gebhart/patrepeval huggingface dataset:
Comparison of Biomarkers in Blood and Saliva in Healthy Adults (2012)

Researchers measure biomarkers as a reflection of patient health status or intervention outcomes. While blood is generally regarded as the best body fluid for evaluation of systemic processes, substitution of saliva samples for blood would be less invasive and more convenient. The concentration of specific biomarkers may differ between blood and saliva. The objective of this study was to compare multiple biomarkers (27 cytokines) in plasma samples, passive drool saliva samples, and filter paper saliva samples in 50 healthy adults. Demographic data and three samples were obtained from each subject: saliva collected on filter paper over 1 minute, saliva collected by passive drool over 30 seconds, and venous blood (3 mL) collected by venipuncture. Cytokines were assayed using Bio-Rad multiplex suspension array technology. Descriptive statistics and pairwise correlations were used for data analysis. The sample was 52% male and 74% white. Mean age was 26 (range = 19-63 years, sd = 9.7). The most consistent and highest correlations were between the passive drool and filter paper saliva samples, although relationships were dependent on the specific biomarker. Correlations were not robust enough to support substitution of one collection method for another. There was little correlation between the plasma and passive drool saliva samples. Caution should be used in substituting saliva for blood, and relationships differ by biomarker.
Compartment pressures after intramedullary nailing of the tibia (1990)

Intracompartmental pressures of 66 patients with 67 tibial fractures treated by intramedullary nailing were monitored. There was no difference in the pressures recorded between the different Tscherne fracture types, between open and closed fractures, between low energy and high energy injuries or between fractures dealt with early and those not treated until more than 24 hours after injury. The overall incidence of acute compartment syndrome was 1.5%. No patient developed any sequelae of compartment syndrome. We conclude that intramedullary nailing does not increase the incidence of acute compartment syndrome in tibial fractures and that delay does not reduce the risk of raised compartment pressures.
Anti-opiate (naloxone) suppression of Cushingoid degenerative changes in obese/SHR. (1985)

Young and mature, genetically obese and non-obese, spontaneously hypertensive rats (SHR) were injected with saline (controls) or naloxone for 12 weeks. Naloxone stilled the hyperphagia to a normal intake in the obese SHR (Obese/SHR) so that young Obese/SHR did not develop their usual massive obesity and mature Obese/SHR that had become massively obese were reduced to leanness. The naloxone-treated young, obese and non-obese SHR (controls) exhibited marked reduction of the weight of their pituitary and adrenal glands, whereas the pituitary and adrenal glands of naloxone-treated mature, obese and non-obese/SHR were greatly increased in weight. The elevated systolic blood pressure of the obese and non-obese rats was reduced after chronic treatment with naloxone. Naloxone treatment caused reduction of blood ACTH, corticosterone, and beta endorphin levels but elevated growth hormone levels. The characteristic hyperinsulinemia, hyperlipidemia, hyperglycemia, elevated BUN levels, and the Cushingoid spectrum of degenerative changes found in Obese/SHR did not appear in naloxone-treated rats.
Differential effects of IL-4 and IL-10 on IL-2-induced IFN-γ synthesis and lymphokine-activated killer activity (1992)

Culture of human peripheral blood mononuclear cells (PBMC) with IL-2 stimulates synthesis of cytokines and generation of lymphokine-activated killer (LAK) activity. Both IL-4 and IL-10 [cytokine synthesis inhibitory factor (CSIF)] inhibit IL-2-induced synthesis of IFN-gamma and tumor necrosis factor (TNF)-alpha by human PBMC. However, unlike IL-4, IL-10 inhibits neither IL-2-induced proliferation of PBMC and fresh natural killer (NK) cells, nor IL-2-induced LAK activity. Moreover, IL-4 inhibits IL-2-induced IFN-gamma synthesis by purified fresh NK cells, while in contrast the inhibitory effect of IL-10 is mediated by CD14+ cells (monocytes/macrophages). IL-10 inhibits TNF-alpha synthesis by monocytes or monocytes plus NK cells, but not by NK cells alone. These results suggest that IL-4 and IL-10 act on NK cells via distinct pathways, and that IL-2-induced cytokine synthesis and LAK activity are regulated via different mechanisms.
Effects of trans -acting Genetic Modifiers on Meiotic Recombination Across the a1–sh2 Interval of Maize (2006)

