gebhart/patrepeval huggingface dataset:
Gold Nanoparticle/Organic Networks as Chemiresistor Coatings: The Effect of Film Morphology on Vapor Sensitivity (2008)

Networked films comprising gold nanoparticles (4 nm core diameter) and dodecanedithiol were deposited via layer-by-layer self-assembly. The film thickness was controlled by the number of deposition cycles and ranged from submonolayer to multilayer coverage with up to 60 nm thickness. FE-SEM and XPS revealed island growth during the first four to five deposition cycles. At room temperature, films based on islands showed slightly nonlinear current−voltage curves, whereas thicker films gave Ohmic behavior. Between 100 and 300 K, the temperature dependence of conductance was consistent with an Arrhenius model for activated charge transport. The chemical sensitivity of the films was characterized by dosing them with vapors of toluene, 4-methyl-2-pentanone, 1-propanol, and water while monitoring their relative differential resistances. Thin films responded with a decrease in the resistance, whereas thicker films responded with a resistance increase. The results indicate that swelling along the film normal may be important for the underlying sensing mechanism of homogeneous multilayer films. Changes in permittivity and/or swelling-induced decrease of the interisland distance can be responsible for the observed decrease in resistance of the thinner films.
Thrombopoietin‐Stimulated ex Vivo Expansion of Human Bone Marrow Megakaryocytes (1996)

The effect of thrombopoietin (TPO) on megakaryocytopoiesis (MKP) has been mainly studied using clonogenic assays in murine systems. In this study, we evaluated MKP in liquid culture using human bone marrow cells. While interleukin 3 (IL-3) and stem cell factor (SCF) are potent activators of TPO-stimulated MKP in the murine system, only IL-3 exhibited synergistic activity with TPO in cultures of human bone marrow. The IL-3 effect on TPO-stimulated megakaryocyte (MK) proliferation, expressed as the absolute number of MKs per seeded CD34+ cell, was more pronounced with purified CD34+ cell (8 +/- 1.6 SE versus 2.8 +/- 0.7 SE in the presence and absence of IL-3, respectively) than with mononuclear cells (MNC) (16 +/- 2.8 SE versus 11 +/- 2.0 SE). This effect of IL-3 on TPO-stimulated MK proliferation was due to a general proliferation of all cell types since the relative frequency of MKs (32.1 +/- 3 SE and 55.8 +/- 3 SE in MNC and CD34+ cells, respectively) was not affected by IL-3. The effect of TPO alone, TPO + IL-3, TPO + SCF, and TPO + IL-3 + SCF on MK proliferation was examined in MNC and CD34+ cultures. Greater numbers of MK per seeded CD34+ were observed in MNC compared to CD34+ cultures under all conditions except when TPO was added with both IL-3 and SCF. The enhancing effect of MNC was also observed on MK ploidy in the presence of TPO and IL-3. While proliferation and ploidy increase with TPO concentration in the murine system, they are inversely related in the human system. A significant 2.5-fold enhancement of TPO-induced MK proliferation was observed when purified CD34+ cells were cultured in inserts separated from human bone marrow stroma, indicating that soluble stimulatory factors are released from the stroma. These observations will be useful for ex vivo expansion of MKs to treat post-transplant or chemotherapy-associated thrombocytopenia.
Synthesis of 1,5-Anhydrohexitol Nucleosides as Mimics of AZT, D4T and DDC (1996)

Abstract 1,5-Anhydrohexitol congeners of AZT, D4T and DDC were synthesized. These compounds did not show anti-HIV activity.
Androgens, insulin resistance and vascular disease in men (2005)

Type 2 diabetes mellitus is increasing globally and is an established risk factor for the development of atherosclerotic vascular disease. Insulin resistance is the hallmark feature of type 2 diabetes and is also an important component of the metabolic syndrome. There is evidence to suggest that testosterone is an important regulator of insulin sensitivity in men. Observational studies have shown that testosterone levels are low in men with diabetes, visceral obesity (which is strongly associated with insulin resistance), coronary artery disease and metabolic syndrome. Short-term interventional studies have also demonstrated that testosterone replacement therapy produces an improvement in insulin sensitivity in men. Thus hypotestosteronaemia may have a role in the pathogenesis of insulin-resistant states and androgen replacement therapy could be a potential treatment that could be offered for improvements in glycaemic control and reduction in cardiovascular risk, particularly in diabetic men.
Active site labeling of a receptor-like protein tyrosine phosphatase. (1992)

