gebhart/patrepeval huggingface dataset:
Comparison of 16S rRNA Gene PCR and BACTEC 9240 for Detection of Neonatal Bacteremia (2000)

Ten percent of infants born in the United States are admitted to neonatal intensive care units (NICU) annually. Approximately one-half of these admissions are from term infants (>34 weeks of gestation) at risk for systemic infection. Most of the term infants are not infected but rather have symptoms consistent with other medical conditions that mimic sepsis. The current standard of care for evaluating bacterial sepsis in the newborn is performing blood culturing and providing antibiotic therapy while awaiting the 48-h preliminary result of culture. Implementing a more rapid means of ruling out sepsis in term newborns could result in shorter NICU stays and less antibiotic usage. The purpose of this feasibility study was to compare the utility of PCR to that of conventional culture. To this end, a total of 548 paired blood samples collected from infants admitted to the NICU for suspected sepsis were analyzed for bacterial growth using the BACTEC 9240 instrument and for the bacterial 16S rRNA gene using a PCR assay which included a 5-h preamplification culturing step. The positivity rates by culture and PCR were 25 (4.6%) and 27 (4.9%) positive specimens out of a total of 548 specimens, respectively. The comparison revealed sensitivity, specificity, and positive and negative predictive values of 96.0, 99. 4, 88.9, and 99.8%, respectively, for PCR. In summary, this PCR-based approach, requiring as little as 9 h of turnaround time and blood volumes as small as 200 microl, correlated well with conventional blood culture results obtained for neonates suspected of having bacterial sepsis.
A Panel of 3 Markers Including p16, ProExC, or HPV ISH is Optimal for Distinguishing Between Primary Endometrial and Endocervical Adenocarcinomas (2010)

Endometrial and endocervical adenocarcinomas may seem histologically identical and it can be difficult to determine primary site of origin based on morphology alone. As the distinction is significant and cannot always be made on the basis of clinical findings, various immunohistochemical panels have been proposed to aid in determining site of origin. Stains for vimentin, estrogen receptor (ER), progesterone receptor (PR), monoclonal carcinoembryonic antigen, p16 and ProExC, and HPV in situ hybridization (ISH), were performed on 283 tissue microarray (TMA) cores and 38 whole sections. The TMA consisted of 214 endometrial carcinomas, 33 endocervical adenocarcinomas, and 36 problematic cases. The endometrial and endocervical carcinomas represented usual endometrioid and mucinous types, and special variants (uterine serous carcinoma, uterine clear cell carcinoma, minimal deviation endocervical adenocarcinoma, cervical small cell carcinoma, adenoid basal cell carcinoma, mesonephric carcinoma). Univariate analysis showed that 6 markers (vimentin, ER, PR, p16, ProExC, and HPV ISH) performed well in distinguishing between endocervical and endometrial origin for the usual endometrioid and mucinous types. Multivariate analysis showed that vimentin, p16, and HPV ISH are the strongest predictors of site. Using a script written in R, the diagnostic accuracy of all possible combinations of markers was evaluated and it was shown that a 3 marker panel including vimentin, ER, or PR, and an HPV marker (p16, ProExC, or HPV ISH) is optimal for determining site of origin for usual endometrial and endocervical adenocarcinomas. However, these panels do not perform well with special variant carcinomas.
[The regulation of microecological disorders of the intestines in newborn infants with perinatal pathology using the new probiotic bifidumbacterin-forte]. (1998)

The study was made on 93 newborn infants with perinatal pathology, among them infants with the perinatal lesion of the central nervous system (52), hemolytic disease of newborns (19) and conjugation jaundice (12). All newborn infants were examined for the presence of intestinal microflora in its dynamics and for the state microbiocenosis, evaluated by the rapid method based on the determination of the caseinolytic activity of fecal supernatants after the correction of normal flora with bifidumbacterin in 55 infants and with bifidumbacterin-forte in 38 infants. The comparative study of these two preparations revealed that the use of probiotics containing Bifidobacterium bifidum was mainly substitutional, promoting the colonization of the intestine by lactobacteria, which later determined the suppression opportunistic microflora. The effectiveness of bifidumbacterin-forte containing live B. bifidum, immobilized on sorbent, proved to be most pronounced.
Identification of the Template-Binding Cleft of T7 RNA Polymerase as the Site for Promoter Binding by Photochemical Cross-linking with Psoralen (1996)