Meiotic recombination rates are potentially affected by cis- and trans-acting factors, i.e., genotype-specific modifiers that do or do not reside in the recombining interval, respectively. Effects of trans modifiers on recombination across the approximately 140-kb maize a1-sh2 interval of chromosome 3L were studied in the absence of polymorphic cis factors in three genetically diverse backgrounds into which a sequence-identical a1-sh2 interval had been introgressed. Genetic distances across a1-sh2 varied twofold among genetic backgrounds. Although the existence of regions exhibiting high and low rates of recombination (hot and cold spots, respectively) was conserved across backgrounds, the absolute rates of recombination in these sequence-identical regions differed significantly among backgrounds. In addition, an intergenic hot spot had a higher rate of recombination as compared to the genome average rate of recombination in one background and not in another. Recombination rates across two genetic intervals on chromosome 1 did not exhibit the same relationships among backgrounds as was observed in a1-sh2. This suggests that at least some detected trans-acting factors do not equally affect recombination across the genome. This study establishes that trans modifier(s) polymorphic among genetic backgrounds can increase and decrease recombination in both genic and intergenic regions over relatively small genetic and physical intervals.
Lactate Metabolism in Anxiety Neurosis (1967)

FOUR investigations conducted in 4 countries during the past twenty-five years have shown excessive lactate production on standard exercise in patients with anxiety neurosis.1 2 3 4 The characteristic anxiety symptoms were often evoked by the exercise and appeared to be concomitant with the extremely rapid rise of blood lactic acid. In general, the patients were unable to perform as much work per unit of time or to maintain as great a workload as normal matched controls.4 5 6 The rise in blood lactate per unit of work output per unit of time in the anxiety neurotics approximates that of patients with arteriosclerotic heart disease . . .
Gases generated from simulated thermal degradation of autotrophic and heterotrophic chlorella (1992)

The content of crude lipid in the cells of heterotrophic Chlorella protothecoides is 4.4 times as high as in the autotrophic algal cells. The gases thermally degraded from autotrophic cells at 200-300[degrees]C contain mainly CO[sub 2], while the heterotrophic algal cells produce hydrocarbon gas at a much higher rate than autotraophic algal cells. With the rise in temperature, both kinds of cells display a rapid drop in the acid/alkane ratio of the gas components and the ratio of ethane to ethylene increases regularly. Their ratio of normal and isomeric alkanes are all above 1. The study reveals that the actual potential of microplanktonic algae in producing oil and natural gas should be much greater than what people have recognized before.
Introduction to Bioinformatics (2003)

to Bioinformatics A Theoretical and Practical Approach Edited by Stephen A. Krawetz, PhD Wayne State University School of Medicine, Detroit MI and David D. Womble, PhD Wayne State University School of
Origin and distribution of terrestrial organic matter in the NW Mediterranean (Gulf of Lions): Exploring the newly developed BIT index (2006)

The Branched and Isoprenoid Tetraether (BIT) index is based on the relative abundance of nonisoprenoidal glycerol dialkyl glycerol tetraethers (GDGTs) derived from organisms living in terrestrial environments versus a structurally related isoprenoid GDGT “crenarchaeol” produced by marine Crenarchaeota. The BIT index varies between 0 and 1, representing marine and terrestrial organic matter (OM) end‐members, respectively (Hopmans et al., Earth Planet. Sci. Lett. , 224 , 107–116, 2004). In this study, the applicability of the BIT index to trace terrestrial OM is tested in combination with other organic parameters (TOC, C/N ratio, δ 13 C org , total lipid, and n ‐alkane) in the Gulf of Lions, a river‐dominated continental margin of the western Mediterranean. We analyzed a variety of soils and riverbed sediments from the continent as well as surface sediments from the shelf and canyons. The BIT index in soils and riverbed sediments shows high values (&gt;0.9), while it varies between 0.02 and 0.83 in marine sediments, decreasing seaward from the inner shelf to the slope. For marine surface sediments, high BIT values are associated with lower δ 13 C org values as well as higher TOC contents and higher n ‐alkane concentrations. Our results confirm that the BIT index can be applied in coastal marine environments in order to characterize terrestrial OM as proposed by Hopmans et al. (2004). Therefore the BIT index is a useful addition to the proxies presently available for studying the origin and distribution of OM in continental margins and especially valuable in multiproxy studies.
Use of an extracellular matrix material as a vaccine carrier and adjuvant. (2008)