The inactivation of the cytoplasmic domain of rat LAR, a receptor-like protein tyrosine phosphatase (PTPase), by iodoacetate and not by iodoacetamide suggested that iodoacetate interacts in a highly selective manner with the enzyme. The data indicate that iodoacetate binds at the active site of the enzyme with a stoichiometry of 0.8 mol of iodoacetate bound per mol of rat LAR. A single [14C]iodoacetate-labeled peptide was isolated following endoproteinase Lys-C digestion of the radiolabeled PTPase. Sequence analysis of the active site labeled peptide demonstrates that Cys-1522 contains the radiolabel. This residue has been shown by site-directed mutagenesis to be essential for rat LAR activity (Pot, D. A., Woodford, T. A., Remboutsika, E., Haun, R. S., and Dixon, J. E. (1991) J. Biol. Chem. 266, 19688-19696). Iodoacetate reacts only with the first domain of this double domain PTPase. These results, for the first time, directly identify the highly reactive cysteine residue at the active site of a PTPase and highlight the ability of this residue to participate as a nucleophile in the hydrolysis of phosphate from tyrosine.
A Multi-Resolution Dynamic Model for Face Aging Simulation (2007)

In this paper we present a dynamic model for simulating face aging process. We adopt a high resolution grammatical face model[1] and augment it with age and hair features. This model represents all face images by a multi-layer And-Or graph and integrates three most prominent aspects related to aging changes: global appearance changes in hair style and shape, deformations and aging effects of facial components, and wrinkles appearance at various facial zones. Then face aging is modeled as a dynamic Markov process on this graph representation which is learned from a large dataset. Given an input image, we firstly compute the graph representation, and then sample the graph structures over various age groups according to the learned dynamic model. Finally we generate new face images with the sampled graphs. Our approach has three novel aspects: (1) the aging model is learned from a dataset of 50,000 adult faces at different ages; (2) we explicitly model the uncertainty in face aging and can sample multiple plausible aged faces for an input image; and (3) we conduct a simple human experiment to validate the simulated aging process.
Addition of interferon‐α to the p53‐SLP® vaccine results in increased production of interferon‐γ in vaccinated colorectal cancer patients: A phase I/II clinical trial (2012)

We previously established safety and immunogenicity of a p53 synthetic long peptides (p53-SLP®) vaccine. In the current trial, we investigated whether combination of interferon-alpha (IFN-α) with p53-SLP® is both safe and able to improve the induced p53-specific IFN-γ response. Eleven colorectal cancer patients successfully treated for metastatic disease were enrolled in this study. Of these, nine patients completed follow-up after two injections with p53-SLP® together with IFN-α. Safety and p53-specific immune responses were determined before and after vaccination. Furthermore, cryopreserved PBMCs were compared head-to-head to cryopreserved PBMCs obtained in our previous trial with p53-SLP® only. Toxicity of p53-SLP® vaccination in combination with IFN-α was limited to Grade 1 or 2, with predominantly small ongoing swellings at the vaccination site. All patients harbored p53-specific T cells after vaccination and most patients showed p53-specific antibodies. Compared to the previous trial, addition of IFN-α significantly improved the frequency of p53-specific T cells in IFN-γ ELISPOT. Moreover, in this trial, p53-specific T cells were detectable in blood samples of all patients in a direct ex vivo multiparameter flowcytometric assay, opposed to only 2 of 10 patients vaccinated with p53-SLP® only. Finally, patients in this trial displayed a broader p53-specific immunoglobulin-G response, indicating an overall better p53-specific T-helper response. Our study shows that p53-SLP® vaccination combined with IFN-α injection is safe and capable of inducing p53-specific immunity. When compared to a similar trial with p53-SLP® vaccination alone the combination was found to induce significantly more IFN-γ producing p53-specific T cells.
Immunization of Monkeys with Baculovirus-Dengue Type-4 Recombinants Containing Envelope and Nonstructural Proteins: Evidence of Priming and Partial Protection (1994)

