gebhart/patrepeval huggingface dataset:
Induction of IFN-γ and IL-17 by Pneumococcal Surface Protein C-Based Vaccines does not Protect Against a Streptococcus pneumoniae Invasive Challenge (2008)

Streptococcus pneumoniae (pneumococcus) is an important pathogen that causes pneumonia, meningitis and otitis media. Invasive diseases usually follow colonization of the respiratory tract and may be favored by factors that cause immunosupression. Several pneumococcal proteins actively participate of these events playing different roles such as facilitating bacterial adhesion to epithelial cells or evasion from the immune system. Pneumococcal Surface protein C (PspC) is a virulence factor that has been implicated both in colonization and in invasive phases of pneumococcal diseases. Antigen delivery systems based on live recombinant lactic acid bacteria represents a promising strategy for mucosal vaccination, since they are able to elicit both systemic and mucosal immune responses. In the present work, we have evaluated the immune response and the protective activity of nasal vaccines composed of recombinant PspC (rPspC) or Lactobacillus casei expressing PspC (L.c.PspC). Nasal immunization of mice with both formulations did not elicit the production of anti-PspC IgG or IgA. On the other hand, ELISPOT and cytokine ELISA analysis of cultures obtained from mice 13 h after intranasal challenge with a virulent pneumococcal strain, showed an increase in IFN-γ secretion in lung cells from mice immunized with L.c.PspC and to a lesser extent, rPspC. This cytokine was also produced by spleen cells from mice immunized with both formulations. Production of IL-17 by lung cells was observed in the group immunized with rPspC whereas immunization with L.c.PspC induced the production of this cytokine only by spleen cells. IL-17 has already been implicated in the protection against colonization conferred by a cellular pneumococcal vaccine. Nevertheless, the induction of this cytokine or IFN-γ by our vaccines did not confer protection against an invasive challenge with pneumococci. Further studies will be necessary for the evaluation of protection against nasal colonization. Financial Support: FAPESP, Fundação Butantan, Millenium Institute-Gene Therapy Network (MCT-CNPq).
Ultrasound elastography assessment of increased carotid artery wall stiffness in human immunodeficiency virus infected patients (2019)

Prevalence of cardiovascular diseases is higher in HIV subjects when compared to the general population. The chronic immune stimulation and low grade inflammation are possible causes. Carotid artery strain and motion are proposed as markers of premature atherosclerosis. Seventy-four HIV infected and 75 age-matched control subjects were recruited from a prospective, controlled cohort study (mean age 56 years ± 8; 128 men). Elastography applied to longitudinal ultrasound images of common and internal carotid arteries quantified the cumulated axial strain, cumulated shear strain, cumulated axial translation, and cumulated lateral translation. Presence of plaque was also assessed. Association between elastography biomarkers and HIV status were evaluated with Mann–Whitney tests and multivariate linear regression models. A higher occurrence of carotid plaques was found in HIV infected individuals (p = 0.011). Lower cumulated lateral translations were found in HIV infected subjects on both common and internal carotid arteries (p = 0.037 and p = 0.026, respectively). These observations remained significant when considering multivariable models including common cardiovascular risk factors and clinical characteristics (p&amp;lt; 0.05). Lower cumulated axial strains were also observed in internal carotid arteries when considering both multivariate models (p&amp;lt; 0.05). Lower translation and strain of the carotid artery wall in HIV infected individuals, which indicate increased vessel wall stiffness, could be new biomarkers of premature atherosclerosis.
2-Alkynyl-N-propargyl Pyridinium Salts:  Pyridinium-Based Heterocyclic Skipped Aza-Enediynes that Cleave DNA by Deoxyribosyl Hydrogen-Atom Abstraction and Guanine Oxidation (2006)