SIS enhanced the efficacy of a tissue vaccine for prostate cancer, demonstrating the potential utility of extracellular matrices as novel vaccine adjuvants.
Production and characterization of recombinant tachycitin, the Cys-rich chitin-binding protein (2002)

Tachycitin is an invertebrate chitin-binding protein with an amidated C-terminus, and possesses antimicrobial activity against both fungi and bacteria. The (1)H-NMR-based tertiary structure of tachycitin was recently determined [Suetake et al. (2000) J. Biol. Chem., 275, 17929-17932]. In order to examine the structural and functional features of tachycitin more closely, we performed for the first time, gene expression, refolding, (15)N-NMR-based characterizations, and antimicrobial activity measurements of a recombinant tachycitin (rTcn) that does not have the amide group at the C-terminus. The NMR analysis indicated that rTcn possesses the same structural construction as the native tachycitin. The backbone (15)N relaxation measurements showed that the molecular motional correlation time of rTcn increases as its concentration increases, indicating that tachycitins have a tendency to aggregate with each other. rTcn exhibits antimicrobial activity against fungi but not against bacteria. The cell surface of fungi contains chitin as an essential constituent, but that of bacteria does not. These results suggest that not only the chitin-binding region but also the C-terminal amide group of tachycitin plays a significant role in its antimicrobial properties.
Synthesis of Control Protocols for Autonomous Systems (2013)

This article provides a review of control protocol synthesis techniques that incorporate methodologies from formal methods and control theory to provide correctness guarantee for different types of autonomous systems, including those with discrete and continuous state space. The correctness of the system is defined with respect to a given specification expressed as a formula in linear temporal logic to precisely describe the desired properties of the system. The formalism presented in this article admits nondeterminism, allowing uncertainties in the system to be captured. A particular emphasis is on alleviating some of the difficulties, e.g., heterogeneity in the underlying dynamics and computational complexity, that naturally arise in the construction of control protocols for autonomous systems.
Dynamics of antigen-specific helper T cells at the initiation of airway eosinophilic inflammation (2001)

Bronchial asthma is characterized by chronic eosinophilic inflammation of the bronchial mucosa in which Th2 cells play crucial roles. Ovalbumin-reactive Th2 clones were labeled with a fluorescent-probe then infused into unprimed mice to elucidate the dynamics of antigen-specific T cells involved in allergic inflammation. Infiltration of not only labeled antigen-specific T cells, but also unlabeled nonspecific CD4(+) T cells into the bronchial mucosa following inhaled antigen challenge was detectable under confocal microscopy and flow cytometry. Accordingly, labeled T cells in the spleen were decreased, whereas those in hilar lymph nodes were increased upon antigen challenge. Approximately 45% of antigen-specific T cells that migrated into the lungs bore CD25, while another early activation marker, CD69, was expressed on 80% of the migrated T cells. Accordingly, antigen challenge to the mice induced in situ proliferation of antigen-specific T cells as well as bronchial epithelial cells in the lungs. Expression of vascular cell adhesion molecule (VCAM)-1, but not intercellular adhesion molecule (ICAM)-1, on the vascular endothelium in the lungs was enhanced following antigen challenge. Nevertheless, treatment with anti-VCAM-1 antibody, and also anti-ICAM-1 antibody strongly suppressed the accumulation of T cells, suggesting that both VCAM-1 and ICAM-1 are essential for antigen-stimulated T cell mobilization into peripheral tissues. Our current study visualized the kinetics and the mechanism of antigen-specific T cell migration in response to local challenge with a protein antigen.
Detection and Quantitation of Human Papillomavirus by Using the Fluorescent 5′ Exonuclease Assay (1999)

