gebhart/patrepeval huggingface dataset:
Quantitative assessment of hematopoietic chimerism after bone marrow transplantation by real-time quantitative polymerase chain reaction (2002)

We have developed a real-time quantitative polymerase chain reaction (PCR) assay using TaqMan technology (Applied Biosystems, Foster City, CA) for monitoring donor cell engraftment in allogenic hematopoietic stem cell transplant recipients. For this purpose, we selected 19 specific sequence polymorphisms belonging to 11 human biallelic loci located on 9 different chromosomes. Using a set of specially designed primers and fluorogenic probes, we evaluated the 19 markers' informativity on a panel of 126 DNA samples from 63 recipient/donor pairs. In more than 90% of these pairs, discrimination between recipient and donor genetic profile was possible. By using serial dilutions of mixed DNAs, we evaluated the linearity and sensitivity of the method. A linear correlation with r higher than 0.98 and a sensitivity of 0.1% proved reproducible. Fluorescent-based PCR of short tandem repeats (STR-PCR) and real-time PCR chimerism assay were compared with a panel of artificial cell mixtures. The main advantage of the real-time PCR method over STR-PCR chimerism assays is the absence of PCR competition and plateau biases, and results evidenced greater sensitivity and linearity with the real-time PCR method. Furthermore, different samples can be tested in the same PCR run with a final result in fewer than 48 hours. Finally, we prospectively analyzed patients who received allografts and present 4 different clinical situations that illustrate the informativity level of our method. In conclusion, this new assay provides an accurate quantitative assessment of mixed chimerism that can be useful in guiding early implementation of additional treatments in hematopoietic stem cell transplantation.
Alternate phase variation in expression of two major surface membrane proteins (MBA and UU376) ofUreaplasma parvumserovar 3 (2009)

Ureaplasma urealyticum and Ureaplasma parvum are commensals and pathogens of the human urogenital tract and of newborn infants. There are four distinct U. parvum serovars and 10 distinct U. urealyticum serovars. Both species possess a distinct immunodominant variable surface protein, the multiple banded antigen (MBA), which shows size variability among isolates as a result of changes in the number of C-terminal repeating units. Adjacent to the MBA gene (UU375) lies UU376, which was annotated as 'Ureaplasma-specific conserved hypothetical gene'. In four different strains of U. parvum serovar 3, we demonstrated expression of UU376 by Western blot analysis and phase variation between UU376, here designated Upvmp376 (Ureaplasma phase-variable membrane protein 376), and MBA after application of selective pressure with hyperimmune antisera directed against either protein. By Southern blot analysis, we found that the switch between MBA and Upvmp376 expression is associated with a DNA inversion event in which the nonrepetitive region of the MBA gene and its putative promoter region are opposed to either the repetitive region of MBA or UU376. We propose that in U. parvum serovar 3, and presumably in all U. parvum and U. urealyticum, an inversion event at specific sites effects an alternate ON/OFF switching of the genes UU375 and UU376.
Noise autocorrelation in high density recording on metal film disks (1986)

This paper presents measurement and analysis of noise associated with closely spaced transitions. The measured noise autocorrelation function is found to be similar to noise calculated with both pulse amplitude variation and position jitter. The amplitude variation is larger for closely spaced transitions.
Modifying the Glycome in Pigs for Xenotransplantation (2016)

In Brief The authors highlight the power of glycome editing of progressive carbohydrate remodeling for reducing the antigenicity of pig xenografts.
Conformationally constrained tachykinin analogs: potent and highly selective neurokinin NK-2 receptor agonists (1992)

The design and synthesis of potent and selective neurokinin NK-2 receptor agonists 12 (GR64349) and 31 are described, together with structure-activity relationships for related analogues. Compound 12 (EC50 = 3.7 nM at NK-2 receptors in the rat colon; selectivity > 1000- and > 300-fold with respect to NK-1 and NK-3 receptors, respectively) was derived by incorporation of a Gly-Leu gamma-lactam conformational constraint into the C-terminal region of the neurokinin A octapeptide analogue [Lys3]-NKA(3-10). Compound 31 (EC50 = 15 nM in rat colon) contains a novel fused-bicyclic constraint at the corresponding site in the substance P hexapeptide analogue [Ava6]-SP(6-11).
Comparison of some fiber optic configurations for measurement of luminescence and Raman scattering (1990)

