gebhart/patrepeval huggingface dataset:
Non-invasive prenatal diagnostics of aneuploidy using next-generation DNA sequencing technologies, and clinical considerations (2012)

Rapidly developing next-generation sequencing (NGS) technologies produce a large amount of data across the whole human genome and allow a large number of DNA samples to be analyzed simultaneously. Screening cell-free fetal DNA (cffDNA) obtained from maternal blood using NGS technologies has provided new opportunities for non-invasive prenatal diagnosis (NIPD) of fetal aneuploidies. One of the major challenges to the analysis of fetal abnormalities is the development of accurate and reliable algorithms capable of analyzing large numbers of short sequence reads. Several such algorithms have recently been developed. Here, we provide a review of recent NGS-based NIPD methods as well as the available algorithms for short-read sequence analysis. We furthermore introduce the practical application of these algorithms for the detection of different types of fetal aneuploidies, and compare the performance, cost and complexity of each approach for clinical deployment. Our review identifies several main technologies and trends in NGS-based NIPD. The main considerations for clinical development for NIPD and screening tests using DNA sequencing are: accuracy, intellectual property, cost and the ability to screen for a wide range of chromosomal abnormalities and genetic defects. The cost of the diagnostic test depends on the sequencing method, diagnostic algorithm and volume of the tests. If the cost of sequencing equipment and reagents remains at or around current levels, targeted approaches for sequencing-based aneuploidy testing and SNP-based methods are preferred.
Genistein potentiates the radiation effect on prostate carcinoma cells. (2001)

We have shown previously that genistein, the major isoflavone in soybean, inhibited the growth of human prostate cancer cells in vitro by affecting the cell cycle and inducing apoptosis. To augment the effect of radiation for prostate carcinoma, we have now tested the combination of genistein with photon and neutron radiation on prostate carcinoma cells in vitro. The effects of photon or neutron radiation alone or genistein alone or both combined were evaluated on DNA synthesis, cell growth, and cell ability to form colonies. We found that neutrons were more effective than photons for the killing of prostate carcinoma cells in vitro, resulting in a relative biological effectiveness of 2.6 when compared with photons. Genistein at 15 microM caused a significant inhibition in DNA synthesis, cell growth, and colony formation in the range of 40-60% and potentiated the effect of low doses of 200-300 cGy photon or 100-150 cGy neutron radiation. The effect of the combined treatment was more pronounced than with genistein or radiation alone. Our data indicate that genistein combined with radiation inhibits DNA synthesis, resulting in inhibition of cell division and growth. Genistein can augment the effect of neutrons at doses approximately 2-fold lower than photon doses required to observe the same efficacy. These studies suggest a potential of combining genistein with radiation for the treatment of localized prostate carcinoma.
Highly Efficient Synthesis of <i>O</i>-(2,4-Dinitrophenyl)hydroxylamine. Application to the Synthesis of Substituted <i>N</i>-Benzoyliminopyridinium Ylides (2003)

An efficient two-step synthesis of O-(2,4-dinitrophenyl)hydroxylamine is described along with a comparison of its aminating efficiency with O-mesitylenesulfonylhydroxylamine (MSH). It was used in an expedient N-amination/benzoylation procedure involving various substituted pyridines, leading to polysubstituted N-benzoyliminopyridinium ylides, and the scope of its amination power was studied.
Cdk5 Modulation of Mitogen-activated Protein Kinase Signaling Regulates Neuronal Survival (2006)

Cdk5, a cyclin-dependent kinase, is critical for neuronal development, neuronal migration, cortical lamination, and survival. Its survival role is based, in part, on "cross-talk" interactions with apoptotic and survival signaling pathways. Previously, we showed that Cdk5 phosphorylation of mitogen-activated protein kinase kinase (MEK)1 inhibits transient activation induced by nerve growth factor (NGF) in PC12 cells. To further explore the nature of this inhibition, we studied the kinetics of NGF activation of extracellular signal-regulated kinase (Erk)1/2 in cortical neurons with or without roscovitine, an inhibitor of Cdk5. NGF alone induced an Erk1/2-transient activation that peaked in 15 min and declined rapidly to baseline. Roscovitine, alone or with NGF, reached peak Erk1/2 activation in 30 min that was sustained for 48 h. Moreover, the sustained Erk1/2 activation induced apoptosis in cortical neurons. Significantly, pharmacological application of the MEK1 inhibitor PD98095 to roscovitine-treated cortical neurons prevented apoptosis. These results were also confirmed by knocking down Cdk5 activity in cortical neurons with Cdk5 small interference RNA. Apoptosis was correlated with a significant shift of phosphorylated tau and neurofilaments from axons to neuronal cell bodies. These results suggest that survival of cortical neurons is also dependent on tight Cdk5 modulation of the mitogen-activated protein kinase signaling pathway.
Rating Journals in Health Care Administration The Use of Bibliometric Measures (1993)

