trials (1993)

The recursive partitioning technique can be employed to refine the stratification and design of malignant glioma trials.
Reaction of staphylococcal alpha-toxin with peptide-induced antibodies (1989)

Two peptides representing separate 13-amino-acid sequences of staphylococcal alpha-toxin have been synthesized and acrylamide gel-purified alpha-toxin monomer and hexamer forms have been prepared and used to produce antisera in rabbits. We report here that each synthetic peptide, P-I and P-II, induces the formation of a specific precipitating antiserum. Moreover, these sera also react with the toxin monomer and sometimes with the hexamer, indicating that each peptide has more than one epitope. The purified toxin monomer can induce antibodies to fragments of toxin but is significantly less potent than the hexamer in inducing antibodies to the toxin monomer and almost not effective in inducing a response to the toxin hexamer. The purified toxin hexamer induces responses that are almost the reciprocals of the monomers, with the antihexamer and -monomer responses dominating and almost no responses to fragments of toxin being induced. These responses are interpreted in terms of the stability of the toxin hexamer to proteolytic degradation, compared with the relative sensitivity of the monomer to proteases. In assays of toxin-neutralization activity, only those sera containing antihexamer antibodies can block toxin hemolytic activity. This is true for both peptide- and toxin-induced antisera. The basis for this apparent association between toxin-neutralizing potency and antihexamer reactivity is being studied. Peptide P-I contains the uniquely reactive tyrosine residue and may be involved in monomer-to-monomer associations required to form hexamers. Peptide P-II is near the carboxyl terminus of alpha-toxin and may be involved in the binding of toxin to membranes. In a study of the ability of each peptide to inhibit the rate of hexamer formation induced by membrane lipoprotein, peptide P-I (as expected) proves to be more efficient than peptide P-II. Finally, one rabbit immunized with the toxin hexamer produces antibodies to peptides P-I and P-II. This finding suggests that the two synthetic peptides selected for study are relevant to the in vivo immunoprocessing of staphylococcal alpha-toxin.
Antisense 2′-O-alkyl oligoribonucleotides are efficient inhibitors of reverse transcription (1995)

Reverse transcription is one step of the retroviral development which can be inhibited by antisense oligonucleotides complementary to the RNA template. 2'-O-Alkyl oligoribonucleotides are of interest due to their nuclease resistance, and to the high stability of the hybrids they form with RNA. Oligonucleotides, either fully or partly modified with 2'-O-alkyl residues, were targeted to an RNA template to prevent cDNA synthesis by the Avian Myeloblastosis Virus reverse transcriptase (AMV RT). Fully-modified 2'-O-allyl 17mers were able to specifically block reverse transcription via an RNase H-independent mechanism, with efficiencies comparable to those observed with phosphodiester (PO) and phosphorothioate oligonucleotides. Sandwich 2'-O-alkyl/PO/2'-O-alkyl oligonucleotides, supposed to combine the properties of 2'-O-alkyl modifications (physical blocking of the RT) to those of the PO window (RNase H-mediated cleavage of the RNA) were quasi-stoichiometric inhibitors when adjacent to the primer, but remained without any effect when non-adjacent. They were not able to compete with the polymerase and inhibited reverse transcription only through RNase H-mediated cleavage of the target.
Improved Traction for a Mobile Robot Traveling on the Heart (2006)

This document describes the effects of several design parameters on the traction generated by the suction pads of a mobile robot that walks on the surface of the heart. HeartLander is a miniature mobile robot that adheres to the epicardial surface of the heart using suction, and can travel to any desired location on the heart to administer therapeutic applications. To maximize the effectiveness of locomotion, the gripper pads must provide sufficient traction to avoid slipping. Our testing setup measured the force applied to the gripper pad adhering to ovine epicardial tissue, and recorded overhead video for tracking of the pad and tissue during an extension. By synchronizing the force and video data, we were able to determine the point at which the pad lost traction and slipped during the extension. Of the pads tested, the pad with no suction grate achieved maximum traction. Increasing the extension speed up to 20 mm/s resulted in a corresponding increase in traction. Increasing the vacuum pressure also improved the traction, but the magnitude of the effect was less than the improvement gained from increasing extension speed.
The Structure of DDB1-CRBN E3 ubiquitin ligase in complex with thalidomide (2014)

