gebhart/patrepeval huggingface dataset:
Non-invasive prenatal diagnosis by massively parallel sequencing of maternal plasma DNA (2012)

The presence of foetal DNA in the plasma of pregnant women has opened up new possibilities for non-invasive prenatal diagnosis. The use of circulating foetal DNA for the non-invasive prenatal detection of foetal chromosomal aneuploidies is challenging as foetal DNA represents a minor fraction of maternal plasma DNA. In 2007, it was shown that single molecule counting methods would allow the detection of the presence of a trisomic foetus, as long as enough molecules were counted. With the advent of massively parallel sequencing, millions or billions of DNA molecules can be readily counted. Using massively parallel sequencing, foetal trisomies 21, 13 and 18 have been detected from maternal plasma. Recently, large-scale clinical studies have validated the robustness of this approach for the prenatal detection of foetal chromosomal aneuploidies. A proof-of-concept study has also shown that a genome-wide genetic and mutational map of a foetus can be constructed from the maternal plasma DNA sequencing data. These developments suggest that the analysis of foetal DNA in maternal plasma would play an increasingly important role in future obstetrics practice. It is thus a priority that the ethical, social and legal issues regarding this technology be systematically studied.
What Can Be Predicted from Six Seconds of Driver Glances? (2017)

We consider a large dataset of real-world, on-road driving from a 100-car naturalistic study to explore the predictive power of driver glances and, specifically, to answer the following question: what can be predicted about the state of the driver and the state of the driving environment from a 6-second sequence of macro-glances? The context-based nature of such glances allows for application of supervised learning to the problem of vision-based gaze estimation, making it robust, accurate, and reliable in messy, real-world conditions. So, it's valuable to ask whether such macro-glances can be used to infer behavioral, environmental, and demographic variables? We analyze 27 binary classification problems based on these variables. The takeaway is that glance can be used as part of a multi-sensor real-time system to predict radio-tuning, fatigue state, failure to signal, talking, and several environment variables.
Coordination of immunoglobulin DJH transcription and D-to-JH rearrangement by promoter-enhancer approximation. (1991)

The genes that encode the variable regions of immunoglobulin (Ig) heavy chains are encoded by three DNA segments: VH, D, and JH. During B-cell development these segments are brought together by a pair of site-specific DNA rearrangements. The first of these joins a D segment to a JH segment; the second brings a VH segment in apposition to a DJH unit. B-cell precursors that have undergone D-to-JH joining express transcripts that initiate at the 5' flanks of rearranged D segments (DJH transcription). In this study we have examined the coordination of D-to-JH rearrangement and DJH transcription. The B-lymphoid progenitor cell line HAFTL-1 cell clone, joining of distal D segments (DSP2 and DFL16) to JH is accompanied by an increase in the steady-state level of transcripts initiating 5' of the D coding region. Steady-state transcription of a DSP2 gene segment was undetectable prior to rearrangement and was observed to increase at least 20-fold upon joining to JH. In contrast, transcription from the 5' flank of DQ52, which lies within 700 bp of the JH cluster, was detected prior to rearrangement and did not increase significantly after rearrangement. The 5' flank of a DSP2 segment was found to support expression of a heterologous gene upon transfection into B progenitor cell lines. Expression from this DSP2 promoter was at least 30-fold higher in the presence of the Ig heavy-chain enhancer, in either orientation, than in its absence. A DNA fragment spanning the interval from -165 to +19 bp relative to the major DSP2 transcriptional start site retained enhancer-dependent promoter activity. These observations imply that activation of DSP12JH and DFL16JH transcription is coordinated with D-to-JH rearrangement by approximation of enhancer-dependent D promoter elements to the Ig heavy-chain enhancer. This interpretation is consistent with our observation that the DQ52 segment, which is closely linked to the JH cluster, is transcribed both before and after rearrangement.
In Vitro Synthesis of Human Brain Proteins Including Tubulin and Actin by Purified Postmortem Polysomes (1981)