We describe a novel method of photo-cross-linking DNA-binding proteins to DNA employing psoralen as a tether. We apply this method for the interaction of T7 RNA polymerase to its promoter. The crystallographic model of T7 RNA polymerase shows a cleft formed by the palm, thumb, and fingers domains. It was proposed that template DNA binds in the cleft. Here we directly and positively identify, in solution, the cleft as the seat of template binding. We photo-cross-linked a 23 bp promoter DNA to T7 RNA polymerase. We then determined the masses of cross-linked tryptic peptides by mass spectrometry and analyzed their amino acid composition. The cross-linked peptides were projected on the crystal structure of T7 RNA polymerase. The peptides nicely decorated the back, front, and side wall of the cleft. In a previous work [Sastry et al. (1993) Biochemistry 32, 5526-5538] we used site-specific psoralen furan-side monoadducts for cross-linking DNAs to DNA-binding proteins. We cross-linked a single-stranded 12-mer oligonucleotide to T7 RNA polymerase. We isolated and purified a DNA cross-linked tryptic peptide. We then used mass spectrometry and amino acid composition analysis to identify the location of this peptide on the T7 RNA polymerase primary sequence. In the present work we have mapped this peptide on the 3-D structure of T7 RNA polymerase. This peptide maps in the fingers domain of the polymerase. On the basis of a comparison of the map positions of peptides that cross-linked to either promoter DNA or single-stranded oligo-DNA, we propose that different functional domains may be involved in binding of double-stranded promoter DNA and nonspecific single-stranded DNA. Whereas the cleft of the polymerase is the seat of double-stranded promoter binding, the fingers domain may be used by the polymerase to grab single-stranded DNA (or RNA) in a nonspecific manner. Alternatively, the single-stranded oligo binding site may be an RNA product-binding site during transcription. The photochemical techniques we have developed [Sastry et al. (1993) Biochemistry 32, 5526-5538; this work] can be applied to other DNA-protein complexes to map DNA-binding domains.
Spatial and temporal control of fungal natural product synthesis (2014)

Despite their oftentimes-elusive ecological role, fungal natural products have, for better or worse, impacted our daily lives tremendously owing to their diverse and potent bioactive properties. This Janus-faced nature of fungal natural products inevitably ushered in a field of research dedicated towards understanding the ecology, organisms, genes, enzymes, and biosynthetic pathways that give rise to this arsenal of diverse and complex chemistry. Ongoing research in fungal secondary metabolism has not only increased our appreciation for fungal natural products as an asset but also sheds light on the pivotal role that these once-regarded "metabolic wastes" play in fungal biology, defense, and stress response in addition to their potential contributions towards human mycoses. Full orchestration of secondary metabolism requires not only the seamless coordination between temporal and spatial control of SM-associated machineries (e.g. enzymes, cofactors, intermediates, and end-products) but also integration of these machineries into primary metabolic processes and established cellular mechanisms. An intriguing, but little known aspect of microbial natural product synthesis lies in the spatial organization of both pathway intermediates and enzymes responsible for the production of these compounds. In this highlight, we summarize some major breakthroughs in understanding the genes and regulation of fungal natural product synthesis and introduce the current state of knowledge on the spatial and temporal control of fungal natural product synthesis.
Investigation of different cell types and gel carriers for cell-based intervertebral disc therapy,<i>in vitro</i>and<i>in vivo</i>studies (2011)