In the 1950s the drug thalidomide administered as a sedative to pregnant women led to the birth of thousands of children with multiple defects. Despite its teratogenicity, thalidomide and its derivatives lenalidomide and pomalidomide (together known as Immunomodulatory Drugs: IMiDs) recently emerged as effective treatments for multiple myeloma and 5q-dysplasia. IMiDs target the CUL4-RBX1-DDB1-CRBN (CRL4CRBN) E3 ubiquitin ligase and promote the ubiquitination of Ikaros/Aiolos transcription factors by CRL4CRBN. Here we present the crystal structure of the DDB1-CRBN complex bound to thalidomide, lenalidomide and pomalidomide. The structure establishes CRBN as a CRL4CRBN substrate receptor, which enantioselectively binds IMiDs. Through an unbiased screen we identify the homeobox transcription factor MEIS2 as an endogenous substrate of CRL4CRBN. Our studies suggest that IMiDs block endogenous substrates (MEIS2) from binding to CRL4CRBN when recruiting Ikaros/Aiolos for degradation.
Pathways in Beta-Cell Stimulus-Secretion Coupling as Targets for Therapeutic Insulin Secretagogues (2004)

Physiologically, insulin secretion is subject to a dual, hierarchal control by triggering and amplifying pathways. By closing ATP-sensitive K+ channels (KATP channels) in the plasma membrane, glucose and other metabolized nutrients depolarize beta-cells, stimulate Ca2+ influx, and increase the cytosolic concentration of free Ca2+ ([Ca2+]i), which constitutes the indispensable triggering signal to induce exocytosis of insulin granules. The increase in beta-cell metabolism also generates amplifying signals that augment the efficacy of Ca2+ on the exocytotic machinery. Stimulatory hormones and neurotransmitters modestly increase the triggering signal and strongly activate amplifying pathways biochemically distinct from that set into operation by nutrients. Many drugs can increase insulin secretion in vitro, but only few have a therapeutic potential. This review identifies six major pathways or sites of stimulus-secretion coupling that could be aimed by potential insulin-secreting drugs and describes several strategies to reach these targets. It also discusses whether these perspectives are realistic or theoretical only. These six possible beta-cell targets are 1) stimulation of metabolism, 2) increase of [Ca2+]i by closure of K+ ATP channels, 3) increase of [Ca2+]i by other means, 4) stimulation of amplifying pathways, 5) action on membrane receptors, and 6) action on nuclear receptors. The theoretical risk of inappropriate insulin secretion and, hence, of hypoglycemia linked to these different approaches is also envisaged.
Variations in Corneal Wound Healing After Radial Keratotomy (1992)

Ultrastructural and histopathologic analysis was performed on three human corneal specimens for variable and complicated refractive outcomes 1-2 years after radial keratotomy. Specimens were obtained immediately postsurgery after microkeratome resection with homoplastic lamellar keratoplasty (two cases) and penetrating keratoplasty (one case) for correction of glare, severe astigmatism, overcorrection, and/or double vision. All three cases showed variability of wound healing and delayed corneal wound healing sites; epithelial retention cysts, and/or absence of stromal scar collagen that was not dependent on the length of time after surgery. Two of the three radial keratotomy specimens also contained extensive duplication of the superficial corneal epithelial basal lamina. When present, the thickened basal lamina (3-6 microns in thickness) was seen between all incisions evaluated and appeared to extend from the central optical zone out to the periphery of the lamellar button. The one full-thickness keratoplasty specimen showed focal loss of underlying endothelial cells with occasional migrating cells seen by scanning electron microscopy. These data support previous findings that delayed corneal wound healing with epithelial retention cysts remains the most common histopathologic alteration after radial keratotomy. The effects of variations and delay in wound healing between individuals could explain the lack of predictability of refractive outcome and continuing refractive instability in long-term follow-up after single or repeat radial keratotomy surgeries.
Improved Production of Tryptophan in Genetically EngineeredEscherichia coliwith TktA and PpsA Overexpression (2012)