Polysomes were prepared from human brain tissue 2-6 h postmortem; the polysomes were active in a cell-free protein synthesis system containing rabbit reticulocyte factors. Protein synthesis was totally dependent upon added MgCl2, ATP, the reticulocyte factor fraction, and the human polysome fraction. Human brain proteins synthesized in the presence of L-[35S]methionine were analyzed by one- and two-dimensional polyacrylamide gel electrophoresis. Over 250 proteins were synthesized and they extended in size up to 250,000 d; many of the most abundant native human brain proteins were synthesized, including tubulin and actin. It was shown that human brain alpha and beta tubulin and actin isomers synthesized in vitro from human postmortem polysomes have the same apparent molecular weights and isoelectric points as the corresponding proteins synthesized by rat polysomes from fresh cortices. The corresponding tubulin and actin synthesized by human and rat brain polysomes also yield the same radioactive methionine-containing peptides after digestion with Staphylococcus aureus V8 protease. These analyses indicate that postmortem polysomes contain active messenger RNA which can direct the partial and/or complete synthesis of actin and tubulin subunits and other human brain proteins.
Hemorrhage and Large Lipid-Rich Necrotic Cores Are Independently Associated With Thin or Ruptured Fibrous Caps (2009)

Hemorrhage and larger %lipid-rich/necrotic core were independently associated with a thin or ruptured fibrous cap status at an early to advanced stage of carotid atherosclerosis.
The Motor Protein KIF14 Inhibits Tumor Growth and Cancer Metastasis in Lung Adenocarcinoma (2013)

The motor protein kinesin superfamily proteins (KIFs) are involved in cancer progression. The depletion of one of the KIFs, KIF14, might delay the metaphase-to-anaphase transition, resulting in a binucleated status, which enhances tumor progression; however, the exact correlation between KIF14 and cancer progression remains ambiguous. In this study, using loss of heterozygosity and array comparative genomic hybridization analyses, we observed a 30% loss in the regions surrounding KIF14 on chromosome 1q in lung adenocarcinomas. In addition, the protein expression levels of KIF14 in 122 lung adenocarcinomas also indicated that approximately 30% of adenocarcinomas showed KIF14 down-regulation compared with the expression in the bronchial epithelial cells of adjacent normal counterparts. In addition, the reduced expression of KIF14 mRNA or proteins was correlated with poor overall survival (P = 0.0158 and <0.0001, respectively), and the protein levels were also inversely correlated with metastasis (P<0.0001). The overexpression of KIF14 in lung adenocarcinoma cells inhibited anchorage-independent growth in vitro and xenograft tumor growth in vivo. The overexpression and silencing of KIF14 also inhibited or enhanced cancer cell migration, invasion and adhesion to the extracellular matrix proteins laminin and collagen IV. Furthermore, we detected the adhesion molecules cadherin 11 (CDH11) and melanoma cell adhesion molecule (MCAM) as cargo on KIF14. The overexpression and silencing of KIF14 enhanced or reduced the recruitment of CDH11 in the membrane fraction, suggesting that KIF14 might act through recruiting adhesion molecules to the cell membrane and modulating cell adhesive, migratory and invasive properties. Thus, KIF14 might inhibit tumor growth and cancer metastasis in lung adenocarcinomas.
Central role of mitochondria in drug-induced liver injury (2011)

A frequent mechanism for drug-induced liver injury (DILI) is the formation of reactive metabolites that trigger hepatitis through direct toxicity or immune reactions. Both events cause mitochondrial membrane disruption. Genetic or acquired factors predispose to metabolite-mediated hepatitis by increasing the formation of the reactive metabolite, decreasing its detoxification, or by the presence of critical human leukocyte antigen molecule(s). In other instances, the parent drug itself triggers mitochondrial membrane disruption or inhibits mitochondrial function through different mechanisms. Drugs can sequester coenzyme A or can inhibit mitochondrial β-oxidation enzymes, the transfer of electrons along the respiratory chain, or adenosine triphosphate (ATP) synthase. Drugs can also destroy mitochondrial DNA, inhibit its replication, decrease mitochondrial transcripts, or hamper mitochondrial protein synthesis. Quite often, a single drug has many different effects on mitochondrial function. A severe impairment of oxidative phosphorylation decreases hepatic ATP, leading to cell dysfunction or necrosis; it can also secondarily inhibit ß-oxidation, thus causing steatosis, and can also inhibit pyruvate catabolism, leading to lactic acidosis. A severe impairment of β-oxidation can cause a fatty liver; further, decreased gluconeogenesis and increased utilization of glucose to compensate for the inability to oxidize fatty acids, together with the mitochondrial toxicity of accumulated free fatty acids and lipid peroxidation products, may impair energy production, possibly leading to coma and death. Susceptibility to parent drug-mediated mitochondrial dysfunction can be increased by factors impairing the removal of the toxic parent compound or by the presence of other medical condition(s) impairing mitochondrial function. New drug molecules should be screened for possible mitochondrial effects.
Study on the camera calibration parameters estimation using the perspective variation ratio (2003)