Measurements are made for a number of dual fiber optic configurations to determine their relative sensitivity using bare fibers and graded-refractive-index lenses. An analysis of the background fiber emission for a typical silica-on-silica fiber (Diaguide, 200-microm core) is presented, and the origin (core or cladding) for several prominent Raman peaks is determined. Also, a forward-scattering fiber geometry is introduced, and the dependence of sensitivity on the type of optical termination and fiber separation is determined.
Parkinson's disease patients show reduced cortical‐subcortical sensorimotor connectivity (2012)

Reduced dopamine input to cortical and subcortical brain structures, particularly those in the sensorimotor network, is a hallmark of Parkinson's disease (PD). The extent to which dopamine dysfunction affects connectivity within this and other brain networks remains to be investigated. The purpose of this study was to measure anatomical and functional connectivity in groups of PD patients and controls to determine whether connectivity deficits within the cortico-basal ganglia thalamocortical system could be attributed to PD, particularly in sensorimotor connections. A neuroimaging paradigm involving diffusion-weighted magnetic resonance imaging (MRI) and resting-state functional MRI was implemented in a large cohort of PD patients and control subjects. Probabilistic tractography and functional correlation analyses were performed to map connections between brain structures and to derive indices of connectivity that were then used to compare groups. Anatomical connectivity deficits were demonstrated in PD patients, specifically for sensorimotor connections. Functional deficits were also found in some of the same connections. In addition, functional connectivity was found to increase in associative and limbic connections in PD patients compared with controls. This study lends support to findings regarding the dysfunction of the sensorimotor circuit in PD. As deficits in anatomical and functional connectivity within this circuit were in some cases concordant in PD patients, a possible link between brain structure and function is suggested. Increases in functional connectivity in other cortico-basal ganglia thalamocortical circuits may be indicative of compensatory effects in response to system deficits elsewhere.
Brain development in children with new onset epilepsy: A prospective controlled cohort investigation (2010)

Children with new and recent-onset epilepsy exhibit an altered pattern of brain development characterized by delayed age-appropriate increase in white matter volume. These findings may affect cognitive development through reduced brain connectivity and may also be related to the impairments in executive function commonly reported in this population.
Multipotent and restricted precursors in the central nervous system (1999)

Acquisition of cell type-specific properties in the nervous system is likely a process of sequential restriction in developmental potential. At least two classes of pluripotent stem cells, neuroepithelial (NEP) stem cells and EGF-dependent neurosphere stem cells, have been identified in distinct spatial and temporal domains. Pluripotent stem cells likely generate central nervous system (CNS) and peripheral nervous system (PNS) derivatives via the generation of intermediate lineage-restricted precursors that differ from each other and from multipotent stem cells. Neuronal precursors termed neuronal-restricted precursors (NRPs), multiple classes of glial precursors termed glial-restricted precursors (GRPs), oligodendrocyte-type 2 astrocytes (O2As), astrocyte precursor cells (APCs), and PNS precursors termed neural crest stem cells (NCSCs) have been identified. Multipotent stem cells and restricted precursor cells can be isolated from embryonic stem (ES) cell cultures providing a non-fetal source of such cells. Analysis in multiple species illustrates similarities between rat, mouse, and human cell differentiation raising the possibility that similar factors and markers may be used to isolate precursor cells from human tissue or ES cells. Anat Rec (New Anat): 257:137–143, 1999. © 1999 Wiley-Liss, Inc.
Basic fibroblast growth factor mediates its effects on committed myeloid progenitors by direct action and has no effect on hematopoietic stem cells (1995)