Biological treatment options for the repair of intervertebral disc damage have been suggested for patients with chronic low back pain. The aim of this study was to investigate possible cell types and gel carriers for use in the regenerative treatment of degenerative intervertebral discs (IVD). In vitro: human mesenchymal cells (hMSCs), IVD cells (hDCs), and chondrocytes (hCs) were cultivated in three gel types: hyaluronan gel (Durolane®), hydrogel (Puramatrix®), and tissue-glue gel (TISSEEL®) in chondrogenic differentiation media for 9 days. Cell proliferation and proteoglycan accumulation were evaluated with microscopy and histology. In vivo: hMSCs or hCs and hyaluronan gel were co-injected into injured IVDs of six minipigs. Animals were sacrificed at 3 or 6 months. Transplanted cells were traced with anti-human antibodies. IVD appearance was visualized by MRI, immunohistochemistry, and histology. Hyaluronan gel induced the highest cell proliferation in vitro for all cell types. Xenotransplanted hMSCs and hCs survived in porcine IVDs for 6 months and produced collagen II in all six animals. Six months after transplantation of cell/gel, pronounced endplate changes indicating severe IVD degeneration were observed at MRI in 1/3 hC/gel, 1/3 hMSCs/gel and 1/3 gel only injected IVDs at MRI and 1/3 hMSC/gel, 3/3 hC/gel, 2/3 gel and 1/3 injured IVDs showed positive staining for bone mineralization. In 1 of 3 discs receiving hC/gel, in 1 of 3 receiving hMSCs/gel, and in 1 of 3 discs receiving gel alone. Injected IVDs on MRI results in 1 of 3 hMSC/gel, in 3 of 3 hC/gel, in 2 of 3 gel, and in 1 of 3 injured IVDs animals showed positive staining for bone mineralization. The investigated hyaluronan gel carrier is not suitable for use in cell therapy of injured/degenerated IVDs. The high cell proliferation observed in vitro in the hyaluronan could have been a negative factor in vivo, since most cell/gel transplanted IVDs showed degenerative changes at MRI and positive bone mineralization staining. However, this xenotransplantation model is valuable for evaluating possible cell therapy strategies for human degenerated IVDs.
Ultimate quantum efficiency of a superconducting hot-electron photodetector (1998)

The quantum efficiency and current and voltage responsivities of fast hot-electron photodetectors, fabricated from superconducting NbN thin films and biased in the resistive state, have been shown to reach values of 340, 220 A/W, and 4×104 V/W, respectively, for infrared radiation with a wavelength of 0.79 μm. The characteristics of the photodetectors are presented within the general model, based on relaxation processes in the nonequilibrium electron heating of a superconducting thin film. The observed, very high efficiency and sensitivity of the superconductor absorbing the photon are explained by the high multiplication rate of quasiparticles during the avalanche breaking of Cooper pairs.
Reactions of boron trichlorides with silylamines containing silicon-hydrogen bonds (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactions of boron trichlorides with silylamines containing silicon-hydrogen bondsRobert H. NeilsonCite this: Inorg. Chem. 1980, 19, 3, 755–758Publication Date (Print):March 1, 1980Publication History Published online1 May 2002Published inissue 1 March 1980https://pubs.acs.org/doi/10.1021/ic50205a035https://doi.org/10.1021/ic50205a035research-articleACS PublicationsRequest reuse permissionsArticle Views127Altmetric-Citations12LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
CXCL12 Is a constitutive and inflammatory chemokine in the intestinal immune system (2009)

CXCL12 is expressed by normal IECs and upregulated and differentially distributed in IBD IECs. CXCR4 is expressed by IECs and LPTs, and CXCR4+ cells are significantly increased in IBD LP. CXCL12 is chemotactic for both PBTs and LPTs. Thus, CXCL12 and CXCR4 have a constitutive and inflammatory role in the intestinal mucosa and their selective therapeutic manipulation may be considered in IBD management.
A Case Study of Scaling Problems in Ship Classification (1993)