With 3-D vision measuring, camera calibration is necessary to calculate parameters accurately. In this paper, we present an algorithm for camera calibration using perspective ratio of a grid type frame with different line widths. It can easily estimate camera calibration parameters such as focal length, scale factor, pose, orientations, and distance. But, radial lens distortion is not modeled. The advantage of this algorithm is that it can estimate the distance of the object. To validate proposed method, we set experiments with a frame on rotator at a distance of 1,2,3,4[m] from camera and rotate the frame from -60 to 60 degrees. We have investigated the distance error affected by scale factor or different line widths and experimentally found an average scale factor that includes the least distance error with each image. The average scale factor tends to fluctuate with small variation and makes distance error decrease. Compared with classical methods that use stereo camera or two or three orthogonal planes, the proposed method is easy to use and flexible. It advances camera calibration one more step from static environments to real world such as autonomous land vehicle use
Heparanase as mediator of angiogenesis: mode of action (2001)

ABSTRACT Extracellular matrix (ECM) and basement membranes (BMs) present a physical barrier that requires enzymatic degradation during endothelial cell (EC) sprouting at early stages of angiogenesis. These multimolecular structures also serve as a storage depot for heparin‐binding angiogenic factors. Heparan sulfate proteoglycans (HSPGs) are responsible for the self‐assembly and integrity of the ECM and BM structure, as well as for sequestration of growth and differentiation factors. Recently, we reported the cloning of heparanase, an endo‐β‐ d ‐glucuronidase degrading heparan sulfate (HS), and provided direct evidence for its role in tumor metastasis. We now demonstrate that heparanase is intimately involved in angiogenesis and elucidate its mode of action. Apart from its direct involvement in ECM degradation and EC migration (vascular sprouting), heparanase releases active basic fibroblast growth factor (bFGF) from the subendothelial ECM, as well as bFGF‐stimulating HS degradation fragments from the EC surface. Interestingly, ECM‐derived HS fragments induced little or no potentiation of the growth‐promoting activity of bFGF. The angiogenic effect of heparanase was demonstrated in vivo (via the Matrigel plug assay) by showing a three‐ to fourfold increase in neovascularization induced by murine T‐lymphoma cells after stable transfection with the heparanase gene. Increased tissue vascularity was also observed in a mouse wound‐healing model in response to topical administration of recombinant heparanase. Immunohistochemical staining of human colon carcinoma tissue revealed a high expression of the heparanase protein in the endothelium of sprouting capillaries and small vessels, but not of mature quiescent blood vessels. The ability of heparanase to promote tumor angiogenesis and its involvement in tumor metastasis make it a promising target for cancer therapy.
Scalable web caching of frequently updated objects using reliable multicast (1999)

Frequently updated web objects reduce the benefit of caching, increase the problem of cache inconsistency, and aggravate the inefficiency of the conventional &amp;quot;repeated unicast&amp;quot; delivery model. In this paper, we investigate multicast invalidation and delivery of popular, frequently updated objects to web cache proxies. Our protocol, MMO, groups objects into volumes, each of which maps to one IP multicast group. We show that, by forming volumes of the appropriate size and/or object correlation, the benefit from reliable multicast outweighs the cost of delivering extraneous data as well as the overhead of multicast reliability. Moreover, tracedriven simulations show that the bandwidth saving over conventional approaches increases significantly as the audience size grows. We conclude that MMO provides efficient bandwidth utilization and service scalability, and makes strong web cache consistency for dynamic objects practical. 1. Introduction Web proxy caching [4] is critical to the conti...
Antioxidant Activity of Apple Peels (2003)