Intracellular precursor supply is a critical factor for amino acid productivity. In the present study, ppsA and tktA genes were overexpressed in genetically engineered Escherichia coli to enhance the availability of two precursor substrates, phosphoenolpyruvate and erythrose-4-phosphate. The engineered strain, TRTH0709 carrying pSV709, produced 35.9 g/L tryptophan from glucose after 40 h in fed-batch cultivation. The two genes were inserted, independently or together, into a low-copy-number expression vector (pSTV28) and transferred to TRTH0709. Fed-batch fermentations at high cell densities of the recombination strains revealed that overexpression of the ppsA gene alone does not significantly increase tryptophan yield. On the other hand, overexpression of the tktA gene, alone or with the ppsA gene, could further improve tryptophan yield to a final tryptophan titer of 37.9 and 40.2 g/L, respectively. These results represent a 5.6% and 11.9% enhancement over the titer achieved by TRTH0709. No evident genetic modifications leading to growth impairment were observed.
Predicting High-Grade Cancer at Ten-Core Prostate Biopsy Using Four Kallikrein Markers Measured in Blood in the ProtecT Study (2015)

A statistical model based on kallikrein markers was validated in a large prospective study and reduces unnecessary biopsies while delaying diagnosis of high-grade cancers in few men.
Intertextuality of retrieval database artworks (2013)

Abstract Retrieval database artwork, unlike other artwork, does not present fixed, preset and stable contents; it is formed as external data are retrieved from different sociocultural contexts and combined into the artworks’ content. This article aims to address the intertextual relationships between retrieval database artworks and the mass-produced texts from which the database artworks retrieve their data. After briefly discussing the difference between retrieval database artwork and participatory database artwork, and exploring the main concept of intertextuality, we address why intertextuality is essential and beneficial in understanding retrieval database artworks. Two selected works are used to demonstrate that, as the artwork is executed, the meanings and relationships of retrieval database artwork are ever-changing, and the authorship is constantly shifting due to the viewer’s participation. Shifting authorship in retrieval database artwork is caused by the daily mass cultural production of original text, which might or might not be retrieved by the database to be incorporated into the artwork. We conclude that retrieval database artworks cannot separate themselves from mass data. The dynamic intertextual relationships between the work and its ongoing retrieval of content from other cultural productions, as well as the viewers’ contributions to the work, simultaneously shape and reshape the work and its authorship.
CO2 Power‐assisted hand‐held syringe: Better visualization during diagnostic and interventional angiography (1990)

Recent technology has produced high-flow and large-lumen catheters as well as other angiographic accessories to enhance the visualization of the coronary arteries during diagnostic and percutaneous transluminal coronary angioplasty (PTCA) procedures. In spite of these technological advances, there are still many cases in which the quality of the coronary angiography could be significantly improved. This paper reports on a clinical evaluation of a hand-held power syringe. The syringe offers the ability to power inject contrast safely and effectively during routine angiograms as well as through guiding catheters with the balloon catheter present during PTCA. At the same time, control of the injection is equal to that associated with manual syringes.
Supercontinuum generation by stimulated Raman scattering and parametric four-wave mixing in photonic crystal fibers (2002)

Supercontinuum generation is investigated experimentally and numerically in a highly nonlinear index-guiding photonic crystal optical fiber in a regime in which self-phase modulation of the pump wave makes a negligible contribution to spectral broadening. An ultrabroadband octave-spanning white-light continuum is generated with 60-ps pump pulses of subkilowatt peak power. The primary mechanism of spectral broadening is identified as the combined action of stimulated Raman scattering and parametric four-wave mixing. The observation of a strong anti-Stokes Raman component reveals the importance of the coupling between stimulated Raman scattering and parametric four-wave mixing in highly nonlinear photonic crystal fibers and also indicates that non-phase-matched processes contribute to the continuum. Additionally, the pump input polarization affects the generated continuum through the influence of polarization modulational instability. The experimental results are in good agreement with detailed numerical simulations. These findings demonstrate the importance of index-guiding photonic crystal fibers for the design of picosecond and nanosecond supercontinuum light sources.
Respiratory epithelial cell invasion by group B streptococci (1992)

Group B streptococci (GBS) are the most common cause of pneumonia and sepsis during the neonatal period; however, the pathogenesis of this infection is poorly understood. We investigated the ability of GBS to enter epithelial cells in culture. Two strains of GBS were capable of invading immortalized respiratory epithelial cell lines in vitro at different levels, suggesting strain differences in invasiveness. Intracellular replication was not observed. Invasion required actin microfilaments but not microtubular cytoskeletal elements. Active bacterial protein, DNA, and RNA syntheses were required for invasion. These findings are consistent with our previous observation of intracellular GBS in the lungs of infected primates. We hypothesize that this organism may access the bloodstream by direct invasion of the epithelial cell barrier.