Groups of rhesus monkeys were immunized with baculovirus-dengue type-4 (DEN-4) recombinant-infected cell extracts. One recombinant contained all of the DEN-4 structural proteins and two nonstructural (NS) proteins (C-M-E-NS1-NS2a), while the other was a fusion protein containing a portion of the respiratory syncytial virus G glycoprotein and DEN-4 envelope glycoprotein (RSVG-E). Both preparations were immunogenic; all monkeys receiving either immunogen responded with the production of antivirion antibodies in enzyme immunoassays. All except one monkey receiving the recombinant b(C-M-E-NS1-NS2a) made antibodies to NS1. One monkey that received b(RSVG-E) showed the production of low levels of neutralizing antibodies. Following challenge with unmodified DEN-4 virus, seven of nine monkeys in the immunized group became infected and were viremic for a mean of 4.1 days. The control, sham-inoculated monkeys were also viremic; the mean number of days of viremia in this group was 4.7 days. The remaining monkeys in the immunized group (n = 7), although not protected, had evidence of priming. Hemagglutination inhibition antibody responses following challenge indicated an anamnestic response in this group of animals. Based on these results, it was concluded that future immunization schedules should be altered to optimize immune responses and that immunization with more potent and purified immunogens would probably result in higher seroconversion rates and antibody levels in monkeys.
A new approach to text searching (1992)

String searching is a very important component of many problems, including text editing, bibliographic retrieval, and symbol manipulation. Recent surveys of string searching can be found in The string-matching problem consists of finding all occurrences of a pattern of length m in a text of length n. We
Topical treatment with a new matrix therapy agent (RGTA, CACICOL‐20) improves epithelial wound healing after penetrating keratoplasty (2014)

Abstract Purpose Complete epithelial wound healing is a milestone in the early post‐operative care after penetrating keratoplasty (PKP). It reduces the infectious risk, allows safe instillation of steroids, and conditions discharge from hospitalization. We assessed a new matrix therapy agent, mimicking heparan sulfates, for the management of post PKP epithelial defects Methods Prospective, open‐label, uncontrolled, single‐centre study on 33 consecutive patients (33 eyes) who benefited from a 8.25 mm PKP for all‐comers indications. Patients were treated with RGTA eye drops (THEA): one drop in the operating theater immediately after graft, then on alternate days. Follow‐up was performed by slit‐lamp examination and photography with fluorescein‐dye testing repeated every day at a fixed time. Dye area was measured using the freeware ImageJ. Main outcome: time of corneal surface healing Results All corneas displayed complete healing after a mean 2.7±1.1 days (median 3, range; 1 to 6). Complete wound healing was obtained at D1 for 15%, D2 for 33%, D3 for 88%, D4 for 94%, and D6 for 100%. Area of epithelial defect decreased by a mean 75±22% between D1 and D2 (n=28) corresponding to a wound healing speed of 11.5±6.5 mm2/D. There were no systemic or local side effects. For comparison, in the series of all‐comers indications of 1003 PKP without RGTA of Borderie, mean wound healing was 4.6+/‐13.2 days (median 2.5, range 1‐210). Conclusion RGTA seems a potentially useful, noninvasive therapeutic approach in PKP management. A controlled double blind clinical trial vs placebo will be soon conducted to answer this question conclusively.
Using phonation time to estimate vital capacity in amyotrophic lateral sclerosis. (1989)

Amyotrophic lateral sclerosis (ALS) is a neuromuscular disease in which progressive respiratory weakness is usually the proximate cause of death. Since continued assessment of respiratory function is important in predicting progression, phonation time was measured in a group of 41 ALS patients and correlated with measured vital capacity. The findings show that the variance in phonation time accounts for nearly 50% of the variability of vital capacity, and therefore, successive measurements of phonation time are a useful means of estimating the loss of vital capacity.
Heat Shock Protein Expression in Cerebral Vessels after Subarachnoid Hemorrhage (2002)