Diradical-generating cyclizations such as the enediyne Bergman cyclization and the enyne allene Myers-Saito cyclization have been exploited by nature in the mechanism of DNA cleavage by a series of potent antitumor antibiotics. Alternative diradical-generating cyclizations have been proposed in the design of selective antitumor agents; however, little information is available concerning the utility of these alternative cyclizations in radical-based DNA cleavage chemistry. One such alternative diradical-generating cyclization, the aza-Myers-Saito cyclization of aza-enyne allenes that are derived from base-promoted isomerization of skipped aza-enediynes, has been recently reported. Here, we report the synthesis and DNA cleavage chemistry of a series of pyridinium skipped aza-enediynes (2-alkynyl-N-propargyl pyridinium salts). Efficient DNA cleavage requires the presence of the skipped aza-enediyne functionality, and optimal DNA cleavage occurs at basic pH. Within this series of compounds, the analogue bearing a p-methoxyphenyl group on the pyridinium 2-alkyne substituents was found to be the most effective DNA cleavage agent, displaying significant supercoiled DNA-nicking activity at concentrations as low as 1 microM. Detailed studies of this analogue show that DNA cleavage occurs through 4'-hydrogen-atom abstraction from the DNA backbone and oxidation of guanine bases. This is the first report of enediyne-like radical-based DNA cleavage by an agent designed to undergo an alternative diradical-generating cyclization.
Enhancing glucose flux into sweat by increasing paracellular permeability of the sweat gland (2018)

Non-invasive wearable biosensors provide real-time, continuous, and actionable health information. However, difficulties detecting diluted biomarkers in excreted biofluids limit practical applications. Most biomarkers of interest are transported paracellularly into excreted biofluids from biomarker-rich blood and interstitial fluid during normal modulation of cellular tight junctions. Calcium chelators are reversible tight junction modulators that have been shown to increase absorption across the intestinal epithelium. However, calcium chelators have not yet been shown to improve the extraction of biomarkers. Here we show that for glucose, a paracellularly transported biomarker, the flux into sweat can be increased by >10x using citrate, a calcium chelator, in combination with electroosmosis. Our results demonstrate a method of increasing glucose flux through the sweat gland epithelium, thereby increasing the concentration in sweat. Future work should examine if this method enhances flux for other paracellularly transported biomarkers to make it possible to detect more biomarkers with currently available biosensors.
A Study of Effect of Cutting Strategy on Surface Generation in Ultra-Precision Machining of Micro-Structured Pattern Rollers (2013)

Plasticfilms with Embossed Micro-Structured Patterns have been Widely Used Inbacklight Guide Panels. the Mass Production of these Films Demands Forultra-Precision Roller Embossing of Micro-Structured Patterns on Plastic Filmsby Precision Pattern Rollers. due to the Heavy Workload and High Precisionrequirements, Ultra-Precision Rollers with Microstructures are very Difficultto be Machined in the Level of Submicrometer Form Accuracy and Surface Finishin Nanometer Range. this Paper Presents Theoretical and Experimental Studies Ofultra-Precision Machining of Precision Rollers with Microstructures. Themachining Mechanism for Precision Roller is Firstly Explained, and Hence Astudy of Effect of Cutting Strategies on Surface Generation in Ultra-Precisionmachining of Micro-Structured Pattern Rollers is Presented. this Includes Thestudy of Different Cutting Trajectories, Length-to-Diameter Ratio of Therollers, Mounting Method for the Rollers, the Number of Cuts in the Formationof the Micro-Structured Patterns, as well as the Time Budgeting for Adoptingdifferent Cutting Trajectories in Ultra-Precision Machining of Micro-Structuredpattern Rollers. the Results of the Study Provide an Important Means Forenhancing the Surface Quality and Optimizing the Time for Machining Precisionrollers.
Mo4Ce4Al7C3: A nanolamellar ferromagnetic Kondo lattice (2020)