*From the Wishard Memorial Hospital, Indianapolis, IN. †From the Graduate Program in Health Administration, School of Public and Environmental Affairs, Indiana University, Indianapolis, IN. ‡From the Regenstrief Institute for Health Care §From the Department of Medicine, School of Medicine, Indiana University, Indianapolis, IN.
Clinical Efficacy of Kitecko Ultrasonic Conductor (1989)

A homogeneous synthetic polymer block (Kitecko) was evaluated for ultrasound imaging of small parts, superficial structures, and the pediatric patient. The block is intended to be used as an offset and replaces the traditional way of scanning with water paths, fluid-filled surgical gloves or IV bags. A randomized paired comparison of the Kitecko pad conductor and a water path system (IV bag) was performed. One hundred pediatric and adult patients were scanned using both conductors. The images were encoded and subsequently evaluated for image quality, including artifact, attenuation, resolution, and distortion. A statistical analysis showed significantly higher scores (P less than .01) with the Kitecko substance when compared to water path scanning when evaluating for reverberation artifact, scatter artifact, and spatial resolution.
Transmission Electron Microscope Studies of LiNi[sub 1/3]Mn[sub 1/3]Co[sub 1/3]O[sub 2] before and after Long-Term Aging at 70°C (2008)

LiNi1/3Mn1/3Co1/3O2 is a potential cathode material for high-power applications in lithium-ion batteries. While cation ordering on a sqrt(3)×sqrt(3) R30° in-plane superlattice was proposed for the layered structure, the experimental data do not fully support this model. Here, we present a systematic electron diffraction study of LiNi1/3Mn1/3Co1/3O2 in the pristine state and after aging. Our results show that a mixture of different phases in the starting material transforms to the O3-type phase and the cubic spinel phase after aging, accompanied by an increase in the percentage of polycrystals.
Ultrasonic Key Recognition: Security Algorithm for Pre-composed High Frequency Sound as a Mode of Unlocking a Security Lock (2012)

Ultrasonic key recognition is a system that uses high-frequency sound as a mode of unlocking a security lock. The password is composed by the user using high-frequency sound and is then embedded in a music file that will serve as the "key". A music player will be used to play and emit this "key" and it is then being detected by a device which will serve as the "lock". The lock's built-in microphone will catch the sound and is then processed and analyzed by the system to compare it with the pre-composed key. Audio fingerprinting algorithm is used in processing and analysis of the sound. If a match is found, the system will allow access, otherwise if not.
Synthesis of 9,11-disubstituted 19-nor-steroids. (1975)

Reaction of a 9α-methyl-11-oxoestrone derivative (I) with methylmagnesium bromide gave the 11α-methyl-11β-hydroxy-compound (II). This could be dehydrated with acid to an olefin, shown to be an 11,11-dimethyl-Δ8,9-steroid, or converted into its acetate and pyrolysed to give a 9α-methyl-11-methylene derivative as the major product. Hydrogenation of this last material gave a 9α, 11β-dimethyl derivative. All three substituted skeletons were converted into other 19-nor-compounds, in particular, the 17α-ethynyl-17β-hydroxyl-4-en-3-ones (XVII), (XXV), and (XXXIX).
Built-In Self-Test of Configurable Cores in SoCs Using Embedded Processor Dynamic Reconfiguration (2005)

Built-In Self-Test (BIST) provides an effective way to test configurable cores in System-on-Chip (SoC) implementations. We present a case study of the use of dynamic reconfiguration from an embedded processor core to implement BIST for the programmable logic and routing resources in configurable cores in commercially available SoCs. Experimental results from actual implementations include speed-up and memory savings obtained and compared to traditional BIST approaches for configurable cores. 1
Lability of Odor Pleasantness: Influence of Mere Exposure (1978)