Basic fibroblast growth factor or fibroblast growth factor-2 (FGF) has been shown to affect myeloid cell proliferation and hypothesized to stimulate primitive hematopoietic cells. We sought to evaluate the effect of FGF on hematopoietic stem cells and to determine if FGF mediated its effects on progenitor cells directly or through the induction of other cytokines. To address the direct effects of FGF, we investigated whether FGF induced production of interleukin-1 beta (IL-1 beta), tumor necrosis factor alpha, IL-6, granulocyte colony-stimulating factor, or granulocyte-macrophage colony-stimulating factor by two types of accessory cells, bone marrow (BM) fibroblasts and macrophages. We further evaluated whether antibodies to FGF-induced cytokines affected colony formation. To determine if FGF was capable of stimulating multipotent progenitors, we assessed the output of different colony types after stimulation of BM mononuclear cells (BMMC) or CD34+ BMMC and compared the effects of FGF with the stem cell active cytokine, kit ligand (KL). In addition, a subset of CD34+ BMMC with characteristics of hematopoietic stem cells was isolated by functional selection and their response to FGF was evaluated using proliferation, colony-forming, and single-cell polymerase chain reaction (PCR) assays. We determined that FGF had a stimulatory effect on the production of a single cytokine, IL-6, but that the effects of FGF on colony formation were not attributable to that induction. FGF was more restricted in its in vitro effects on BM progenitors than KL was, having no effect on erythroid colony formation. FGF did not stimulate stem cells and FGF receptors were not detected on stem cells as evaluated by single-cell reverse transcription PCR. In contrast, FGF receptor gene expression was detected in myeloid progenitor populations. These data support a directly mediated effect for FGF that appears to be restricted to lineage-committed myeloid progenitor cells. FGF does not appear to modulate the human hematopoietic stem cell.
Hydrodynamic Radii of Ranibizumab, Aflibercept and Bevacizumab Measured by Time-Resolved Phosphorescence Anisotropy (2016)

Time-resolved phosphorescence anisotropy is a relatively simple and straightforward method that allows experimental measurement of the hydrodynamic radius of individual proteins, and is superior to theoretical calculations which cannot give the required accuracy for a particular protein.
Periodic arrays of deep nanopores made in silicon with reactive ion etching and deep UV lithography (2008)

We report on the fabrication of periodic arrays of deep nanopores with high aspect ratios in crystalline silicon. The radii and pitches of the pores were defined in a chromium mask by means of deep UV scan and step technology. The pores were etched with a reactive ion etching process with SF(6), optimized for the formation of deep nanopores. We have realized structures with pitches between 440 and 750 nm, pore diameters between 310 and 515 nm, and depth to diameter aspect ratios up to 16. To the best of our knowledge, this is the highest aspect ratio ever reported for arrays of nanopores in silicon made with a reactive ion etching process. Our experimental results show that the etching rate of the nanopores is aspect-ratio-dependent, and is mostly influenced by the angular distribution of the etching ions. Furthermore we show both experimentally and theoretically that, for sub-micrometer structures, reducing the sidewall erosion is the best way to maximize the aspect ratio of the pores. Our structures have potential applications in chemical sensors, in the control of liquid wetting of surfaces, and as capacitors in high-frequency electronics. We demonstrate by means of optical reflectivity that our high-quality structures are very well suited as photonic crystals. Since the process studied is compatible with existing CMOS semiconductor fabrication, it allows for the incorporation of the etched arrays in silicon chips.
Silicon Carbide as a Material for Biomedical Microsystems (2009)

Abstract- Silicon Carbide (SiC) is emerging as an enabling material for biomedical microsystems due to its unique combination of electrical, mechanical and chemical properties combined with its compatibility with Si micromachining techniques. This paper presents an overview of the latest advancements in this area including on-going research to develop SiC for biosensing, bio-microdevice packaging, biofiltering, biomedical imaging and other related biomedical applications. I.
1163. The crystal and molecular structure of aspirin (1964)

P. J. Wheatley, J. Chem. Soc., 1964, 6036 DOI: 10.1039/JR9640006036
Oats induced villous atrophy in coeliac disease (2003)