A method for the detection and quantitation of oncogenic human papillomavirus (HPV) was developed by using the fluorescent 5' exonuclease assay. The method is based on the amplification of a 180-bp fragment from the 3' part of the E1 open reading frame in a single PCR with type-specific probes for HPV types 16, 18, 31, 33, and 35. The probes can be used separately or in combinations of up to three probes per assay. Quantitation over a range of 10(1) to 10(6) initial HPV copies was possible by using real-time detection of the accumulation of fluorescence with cycle number. Reconstitution experiments, performed to mimic mixed infections, showed that individual HPV types can be detected down to a ratio of about 1% in a mixture. The performance of the assay depends on DNA quality, the presence of PCR inhibitors, and the number of different probes used simultaneously. This homogeneous assay provides a fast and sensitive way of screening for oncogenic HPV types in biopsy specimens as well as cervical smear samples. The closed-tube nature of the assay and the inclusion of uracil N'-glycosylase reduces cross contamination of PCR products to a minimum. A similar assay for beta-actin was used in parallel for quantitation of genomic DNA. After normalizing the samples for genomic DNA content, the mean number of HPV copies per cell could be calculated.
Desketoneoenactin-Siderophore Conjugates for Candida : Evidence of Iron Transport-Dependent Species Selectivity (2004)

We investigated the inhibitory activity of synthetic isocyanurate-based as well as linear mono- and trihydroxamate siderophore-drug conjugates against Candida spp. The conjugated drug was 13C-desketoneoenactin (DE). The MICs of siderophore-drug conjugates were determined in the absence and presence of 2,2'-dipyridyl to restrict iron availability. The ability of various siderophore types to promote growth in an iron-restricted medium was also assayed. Addition of a siderophore portion to the drug strongly impaired the inhibitory activity of DE. However, the activity of the drug conjugates was increased by up to 16-fold in iron-depleted medium for species having their growth strongly promoted by most hydroxamate-type siderophores (C. albicans, C. stellatoidea, and C. pseudotropicalis). The uptake of (55)Fe from ferrichrome and from two siderophore-drug conjugates was improved when C. albicans cells were grown in a low-iron medium. In the same assay, unlabeled ferrichrome was able to compete with the uptake of (55)Fe from both conjugates, indicating a common mechanism of uptake. A C. albicans strain lacking the siderophore transporter CaSit1/CaArn1 was not able to use ferrichrome or the synthetic ornithine-based trihydroxamate siderophore for growth promotion and was much less susceptible to the siderophore-drug conjugates than its isogenic parent strain. In summary, the ability of some Candida spp. to use ferrichrome-like siderophores for growth promotion explains the selective activity of hydroxamate-drug conjugates, and this activity seems to be related to the presence, in C. albicans, of the siderophore transporter CaSit1/CaArn1. New conjugate designs are necessary to fully restore or improve the initial DE activity.
Relative binding affinities of distamycin and its analog to d(CGCAAGTTGGC).d(GCCAACTTGCG): comparison of simulation results with experiment. (1994)

We report here an effort to use molecular dynamics/free energy perturbation methodology to calculate relative binding affinities of two related drugs to DNA. Specifically, we focus on the relative binding free energies of distamycin (Dst) and its analog, 2-imidazoledistamycin (2-ImD), to d(CGCAAGTTGGC).d(GCCAACTTGCG). The pyrrole (Dst) and the imidazole variant (2-ImD) differ only in that the C-H is substituted by an N in the central ring. The starting conformation for these calculations was the previously determined solution structure of two 2-ImD molecules in the minor groove of the above 11-residue DNA. In this complex both the ligands have the imidazole nitrogen (N3) oriented toward the amino group of G6. However only ligand 1 (site I) has N3 within the hydrogen bonding distance from N2 amino proton of G6. We have calculated the difference in free energy of binding of 2-ImD versus Dst in three different cases by mutating 2-ImD-->Dst reversibly. In the first case ligand 1 (site I) is mutated, in the second case ligand 2 (site II) is mutated, and in the third case both the ligands are mutated. These calculations show that at site I Dst has weaker binding affinity than 2-ImD by 0.7 kcal/mol, at site II Dst has stronger binding affinity than 2-ImD by 2.9 kcal/mol, and when occupying both site I and site II, Dst binds with greater affinity than 2-ImD by 1.8 kcal/mol. Recent experimental findings agree semiquantitatively (within 1 kcal/mol) with the calculations presented here. Hence the methodology presented here can be used to predict relative binding energies of two or more closely related molecules to DNA.
Preventive magnesium supplement protects the inner ear against noise-induced impairment of blood flow and oxygenation in the guinea pig. (2002)