Subjects judged the pleasantness of various odorants both before and after intensive exposure to a pleasant, a neutral, or an unpleasant odorant, or a short period of relaxation. Intensive exposure comprised a 30 min task of intensity discrimination. The outcome implied that exposure to an odorant can modify its own pleasantness readily, but not so readily that of other odorants. Exposure to the pleasant lemon-smelling substance citral reduced its subsequent pleasantness, whereas exposure to the unpleasant rancid-smelling substance isobutyric acid reduced its subsequent unpleasantness. The results were compatible with the notion of affective habituation. Variability of the pleasantness judgments was uniform throughout the hedonic continuum. That is, subjects agreed as much about hedonically neutral odors as about extremely pleasant and unpleasant odors.
Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment (1994)

This study reports improvements in two of the key steps, lysis of indigenous cells and DNA purification, required for achieving a rapid nonselective protocol for extracting nucleic acids directly from sodium dodecyl sulfate (SDS)-treated sediment rich in organic matter. Incorporation of bead-mill homogenization into the DNA extraction procedure doubled the densitometrically determined DNA yield (11.8 micrograms of DNA.g [dry weight] of sediment-1) relative to incorporation of three cycles of freezing and thawing (5.2 micrograms of DNA.g [dry weight] of sediment-1). The improved DNA extraction efficiency was attributed to increased cell lysis, measured by viable counts of sediment microorganisms which showed that 2 and 8%, respectively, survived the bead-mill homogenization and freeze-thaw procedures. Corresponding measurements of suspensions of viable Bacillus endospores demonstrated that 2 and 94% of the initial number survived. Conventional, laser scanning epifluorescence phase-contrast, and differential interference-contrast microscopy revealed that small coccoid bacterial cells (1.2 to 0.3 micron long) were left intact after combined SDS and bead-mill homogenization of sediment samples. Estimates of the residual fraction of the fluorescently stained cell numbers indicated that 6% (2.2 x 10(8) cells.g [dry weight] of sediment-1) of the original population (3.8 x 10(9) cells.g [dry weight] of sediment-1) remained after treatment with SDS and bead-mill homogenization. Thus, lysis of total cells was less efficient than that of cells which could be cultured. The extracted DNA was used to successfully amplify nahR, the regulatory gene for naphthalene catabolism in Pseudomonas putida G7, by PCR.(ABSTRACT TRUNCATED AT 250 WORDS)
Beauty (Essay 8 of Seeing: When Art and Faith Intersect) (2002)

Excerpt: "Beauty as a concept has given twentieth century writers, especially art critics and art historians, a great deal of difficulty. Why is this so?Answering would take several volumes--! will settle for less. The traditional idea of beauty has all the trappings of a universal concept. For Plato, one of the earliest and most prominent supporters of such universals, beauty, along with other concepts, had the mind of the creator as its source. For much of Christianity's existence Plato's idea of beauty was accepted--with some alterations. For one, the creator became Yahweh, creator of the universe. Secondly, though spiritual beauty might inhabit physical beauty, the reverse was not necessarily the case."
<i>In vitro</i>volatile organic compound profiling using GC×GC-TOFMS to differentiate bacteria associated with lung infections: a proof-of-concept study (2016)

Chronic pulmonary infections are the principal cause of morbidity and mortality in individuals with cystic fibrosis (CF). Due to the polymicrobial nature of these infections, the identification of the particular bacterial species responsible is an essential step in diagnosis and treatment. Current diagnostic procedures are time-consuming, and can also be expensive, invasive and unpleasant in the absence of spontaneously expectorated sputum. The development of a rapid, non-invasive methodology capable of diagnosing and monitoring early bacterial infection is desired. Future visions of real-time, in situ diagnosis via exhaled breath testing rely on the differentiation of bacteria based on their volatile metabolites. The objective of this proof-of-concept study was to investigate whether a range of CF-associated bacterial species (i.e. Pseudomonas aeruginosa, Burkholderia cenocepacia, Haemophilus influenzae, Stenotrophomonas maltophilia, Streptococcus pneumoniae and Streptococcus milleri) could be differentiated based on their in vitro volatile metabolomic profiles. Headspace samples were collected using solid phase microextraction (SPME), analyzed using comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC×GC-TOFMS) and evaluated using principal component analysis (PCA) in order to assess the multivariate structure of the data. Although it was not possible to effectively differentiate all six bacteria using this method, the results revealed that the presence of a particular pattern of VOCs (rather than a single VOC biomarker) is necessary for bacterial species identification. The particular pattern of VOCs was found to be dependent upon the bacterial growth phase (e.g. logarithmic versus stationary) and sample storage conditions (e.g. short-term versus long-term storage at -18 °C). Future studies of CF-associated bacteria and exhaled breath condensate will benefit from the approaches presented in this study and further facilitate the production of diagnostic tools for the early detection of bacterial lung infections.
Bisphosphonate-modified biomaterials for drug delivery and bone tissue engineering (2015)