The current trend is to allow coeliac disease (CD) patients to introduce oats to their gluten free diet. We sought further data from the clinical setting with regards to oats consumption by coeliac patients. Several oat products were tested for wheat contamination using a commercial enzyme linked immunoassay (ELISA) kit, and six samples were examined by an ELISA using a cocktail of monoclonal antibodies, mass spectrometry, and western blot analysis. Nineteen adult CD patients on a gluten free diet were challenged with 50 g of oats per day for 12 weeks. Serological testing and gastroduodenoscopy was performed before and after the challenge. Biopsies were scored histologically and levels of mRNA specific for interferon gamma were determined by reverse transcription-polymerase chain reaction analysis. Oats were well tolerated by most patients but several reported initial abdominal discomfort and bloating. One of the patients developed partial villous atrophy and a rash during the first oats challenge. She subsequently improved on an oats free diet but developed subtotal villous atrophy and dramatic dermatitis during a second challenge. Five of the patients showed positive levels of interferon gamma mRNA after challenge. Some concerns therefore remain with respect to the safety of oats for coeliacs.
Biosynthetic Gene Clusters of Benzoisochromanequinone Antibiotics in Streptomyces spp. Identification of Genes Involved in Post-PKS Tailoring Steps. (1998)

Benzoisochromanequinone (BIQ) antibiotics are a class of aromatic polyketides produced by Streptomyces spp. A polyketide synthase (PKS, Type II) is involved in the formation of each BIQ chromophore. The first PKS genes were cloned in S. coelicolor A3(2), producer of the typical BIQ antibiotic, actinorhodin; sequence analysis of the PKS genes revealed their clustering with all the other relevant biosynthetic genes (the act cluster). A number of PKS genes have been discovered in the producers not only of other BIQs, but also of other classes of aromatic polyketides, using the act PKS genes as hybridisation probes. Among them similar genetic organisations were identified for the genes encoding the minimal PKS components -KS (ketosynthase), CLF (chain length factor), ACP (acyl carrier protein)- and their closely associated proteins: KR (ketoreductase), ARO (aromatase), and CYC (cyclase). In spite of the increasing knowledge of PKS genes themselves, various biosynthetic problems remain to be solved. As one of the most extensively studied examples at the genetic level, BIQ antibiotics are useful model compounds to be studied to understand the whole biosynthetic pathways of aromatic polyketides. This review describes the genes from the act and gra (granaticin biosynthetic gene cluster in S. violaceoruber Tü22) clusters involved in post-PKS modifying (tailoring) steps to complete BIQ biosynthesis.
A multichannel electromagnetic flowmeter telemetry system. (1972)

An eight-channel biomedical telemetry system provides four channels of blood flow measurements in addition to blood-pressure and EKG data. Emphasis is placed on the amplifiers and signal conditioning circuitry required for interfacing of the electromagnetic flow transducers with the transmission and modulation subsystems. The large number of data channels permits measurement of flow distribution as well as total cardiac output. The batteries and electronics for four channels (blood flow) weigh about 500 g and have a volume of 250 cu cm.
Buffer constraints for rate-distortion optimization in mobile video communications (2006)

In this contribution, a theoretical model of buffer constraints for rate-distortion (R-D) optimization in mobile video communications is presented and analyzed. The analytical model is based on quantitative buffer underflow time and allows for various video transmission scenarios over ad-hoc networks. By considering the play-out probability and the actual "filling" state of the buffer, the constraints estimate the packet loss effects on the displayed video due to buffer underflow. The distortions in the video due to these buffer errors are then categorized and the overall increment in the R-D performance is substantiated. Furthermore, the model accounts for other key implementation issues and the dynamic changes in real-time ad-hoc channel conditions.
TSC1 regulates the balance between effector and regulatory T cells (2013)

Mammalian target of rapamycin (mTOR) plays a crucial role in the control of T cell fate determination; however, the precise regulatory mechanism of the mTOR pathway is not fully understood. We found that T cell-specific deletion of the gene encoding tuberous sclerosis 1 (TSC1), an upstream negative regulator of mTOR, resulted in augmented Th1 and Th17 differentiation and led to severe intestinal inflammation in a colitis model. Conditional Tsc1 deletion in Tregs impaired their suppressive activity and expression of the Treg marker Foxp3 and resulted in increased IL-17 production under inflammatory conditions. A fate-mapping study revealed that Tsc1-null Tregs that lost Foxp3 expression gained a stronger effector-like phenotype compared with Tsc1-/- Foxp3+ Tregs. Elevated IL-17 production in Tsc1-/- Treg cells was reversed by in vivo knockdown of the mTOR target S6K1. Moreover, IL-17 production was enhanced by Treg-specific double deletion of Tsc1 and Foxo3a. Collectively, these studies suggest that TSC1 acts as an important checkpoint for maintaining immune homeostasis by regulating cell fate determination.
A novel chitosan CpG nanoparticle regulates cellular and humoral immunity of mice. (2006)