Abstract : The scaling problem is an active and challenging research topic in the area of artificial intelligence. The purpose is to solve real world problems by means of AI technologies, in cases where the complexity of representation of the real world problem is potentially combinatorial. In this paper, we present a novel approach to cope with the scaling issues in Bayesian belief networks for ship classification. The proposed approach divides the conceptual model of the complex ship classification problem into a set of small modules that work together to solve the classification problem while preserving the functionality of the original model. The possible ways of explaining sensor returns (e.g., the evidence) for some features, such as portholes along the length of a ship, are combinatorial. Thus, using an exhaustive approach, which entails the enumeration of all possible explanations, is impractical for larger problems. We present a network structure (referred to as Sequential Decomposition, SD) in which each observation is associated with a set of legitimate outcomes which are consistent with the allows one to represent feature-observation relations in a manageable way and achieve the same explanatory power as the exhaustive approach.
Data quality assessment of ungated flow cytometry data in high throughput experiments (2007)

Graphical exploratory data analytic tools are quick and useful means of assessing data quality. We propose that the described visualizations should be used as quality assessment tools and where possible, be used for quality control.
Light polarization control due to electrooptic effect (1985)

Abstract An analysis and experimental results are described for the automatic polarization control of the polarization plane of the output light from a single‐mode fiber with a standard axisymmetric core. This automatic polarization control device consists of two phase shifters made of z ‐cut LiNbO 3 exhibiting the electrooptic effect. The phase shifters are oriented with their transverse planes inclined to each other. The state of the polarization is detected by two Rochon prisms and is fed back to the phase shifters. The analysis has been done for the change of the polarization of the incident light in the polarization control device. The range of the voltage applied to the phase shifter for the control and the condition of the angle between the phase shifters are clarified. Next, experiments have been performed and the single polarization control in the desired direction has been attained. A proposal is made to simplify the control mechanism.
Inhibition of Serotonin But Not Norepinephrine Transport during Development Produces Delayed, Persistent Perturbations of Emotional Behaviors in Mice (2008)

Serotonin (5-HT) acts as a neurotransmitter, but also modulates brain maturation during early development. The demonstrated influence of genetic variants on brain function, personality traits, and susceptibility to neuropsychiatric disorders suggests a critical importance of developmental mechanisms. However, little is known about how and when developmentally perturbed 5-HT signaling affects circuitry and resulting behavior. The 5-HT transporter (5-HTT) is a key regulator of extracellular 5-HT levels and we used pharmacologic strategies to manipulate 5-HTT function during development and determine behavioral consequences. Transient exposure to the 5-HTT inhibitors fluoxetine, clomipramine, and citalopram from postnatal day 4 (P4) to P21 produced abnormal emotional behaviors in adult mice. Similar treatment with the norepinephrine transporter (NET) inhibitor, desipramine, did not adversely affect adult behavior, suggesting that 5-HT and norepinephrine (NE) do not share the same effects on brain development. Shifting our period of treatment/testing to P90/P185 failed to mimic the effect of earlier exposure, demonstrating that 5-HT effects on adult behavior are developmentally specific. We have hypothesized that early-life perturbations of 5-HT signaling affect corticolimbic circuits that do not reach maturity until the peri-adolescent period. In support of this idea, we found that abnormal behaviors resulting from postnatal fluoxetine exposure have a post-pubescent onset and persist long after reaching adult age. A better understanding of the underlying 5-HT sensitive circuits and how they are perturbed should lead to new insights into how various genetic polymorphisms confer their risk to carriers. Furthermore, these studies should help determine whether in utero exposure to 5-HTT blocking drugs poses a risk for behavioral abnormalities in later life.
Faraday Rotation Measurements on Thin Films of Regioregular Alkyl-Substituted Polythiophene Derivatives (2008)

The authors describe a magneto-optic measurement system for the determination of Faraday rotation from ultrathin films relative to a substrate reference. The setup is intrinsically immune to reciprocal effects such as circular birefringence and thermal fluctuations. Faraday rotation measurements on thin films of 3-hexyl and 3-dodecyl derivatives of regioregular polythiophene are reported. The authors show that the Faraday rotation from these films is largely dependent on the supramolecular organization within the thin films of these polymers.
Joint covariate selection and joint subspace selection for multiple classification problems (2009)