Calcium-binding properties of BPs can be successfully extended via different conjugation strategies not only for purposes of bone targeting, but also in supramolecular assembly affording either new nanocarriers or bulk nanocomposite scaffolds. Interaction between carrier-linked BPs and drug molecules should also be considered for the control of release of these molecules and their optimized delivery. Bone-targeting properties of BP-functionalized nanomaterials should correspond to bone adhesive properties of their bulk analogs.
Strategies to Eliminate HBV Infection (2014)

Chronic HBV infection is a major public health concern affecting over 240 million people worldwide. Although suppression of HBV replication is achieved in the majority of patients with currently available newer antivirals, discontinuation of therapy prior to hepatitis B surface antigen loss or seroconversion is associated with relapse of HBV in the majority of cases. Thus, new therapeutic modalities are needed to achieve eradication of the virus from chronically infected patients in the absence of therapy. The basis of HBV persistence includes viral and host factors. Here, we review novel strategies to achieve sustained cure or elimination of HBV. The novel approaches include targeting the viral and or host factors required for viral persistence, and novel immune-based therapies, including therapeutic vaccines.
Catalytic site of F1-ATPase of Escherichia coli. Lys-155 and Lys-201 of the beta subunit are located near the gamma-phosphate group of ATP in the presence of Mg2+. (1991)

The catalytic site of Escherichia coli F1 was probed using a reactive ATP analogue, adenosine triphosphopyridoxal (AP3-PL). For complete loss of enzyme activity, about 1 mol of AP3-PL bound to 1 mol of F1 was estimated to be required in the presence or absence of Mg2+. About 70% of the label was bound to the alpha subunit and the rest to the beta subunit in the absence of Mg2+, and the alpha Lys-201 and beta Lys-155 residues, respectively, were the major target residues (Tagaya, M., Noumi, T., Nakano, K., Futai, M., and Fukui, T. (1988) FEBS Lett. 233, 347-351). Addition of Mg2+ decreased the AP3-PL concentration required for half-maximal inhibition, and predominant labeling of the beta subunit (beta Lys-155 and beta Lys-201) with the reagent. ATP and ADP were protective ligands in the presence and absence of Mg2+. The alpha subunit mutation (alpha Lys-201----Gln or alpha Lys-201 deletion) were active in oxidative phosphorylation. However, purified mutant F1s showed impaired low multi-site activity, although their uni-site catalyses were essentially normal. Thus alpha Lys-201 is not a catalytic residue, but may be important for catalytic cooperativity. Mutant F1s were inhibited less by AP3-PL in the absence of Mg2+, and consistent with this, modifications of their alpha subunits by AP3-PL were reduced. AP3-PL was more inhibitory to the mutant enzymes in the presence of Mg2+, and bound to the beta Lys-155 and beta Lys-201 residues of mutant F1 (alpha Lys-201----Gln). These results strongly suggest that alpha Lys-201, beta Lys-155, and beta Lys-201 are located close together near the gamma-phosphate group of ATP bound to the catalytic site, and that the two beta residues and the gamma-phosphate group become closer to each other in the presence of Mg2+.
Twelve month comparison of salmeterol and salbutamol as dry powder formulations in asthmatic patients. European Study Group. (1993)

In this study salmeterol (50 micrograms twice daily) was more effective than salbutamol (400 micrograms four times daily) in the control of asthma over three months, and more effective than salbutamol (400 micrograms twice daily) over a further nine months. Neither salmeterol nor salbutamol was associated with any worsening of control of asthma.
Pulsed ultraviolet laser deposition of SiO2 films at 248 nm (1995)