Herein we show that ${\mathrm{Mo}}_{4}{\mathrm{Ce}}_{4}{\mathrm{Al}}_{7}{\mathrm{C}}_{3}$, a recently discovered nanolamellar compound displaying mixed valence, combines Kondo lattice behavior with ferromagnetism. A sizeable magnetization is carried by $3p$ states of Al as evidenced by a strong x-ray magnetic circular dichroism signal at the $K$ edge of aluminum, whereas no detectable signal was observed at the $K$ edge of carbon and ${L}_{2,3}$ edges of molybdenum. These results point out that the ferromagnetic behavior originates in the Ce atoms with $4{f}^{1}$ electronic configuration lying within the Al planes. The evolution with pressure of the mixed valence of Ce atoms in the Mo-C planes determined via Ce ${L}_{3}$ x-ray-absorption spectra along with the magnetoresistance measurements across the ferromagnetic transition unambiguously reveal a Kondo behavior. Angle-resolved photoemission spectroscopy and density functional theory confirm a certain degree of Ce $4f$ electron delocalization. More generally, conduction electrons are not restricted to lie in the MoC planes but are also delocalized in the Al planes.
Voting Reform can Include Everyone: Average Citizens, the Aging Population, and People with Disabilities (2001)

“If people with disabilities voted at the same rate as the non-disabled, 7 million more votes would have been cast in the last presidential election” (National Organization on Disability, October 1999). When interface technologies and/or the voting process as a whole are not flexible enough to meet the needs of those with temporary or permanent disabilities, obtained through aging or otherwise, citizens may experience various problems which may affect or prevent their vote. The authors will be demonstrating a proposed cross-disability accessible interface approach for electronic voting machines. The approach uses private speech output and a simple 3-button interface to supplement a touchscreen or selection wheel.
Proteomic Analysis of 3T3-L1 Adipocyte Mitochondria during Differentiation and Enlargement (2011)

The increase in adipose tissue mass arises in part from progressive lipid loading and triglyceride accumulation in adipocytes. Enlarged adipocytes produce the highest levels of pro-inflammatory molecules and reactive oxygen species (ROS). Since mitochondria are the site for major metabolic processes (e.g., TCA cycle) that govern the extent of triglyceride accumulation as well as the primary site of ROS generation, we quantitatively investigated changes in the adipocyte mitochondrial proteome during different stages of differentiation and enlargement. Mitochondrial proteins from 3T3-L1 adipocytes at different stages of lipid accumulation (days 0-18) were digested and labeled using the iTRAQ 8-plex kit. The labeled peptides were fractionated using a liquid phase isoelectric fractionation system (MSWIFT) to increase the depth of proteome coverage and analyzed using LC-MS/MS. A total of 631 proteins in the mitochondrial fraction, including endoplasmic reticulum-associated and golgi-related mitochondrial proteins, were identified and classified into 12 functional categories. A total of 123 proteins demonstrated a statistically significant change in expression in at least one of the time points over the course of the experiment. The identified proteins included enzymes and transporters involved in the TCA cycle, fatty acid oxidation, and ATP synthesis. Our results indicate that cultured adipocytes enter a state of metabolic-overdrive where increased flux through the TCA cycle and increased fatty acid oxidation occur simultaneously. The proteomic data also suggest that accumulation of reduced electron carriers and the resultant oxidative stress may be attractive targets for modulating adipocyte function in metabolic disorders.
Stress-limiting test structures for rapid low-cost strength and stiffness assessment (2015)

Purpose – The purpose of this paper is to evaluate the use of a simple printed geometry to estimate mechanical properties (elastic modulus, yield strength) with inexpensive test equipment. Design/methodology/approach – Test geometry is presented that enables controlled strains with manual deformation and repeatable measurement of vibrational frequencies. This is tested with multiple fused deposition modeling (FDM) machines to assess measurement accuracy and repeatability. Printing orientation and some printing parameters are varied to assess the measurement sensitivity. Findings – The test methods show good correlation with manufacturer material specifications in the X-Y plane and reported elastic strain limits. It is also sensitive to printing orientation and printing parameters. Research limitations/implications – Further work is needed to assess the sensitivity of the method to particular defects and parameter errors expected in particular applications. Originality/value – This method supports process monitoring in production environments and inexpensive assessments of material properties for hobbyist and do-i- yourself users. While it is tested with FDM, it should be applicable to other additive manufacturing processes.
Complications with Controlling Insect Eggs (2016)