In this model, impaired relaxation of cerebral vessels after SAH was associated with increases in the amount of phosphorylated HSP27 and decreases in the expression and phosphorylation of HSP20. These data are consistent with alterations in the expression and phosphorylation of these small HSPs in other models of vasospasm.
Construction of asymptotically good low-rate error-correcting codes through pseudo-random graphs (1992)

A novel technique, based on the pseudo-random properties of certain graphs known as expanders, is used to obtain novel simple explicit constructions of asymptotically good codes. In one of the constructions, the expanders are used to enhance Justesen codes by replicating, shuffling, and then regrouping the code coordinates. For any fixed (small) rate, and for a sufficiently large alphabet, the codes thus obtained lie above the Zyablov bound. Using these codes as outer codes in a concatenated scheme, a second asymptotic good construction is obtained which applies to small alphabets (say, GF(2)) as well. Although these concatenated codes lie below the Zyablov bound, they are still superior to previously known explicit constructions in the zero-rate neighborhood.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector (2014)

Engineered DNA-binding proteins that manipulate the human genome and transcriptome have enabled rapid advances in biomedical research. In particular, the RNA-guided CRISPR/Cas9 system has recently been engineered to create site-specific double-strand breaks for genome editing or to direct targeted transcriptional regulation. A unique capability of the CRISPR/Cas9 system is multiplex genome engineering by delivering a single Cas9 enzyme and two or more single guide RNAs (sgRNAs) targeted to distinct genomic sites. This approach can be used to simultaneously create multiple DNA breaks or to target multiple transcriptional activators to a single promoter for synergistic enhancement of gene induction. To address the need for uniform and sustained delivery of multiplex CRISPR/Cas9-based genome engineering tools, we developed a single lentiviral system to express a Cas9 variant, a reporter gene and up to four sgRNAs from independent RNA polymerase III promoters that are incorporated into the vector by a convenient Golden Gate cloning method. Each sgRNA is efficiently expressed and can mediate multiplex gene editing and sustained transcriptional activation in immortalized and primary human cells. This delivery system will be significant to enabling the potential of CRISPR/Cas9-based multiplex genome engineering in diverse cell types.
Mechanisms Regulating The Reactions Of Human Hemoglobin With Oxygen And Carbon Monoxide (1990)

The reactions of hemoglobin with oxygen and carbon monoxide are subject to regulation by the heme and the residues surrounding it and by the effectors, also known as heterotropic ligands (H + , Cl-, CO2 and 2,3-diphospho glycerate), that regulate the equilibrium between its two forms, the oxy or R-structure with high, and the deoxy or T-structure with low oxygen affinity. The stereochemical mechanisms of regulation have been studied for many years by a variety of methods. What is new since the subject had last been surveyed in Annual Review of Biochemistry (
The Genome of Non-O1 Vibrio cholerae NRT36S Demonstrates the Presence of Pathogenic Mechanisms That Are Distinct from Those of O1 Vibrio cholerae (2007)

Vibrio cholerae NRT36S is a non-cholera toxin-producing, non-O1 strain that causes diarrhea in volunteers. The genome of NRT36S was sequenced to create a draft containing 174 contigs plus the superintegron region. Our analysis of the draft genome revealed several putative toxin genes and colonization factors. Besides confirming the existence of nonagglutinable heat-stable toxin, we also identified the genes for a type three secretion system, a putative exotoxin, two different RTX toxins, and four pilus systems.
Virulence of enterococci (1994)