CpG-CNP can significantly promote cellular and humoral immunity and resistance of mice against E. coil infection, and can be utilized as an effective adjuvant to improve the immunoprotection and resistance of porcine against infectious disease.
The Bkb (Bamford-Kowal-Bench) Sentence Lists for Partially-Hearing Children (1979)

Linguistic guidelines for the design of sentences for speech audiometry with children are described, and new lists of test sentences which are based on such guidelines--the Bamford-Kowal-Bench Sentence Lists for Children--are introduced. Audiometric data relating to the use of the new lists are presented and discussed.
Predictive and adaptive bandwidth reservation for hand-offs in QoS-sensitive cellular networks (1998)

How to control hand-off drops is a very important Quality-of-Service (QoS) issue in cellular networks. In order to keep the hand-off dropping probability below a pre-specified target value (thus providing a probabilistic QoS guarantee), we design and evaluate predictive and adaptive schemes for the bandwidth reservation for the existing connections' handoffs and the admission control of new connections.We first develop a method to estimate user mobility based on an aggregate history of hand-offs observed in each cell. This method is then used to predict (probabilistically) mobiles' directions and hand-off times in a cell. For each cell, the bandwidth to be reserved for hand-offs is calculated by estimating the total sum of fractional bandwidths of the expected hand-offs within a mobility-estimation time window. We also develop an algorithm that controls this window for efficient use of bandwidth and effective response to (1) time-varying traffic/mobility and (2) inaccuracy of mobility estimation. Three different admission-control schemes for new connection requests using this bandwidth reservation are proposed. Finally, we evaluate the performance of the proposed schemes to show that they meet our design goal and outperform the static reservation scheme under various scenarios.
Caspase-3 has a nonapoptotic function in erythroid maturation (2004)

Caspase-3 plays a central role in apoptosis. It is also activated in normal erythropoiesis, with its activity peaking early during development (erythroid colony-forming unit [CFU-E] stage). In the present study, we have reduced the expression and subsequent enzymatic activity of caspase-3 by transfection of small interfering RNA (siRNA) directed to caspase-3 in a differentiating human erythroid culture system. We find that siRNA treatment yields a 50% reduction in cells that undergo enucleation with no change in the fraction of cells that undergo apoptosis, measured throughout the culture. Furthermore, a substantial fraction of treated cells are unable to complete the transition from pronormoblasts to basophilic normoblasts. These results demonstrate that caspase-3 is required for efficient erythropoiesis in this model system.
Mutations conferring resistance to phenamil and amiloride, inhibitors of sodium-driven motility of Vibrio parahaemolyticus (1999)

The bacterial flagellum is powered by a rotary motor capable of turning the helical flagellar propeller at very high speeds. Energy to drive rotation is derived from the transmembrane electrochemical potential of specific ions. Ions passing through a channel component are thought to generate the force to power rotation. Two kinds of motors, dependent on different coupling ions, have been described: proton-driven and sodium-driven motors. There are four known genes encoding components of the sodium-powered polar flagellar motor in Vibrio parahaemolyticus. Two, which are characterized here, are homologous to genes encoding constituents of the proton-type motor (motA and motB), and two encode components unique to the sodium-type motor (motX and motY). The sodium-channel-blocking drugs phenamil and amiloride inhibit rotation of the polar flagellum and therefore can be used to probe the architecture of the motor. Mutants were isolated that could swim in the presence of phenamil or amiloride. The majority of the mutations conferring phenamil-resistant motility alter nucleotides in the motA or motB genes. The resultant amino acid changes localize to the cytoplasmic face of the torque generator and permit identification of potential sodium-interaction sites. Mutations that confer motility in the presence of amiloride do not alter any known component of the sodium-type flagellar motor. Thus, evidence supports the existence of more than one class of sodium-interaction site at which inhibitors can interfere with sodium-driven motility.