We have recently demonstrated in the guinea pig that preventive dietary magnesium supplement can significantly reduce hearing loss caused by acute impulse noise exposure. To elucidate the underlying protective mechanisms of magnesium, the present study examined its effect on noise-induced impairment of cochlear blood flow (CoBF) and perilymphatic oxygen partial pressure (pO2) in two groups of guinea pigs maintained on optimal or suboptimal dietary magnesium status. While laser Doppler flowmetry was used to determine CoBF, perilymphatic pO2 was measured polarographically using micro-coaxial platinum needle electrodes. Auditory function was tested by recording compound action potentials. Animals were exposed to a selected high-intensity impulse noise series (L(peak) 167 dB, 1/s, 38 min). In the low magnesium groups, the noise exposure resulted in a mean decrease of CoBF and perilymphatic PO2 by about 10 and 35 per cent of the initial value, respectively. In contrast, in the high magnesium groups, neither parameter displayed any noise-induced decreases, and there was even a tendency to a slight increase. Magnesium also reduced the hearing loss significantly by 10 to 35 dB over the frequency range (2-16 kHz) tested. Both the CoBF and the perilymphatic pO2 were found to correlate with the serum magnesium. The piesent findings show that in the guinea pig preventive dietary magnesium supplement can protect the inner ear against noise-induced impairment of blood flow and oxygenation, which may partly be responsible for noise-induced hearing loss.
Laser chimeras as a paradigm for multistable patterns in complex systems (2015)

A chimera state is a rich and fascinating class of self-organized solutions developed in high-dimensional networks. Necessary features of the network for the emergence of such complex but structured motions are non-local and symmetry breaking coupling. An accurate understanding of chimera states is expected to bring important insights on deterministic mechanism occurring in many structurally similar high-dimensional dynamics such as living systems, brain operation principles and even turbulence in hydrodynamics. Here we report on a powerful and highly controllable experiment based on an optoelectronic delayed feedback applied to a wavelength tuneable semiconductor laser, with which a wide variety of chimera patterns can be accurately investigated and interpreted. We uncover a cascade of higher-order chimeras as a pattern transition from N to N+1 clusters of chaoticity. Finally, we follow visually, as the gain increases, how chimera state is gradually destroyed on the way to apparent turbulence-like system behaviour.
Allogeneic Bone Marrow Transplantation for Chronic Myeloid Leukemia Using Sibling and Volunteer Unrelated Donors: A Comparison of Complications in the First 2 Years (1993)

Results appear to justify the continued use of volunteer donors in chronic-phase chronic myeloid leukemia, but infection and chronic GVHD are still major problems.
Fluidic Heterogeneous Microsystems Assembly and Packaging (2006)

The nonrobotic fabrication of packaged microsystems that contain nonidentical parts has been accomplished by a directed self-assembly process. The self-assembly process uses geometrical shape recognition to identify different components and subsequent bond formation between liquid solder and metal-coated areas to form mechanical and electrical connections. We applied this concept of shape recognition and subsequent formation of contacts to assemble and package microsystems that contained nonidentical subunits. The self-assembly of three-component assemblies is demonstrated by sequentially adding device segments to the assembly solution including 200-mum-sized light-emitting diodes. Six hundred AlGaInP-GaAs light-emitting diode segments self-assembled onto device carriers in 2min without defects. Encapsulation units self-assembled onto the LED-carrier assemblies to form a three-dimensional (3-D) circuit path to operate the final device. The reported procedure provides a new route to the creation of autonomous heterogeneous microsystems including the realization of autonomous wireless sensor system that requires nonidentical units: CMOS circuitry, Non-CMOS sensor unit for sensing, III-V components for communication, and encapsulation units to form 3-D electrical interconnects. The creation of such systems is being discussed and a proof of concept experiment is being demonstrated