Photochemical laser-induced deposition of silicon dioxide thin films is reported with excimer laser radiation at 248 nm. A deposition rate of 0.25 A/pulse was obtained at room temperature. The deposited films were characterized by scanning electron microscopy, x-ray photoelectron spectroscopy, ellipsometry and optical microscopy. The films exhibited excellent properties (n=1.47, k=0.05) derived from ellipsometry data. The deposition required no oxidizing coreactant.
Phototaxis mutants of Chlamydomonas reinhardtii (1977)

A group of 31 mutants of Chlamydomonas reinhardtii with altered phototactic responses was isolated. Growth of all the mutants was normal and, with one exception, they had no gross morphological aberrations. One mutant produced supernumerary flagella. The mutants can be subdivided into five phenotypic classes on the basis of their abnormal responses: slow positive, no reponse, slow negative, fast negative, and variable. Random motility of the mutants was also characterized. About half were indistinguishable from wild type; the others exhibited "jerky" or "twirly" movements instead of relatively straight paths. These mutants can now be used for genetic and biochemical studies of the cellular basis of phototaxis.
Targeted disruption of the voltage-dependent calcium channel α<sub>2</sub>/δ-1-subunit (2009)

Cardiac L-type voltage-dependent Ca(2+) channels are heteromultimeric polypeptide complexes of alpha(1)-, alpha(2)/delta-, and beta-subunits. The alpha(2)/delta-1-subunit possesses a stereoselective, high-affinity binding site for gabapentin, widely used to treat epilepsy and postherpetic neuralgic pain as well as sleep disorders. Mutations in alpha(2)/delta-subunits of voltage-dependent Ca(2+) channels have been associated with different diseases, including epilepsy. Multiple heterologous coexpression systems have been used to study the effects of the deletion of the alpha(2)/delta-1-subunit, but attempts at a conventional knockout animal model have been ineffective. We report the development of a viable conventional knockout mouse using a construct targeting exon 2 of alpha(2)/delta-1. While the deletion of the subunit is not lethal, these animals lack high-affinity gabapentin binding sites and demonstrate a significantly decreased basal myocardial contractility and relaxation and a decreased L-type Ca(2+) current peak current amplitude. This is a novel model for studying the function of the alpha(2)/delta-1-subunit and will be of importance in the development of new pharmacological therapies.
Cryptosporidium parvum (2003)

I. BACKGROUND Although Cryptosporidium was first described in the laboratory mouse by Tyzzer in 1907 (1), the medical and veterinary significance of this protozoan was not fully appreciated for another 70 years. The interest in Cryptosporidium has escalated tremendously over the last two decades as reflected in the number of publications, which increased from 80 in 1983 to 3150 citations in 2002 listed in MEDLINE. The early history of Cryptosporidium is extensively documented in several review articles and book chapters published recently (2-4). Taxonomically, C. parvum belongs to the phylum Apicomplexa (possessing apical complex), class Sporozoasida (reproduce by asexual and sexual cycles, with oocyst formation), subclass Coccidiasina (life cycle involving merogony, gametogeny, and sporogeny), order Eucoccidiida (schizogony occurs), suborder Eimeriina (independent microand macrogamy develop), family Cryptosporidiae (4 naked sporozoites within occysts-no sporocyst) (5). Like other enteric coccidia of vertebrates, Cryptosporidium has a monoxenous life cycle that is primarily completed within the gastrointestinal tract of a single host. It has, however, many unique features which distinguishes Cryptosporidium from other coccidia, of which the most obvious are the lack of host and organ specificity, resistance to antimicrobial agents, ability for autoinfection, and the curious location it occupies within the host cell membrane (6).
OFDM Pulse-Shaped Waveforms for Dynamic Spectrum Access Networks (2010)

In dynamic spectrum access networks (DySPANs), users share access to available spectrum while minimizing the likelihood of harmful interference. In this demonstration we present a dynamic spectrum access network which employs a reconfigurable orthogonal frequency-division multiplexing (OFDM) based waveform. In order to avoid the creation of harmful interference, the out-of-band (OOB) emissions of the waveform are dynamically tailored to the properties of spectrum neighbours through the use of OFDM pulse shaping. The demonstration network is built upon the highly reconfigurable Iris 2.0 software radio platform and illustrates the capabilities of this platform as well as the utility of OFDM pulse shaping in the context of dynamic spectrum access networks.