Eggs are difficult to kill because of the unique structure of the eggshell, comprised of multiple layers that have evolved to allow the embryo to breathe while simultaneously limiting water loss. The eggshell has been shown to be an excellent barrier to insecticides, fungal pathogens, and some fumigants. The insect eggshell contains only a few areas that could allow penetration of insecticides, the aeropyles and micropyles, which seem to be either so few in number or small in size that they do not allow a sufficient amount of insecticide through the eggshell. Resistance is also a contributing factor to control failures of insect eggs. Resistance in eggs has been documented in several insect species and a few studies have shown that some insect eggs produce elevated numbers of enzymes to break down insecticides. This chapter focuses on the structure and respiration of the insect eggshell as a barrier to insecticides and also covers various management strategies against insect eggs. Lastly, we discuss the few documentations of resistance in insect eggs thus far.
<title>From batch to continuous manufacturing of microbiomedical and microanalytical devices</title> (1999)

We demonstrate how manufacture of miniaturized biosensors, fluidic platforms, drug delivery systems and other micro biomedical devices is relying more and more on non-Si micromanufacturing techniques. The new methodologies are hybrid in nature and merge IC fabrication methods (e.g. lithography) with more traditional manufacturing (e.g. lamination, plastic molding and electroplating). These proposed methods may involve large sheets of materials or may even be continuous, i.e., the number of devices that can be produced per single substrate is larger than that of a Si batch. The techniques are also modular rather than integrated and involve methods such as lamination, drop delivery, pick and place, laser drilling and cutting and other methods borrowed from the IC packaging and PC board industries. These new processes will afford for the first time miniaturized sensors, fluidics and other micro- biomedical devices at a cost that will enable them to become pervasive in our daily lives. The greater modularity in combining different components and the wider choice of materials with the required properties (e.g. biocompatibility, toughness, and optical transparency) will further accelerate the advent of many more innovative micro biomedical devices. In this paper we first discuss four important technology needs crucial to the realization of inexpensive disposable micro biomedical devices and then show early results obtained in our own laboratories towards the manufacture of three micro-biomedical and micro- analytical devices: disposable biosensors, CD based microfluidic platforms and responsive drug delivery pills.
Hepatitis C subtype distribution in chronically infected patients with mild liver fibrosis in France: the GEMHEP study (2019)

Treatment options for Hepatitis C infection have greatly improved with direct-acting antiviral (DAA) combinations achieving high cure rates. Nevertheless, the cost of this treatment is still high and access to treatment in many countries has been preferentially reserved for patients with more severe fibrosis (F3 and F4). In this French nationwide study, we investigated the epidemiological characteristics and genotype distribution of hepatitis C virus (HCV) in treatment-naive patients with METAVIR fibrosis stages between F0 and F2 in order to identify patient profiles that became eligible for unrestricted treatment in a second period. Between 2015 and 2016 we collected data from nine French university hospitals on a total of 584 HCV positive patients with absent, mild or moderate liver fibrosis. The most represented genotypes were genotype 1b (159/584; 27.2%), followed by genotype 1a (150/584; 25.7%); genotype 3 (87/584: 14.9%); genotype 4 (80/584; 13.7%). Among genotype 4: 4a was predominantly encountered with 22 patients (27.5% of genotype 4). Genotypes 1b and 1a are currently the most frequent virus types present in treatment-naive patients with mild fibrosis in France. They can be readily cured using the available DAA. Nevertheless, non-a/non-d genotype 4 is also frequent in this population and clinical data on the efficacy of DAA on these subtypes is missing. The GEMHEP is the French group for study and evaluation of viral hepatitis on a national scale. Data collection on epidemiological and molecular aspects of viral hepatitis is performed on a regular basis in all main French teaching hospitals and serves as a basis for surveillance of these infections. Analysis and trends are regularly published on behalf of the GEMHEP group. Data collection was performed retrospectively over the 2015-2016 period, covering nine main university hospitals in France. A total of 584 hepatitis C positive patients were included in this study. Genotyping of the circulating viruses showed a high prevalence of genotypes 1b and 1a in our population. The epidemiology of hepatitis C is slowly changing in France, particularly as a consequence of the rise of 'non-a non-d' genotype 4 viruses mainly originating from African populations. More data concerning treatment efficacy of these genotypes is needed in order to guide clinical care.
Secure Distributed Membership Tests via Secret Sharing How to Hide Your Hostile Hosts: Harnessing Shamir Secret Sharing. (2016)