We address the problem of recovering a common set of covariates that are relevant simultaneously to several classification problems. By penalizing the sum of ℓ 2 norms of the blocks of coefficients associated with each covariate across different classification problems, similar sparsity patterns in all models are encouraged. To take computational advantage of the sparsity of solutions at high regularization levels, we propose a blockwise path-following scheme that approximately traces the regularization path. As the regularization coefficient decreases, the algorithm maintains and updates concurrently a growing set of covariates that are simultaneously active for all problems. We also show how to use random projections to extend this approach to the problem of joint subspace selection, where multiple predictors are found in a common low-dimensional subspace. We present theoretical results showing that this random projection approach converges to the solution yielded by trace-norm regularization. Finally, we present a variety of experimental results exploring joint covariate selection and joint subspace selection, comparing the path-following approach to competing algorithms in terms of prediction accuracy and running time.
Rapid MR image acquisition in the presence of background gradients (2003)

Image acquisition in magnetic resonance imaging (MRI) is based on the application of external gradients to traverse the 2D Fourier domain of the object, known as k-space. This model holds up very well provided the underlying magnetic field is highly homogeneous, however, this is often not the case, particularly for higher field MRI. The constant component of magnetic field inhomogeneity can lead to blurring or geometric shifting in rapid imaging methods, such as spiral and echo planar imaging. The gradient of this background magnetic field variation leads to a local distortion of the acquisition trajectory. This distortion can lead to local sample density variations and shifts in the k-space trajectory that can lead to signal loss. This paper presents an analysis of background gradients, their impact on image quality, and some acquisition and image reconstruction approaches to reduce their effects.
The histone deacetylase inhibitor MS-275 promotes differentiation or apoptosis in human leukemia cells through a process regulated by generation of reactive oxygen species and induction of p21CIP1/WAF1 1. (2003)

Effects of the histone deacetylase (HDAC) inhibitor MS-275 have been examined in human leukemia and lymphoma cells (U937, HL-60, K562, and Jurkat) as well as in primary acute myelogenous leukemia blasts in relation to differentiation and apoptosis. MS-275 displayed dose-dependent effects in each of the cell lines. When administered at a low concentration (e.g., 1 micro M), MS-275 exhibited potent antiproliferative activity, inducing p21(CIP1/WAF1)-mediated growth arrest and expression of differentiation markers (CD11b) in U937 cells. These events were accompanied by an increase in hypophosphorylated retinoblastoma protein and down-regulation of cell cycle-related proteins including cyclin D1. However, at higher concentrations (e.g., 5 micro M), MS-275 potently induced cell death, triggering apoptosis in approximately 70% of cells at 48 h. In contrast to other HDAC inhibitors such as apicidin, the extrinsic, receptor-mediated pathway played a minimal role in MS-275 lethality. However, MS-275 potently induced a very early (e.g., within 2 h) increase in reactive oxygen species (ROS), followed by the loss of mitochondrial membrane potential (Delta psi(m)) and cytosolic release of cytochrome c. These events culminated in activation of the caspase cascade, manifested by poly(ADP-ribose) polymerase, p21(CIP1/WAF1), p27(KIP), Bcl-2, and retinoblastoma protein degradation. MS-275 exposure also resulted in diminished expression of cyclin D1 and the antiapoptotic proteins Mcl-1 and XIAP. Administration of the free radical scavenger L-N-acetylcysteine blocked MS-275-mediated mitochondrial injury and apoptosis, suggesting a primary role for ROS generation in MS-275-associated lethality. Lastly, U937 cells stably expressing a p21(CIP1/WAF1) antisense construct were significantly more sensitive to MS-275-mediated apoptosis than controls, but they were impaired in their differentiation response. Together, these findings demonstrate that MS-275 exerts dose-dependent effects in human leukemia cells, i.e., p21(CIP1/WAF1)-dependent growth arrest and differentiation at low drug concentrations and a marked induction of ROS, mitochondrial damage, caspase activation, and apoptosis at higher concentrations.