Enterococci are commensal organisms well suited to survival in intestinal and vaginal tracts and the oral cavity. However, as for most bacteria described as causing human disease, enterococci also possess properties that can be ascribed roles in pathogenesis. The natural ability of enterococci to readily acquire, accumulate, and share extrachromosomal elements encoding virulence traits or antibiotic resistance genes lends advantages to their survival under unusual environmental stresses and in part explains their increasing importance as nosocomial pathogens. This review discusses the current understanding of enterococcal virulence relating to (i) adherence to host tissues, (ii) invasion and abscess formation, (iii) factors potentially relevant to modulation of host inflammatory responses, and (iv) potentially toxic secreted products. Aggregation substance, surface carbohydrates, or fibronectin-binding moieties may facilitate adherence to host tissues. Enterococcus faecalis appears to have the capacity to translocate across intact intestinal mucosa in models of antibiotic-induced superinfection. Extracellular toxins such as cytolysin can induce tissue damage as shown in an endophthalmitis model, increase mortality in combination with aggregation substance in an endocarditis model, and cause systemic toxicity in a murine peritonitis model. Finally, lipoteichoic acid, superoxide production, or pheromones and corresponding peptide inhibitors each may modulate local inflammatory reactions.
Nonsteroid Anti-Inflammatory Drugs Inhibit Both the Activity and the Inflammation-Induced Expression of Acid-Sensing Ion Channels in Nociceptors (2001)

Nonsteroid anti-inflammatory drugs (NSAIDs) are major drugs against inflammation and pain. They are well known inhibitors of cyclooxygenases (COXs). However, many studies indicate that they may also act on other targets. Acidosis is observed in inflammatory conditions such as chronic joint inflammation, in tumors and after ischemia, and greatly contributes to pain and hyperalgesia. Administration of NSAIDs reduces low-pH-induced pain. The acid sensitivity of nociceptors is associated with activation of H(+)-gated ion channels. Several of these, cloned recently, correspond to the acid-sensing ion channels (ASICs) and others to the vanilloid receptor family. This paper shows (1) that ASIC mRNAs are present in many small sensory neurons along with substance P and isolectin B4 and that, in case of inflammation, ASIC1a appears in some larger Abeta fibers, (2) that NSAIDs prevent the large increase of ASIC expression in sensory neurons induced by inflammation, and (3) that NSAIDs such as aspirin, diclofenac, and flurbiprofen directly inhibit ASIC currents on sensory neurons and when cloned ASICs are heterologously expressed. These results suggest that the combined capacity to block COXs and inhibit both inflammation-induced expression and activity of ASICs present in nociceptors is an important factor in the action of NSAIDs against pain.
A Ranking Approach for Human Ages Estimation Based on Face Images (2010)

In our daily life, it is much easier to distinguish which person is elder between two persons than how old a person is. When inferring a person's age, we may compare his or her face with many people whose ages are known, resulting in a series of comparative results, and then we conjecture the age based on the comparisons. This process involves numerous pairwise preferences information obtained by a series of queries, where each query compares the target person's face to those faces in a database. In this paper, we propose a ranking-based framework consisting of a set of binary queries. Each query collects a binary-classification-based comparison result. All the query results are then fused to predict the age. Experimental results show that our approach performs better than traditional multi-class-based and regression-based approaches for age estimation.
Image analysis with deep learning to predict breast cancer grade, ER status, histologic subtype, and intrinsic subtype (2018)

RNA-based, multi-gene molecular assays are available and widely used for patients with ER-positive/HER2-negative breast cancers. However, RNA-based genomic tests can be costly and are not available in many countries. Methods for inferring molecular subtype from histologic images may identify patients most likely to benefit from further genomic testing. To identify patients who could benefit from molecular testing based on H&E stained histologic images, we developed an image analysis approach using deep learning. A training set of 571 breast tumors was used to create image-based classifiers for tumor grade, ER status, PAM50 intrinsic subtype, histologic subtype, and risk of recurrence score (ROR-PT). The resulting classifiers were applied to an independent test set (<i>n</i> = 288), and accuracy, sensitivity, and specificity of each was assessed on the test set. Histologic image analysis with deep learning distinguished low-intermediate vs. high tumor grade (82% accuracy), ER status (84% accuracy), Basal-like vs. non-Basal-like (77% accuracy), Ductal vs. Lobular (94% accuracy), and high vs. low-medium ROR-PT score (75% accuracy). Sampling considerations in the training set minimized bias in the test set. Incorrect classification of ER status was significantly more common for Luminal B tumors. These data provide proof of principle that molecular marker status, including a critical clinical biomarker (i.e., ER status), can be predicted with accuracy >75% based on H&E features. Image-based methods could be promising for identifying patients with a greater need for further genomic testing, or in place of classically scored variables typically accomplished using human-based scoring.