Abstract not provided.
Analysis of genetic relatedness between gastric and oral H. pylori in patients with early gastric cancer using multilocus sequence typing (2022)

Abstract Although oral cavity is the second most colonized site after the stomach, the association between gastric and oral Helicobacter pylori remains unclear. This study aimed to compare the genetic relatedness between gastric and oral H. pylori in Japanese patients with early gastric cancer by multilocus sequence typing (MLST) analysis using seven housekeeping genes. Gastric biopsy specimens and oral samples, including saliva, supragingival dental biofilm, and superficial layers of the tongue, were collected from 21 patients positive for H. pylori by a fecal antigen test. The number of H. pylori allelic profiles of seven loci obtained from oral and gastric samples ranged from zero to seven since the yield of DNA was small even when the nested PCR was performed. The alleles of seven loci from both collection sites were determined from only one patient, and two out of seven alleles matched between oral and gastric samples. MLST analysis revealed that only one sample had a matching oral and gastric H. pylori genotype, suggesting that different genotypes of H. pylori inhabit the oral cavity and gastric mucosa. The phylogenetic analysis showed that oral H. pylori in two patients was markedly similar to gastric H. pylori , implying that the the origins of two strains may be the same, and the stomach and the oral cavity may be infected at the same time. In brief, although different genotypes of H. pylori exist in the oral cavity independently of H. pylori present in the stomach, there are rare cases in which the same H. pylori is present in the stomach and the oral cavity. It is necessary to establish a culture method for oral H. pylori for elucidating whether the oral cavity will act as the source of the gastric infection, as our analysis was based on a limited number of allele sequences. Author summary Hericobacter pylori is a clinically important pathogen that causes chronic gastritis and peptic ulcers, which are associated with gastric carcinoma. Oral H. pylori DNA has also been detected in a range of oral specimens, including saliva, supra- or sub-gingival biofilm, dentin caries, dental pulp, infected root canal, and coating of the tongue. Thus, researchers speculate that the main route of transmission of gastric H. pylori infections is via the oral cavity, however, there is inadequate evidence to support this suggestion. This study aimed to investigate if the oral and gastric H. pylori have the same origin using multilocus sequence typing. The results of this study provided some insight into the role of oral cavity as the source of H. pylori infections in stomach.
Table S5 from MicroRNA Array Analysis Finds Elevated Serum miR-1290 Accurately Distinguishes Patients with Low-Stage Pancreatic Cancer from Healthy and Disease Controls (2023)

&lt;p&gt;Table S5 - XLSX file 31K, Supplemental Table S5. MicroRNAs elevated in serum of patients with pancreatic cancer relative to combined controls by microarray analysis&lt;/p&gt;
Identification of tRNA‐derived small RNA (tsRNA) responsive to the tumor suppressor, RUNX1, in breast cancer (2020)

Despite recent advances in targeted therapies, the molecular mechanisms driving breast cancer initiation, progression, and metastasis are minimally understood. Growing evidence indicate that transfer RNA (tRNA)-derived small RNAs (tsRNA) contribute to biological control and aberrations associated with cancer development and progression. The runt-related transcription factor 1 (RUNX1) transcription factor is a tumor suppressor in the mammary epithelium whereas RUNX1 downregulation is functionally associated with breast cancer initiation and progression. We identified four tsRNA (ts-19, ts-29, ts-46, and ts-112) that are selectively responsive to expression of the RUNX1 tumor suppressor. Our finding that ts-112 and RUNX1 anticorrelate in normal-like mammary epithelial and breast cancer lines is consistent with tumor-related activity of ts-112 and tumor suppressor activity of RUNX1. Inhibition of ts-112 in MCF10CA1a aggressive breast cancer cells significantly reduced proliferation. Ectopic expression of a ts-112 mimic in normal-like mammary epithelial MCF10A cells significantly increased proliferation. These findings support an oncogenic potential for ts-112. Moreover, RUNX1 may repress ts-112 to prevent overactive proliferation in breast epithelial cells to augment its established roles in maintaining the mammary epithelium.