Consumption of fruits and vegetables has been shown to be effective in the prevention of chronic diseases. These benefits are often attributed to the high antioxidant content of some plant foods. Apples are commonly eaten and are large contributors of phenolic compounds in European and North American diets. The peels of apples, in particular, are high in phenolics. During applesauce and canned apple manufacture, the antioxidant-rich peels of apples are discarded. To determine if a useful source of antioxidants is being wasted, the phytochemical content, antioxidant activity, and antiproliferative activity of the peels of four varieties of apples (Rome Beauty, Idared, Cortland, and Golden Delicious) commonly used in applesauce production in New York state were investigated. The values of the peels were compared to those of the flesh and flesh + peel components of the apples. Within each variety, the total phenolic and flavonoid contents were highest in the peels, followed by the flesh + peel and the flesh. Idared and Rome Beauty apple peels had the highest total phenolic contents (588.9 +/- 83.2 and 500.2 +/- 13.7 mg of gallic acid equivalents/100 g of peels, respectively). Rome Beauty and Idared peels were also highest in flavonoids (306.1 +/- 6.7 and 303.2 +/- 41.5 mg of catechin equivalents/100 g of peels, respectively). Of the four varieties, Idared apple peels had the most anthocyanins, with 26.8 +/- 6.5 mg of cyanidin 3-glucoside equivalents/100 g of peels. The peels all had significantly higher total antioxidant activities than the flesh + peel and flesh of the apple varieties examined. Idared peels had the greatest antioxidant activity (312.2 +/- 9.8 micromol of vitamin C equivalents/g of peels). Apple peels were also shown to more effectively inhibit the growth of HepG(2) human liver cancer cells than the other apple components. Rome Beauty apple peels showed the most bioactivity, inhibiting cell proliferation by 50% at the low concentration of 12.4 +/- 0.4 mg of peels/mL. The high content of phenolic compounds, antioxidant activity, and antiproliferative activity of apple peels indicate that they may impart health benefits when consumed and should be regarded as a valuable source of antioxidants.
Metronidazole in prevention and treatment of bacteroides infections after appendicectomy. (1976)

The frequency of non-clostridial anaerobic infection was studied in 95 patients who had undergone acute appendicectomy: 49 received prophylactic metronidazole and 46 received placebo. Anaerobic infection did not develop in any of the metronidazole-treated patients, but infections did develop in nine (19%) of the 46 controls. Metronidazole is conveniently administered by suppository to patients who cannot take oral drugs. Five patients with intra-abdominal infections caused by non-clostridial anaerobes were successfully treated with metronidazole.
High frequency of yeast carriage on hands of hospital personnel (1994)

The hands of 36 nurses and 21 nonnursing hospital employees were tested by culture with a modification of the broth wash technique. Seventy-five percent of the nurses and 81% of the nonnurses were found to harbor yeasts on their hands; 58% of nurses and 38% of nonnurses were carrying Candida spp.
Artificial Neural Network model design and topology analysis for FPGA implementation of Lorenz chaotic generator (2017)

This paper presents an Artificial Neural Network (ANN) design for a chaotic generator, and the training performances for a three layer ANN architecture with different number of hidden neurons. Chaotic systems can be synchronized and used for secure communication. Chaotic systems such as Lorenz attractor, Rossler attractor and Chen's system are generally implemented directly based on their definitions represented by a unique group of ordinary differential equations (ODEs). An feed forward ANN can be trained using the output values of a chaotic system. The training process is carried out on a computer and the weights are generated for all neurons in an ANN architecture. These weights are then used for a trained ANN architecture model to generate the expected output for the target chaotic system. The complexity of the ANN architecture defines the implementation cost and speed. Therefore it is beneficial to use less number of hidden neurons to achieve the target training performance. Lorenz attractor has its significance in studying chaotic systems and is used as the design subject in this paper. The 3-layer ANN has one input, one hidden and one output layer. The ANN architecture with 1 to 16 hidden neurons is designed and trained respectively using MATLAB Neural Network Toolbox with three training algorithms: Levenberg-Marquardt, Scaled Conjugate Gradient algorithm and Bayesian Regulation. The optimized ANN architecture can be used to improve the efficiency of the fixed-point implementation on an Field Programmable Gates Array (FPGA) device.
Uncoupling of mRNA 3' cleavage and polyadenylation by expression of a hammerhead ribozyme in yeast. (1994)

An artificial messenger RNA containing a derivative of a tobacco ringspot virus ribozyme was expressed in the bakers' yeast Saccharomyces cerevisiae. This mRNA was able to cleave itself efficiently in vivo. Using this system, the two steps of mRNA 3' processing, i.e. cleavage and the addition of a poly(A) tail, can be separated in yeast in vivo. The ribozyme-cleaved transcript was shown to be polyadenylated. The poly(A) tail length was similar to the poly(A) tail length of an endogenous yeast mRNA. Therefore, cleavage of the precursor RNA at the polyadenylation site and the addition of adenosine residues to the 5' product require independent cellular machineries in yeast and can be separately analyzed. This is in contrast to higher eukaryotes where both processes are coupled.
Transcardiac serotonin concentration is increased in selected patients with limiting angina and complex coronary lesion morphology. (1989)

Serotonin is released by activated platelets and may act as a mediator to initiate or sustain certain unstable syndromes of ischemic heart disease in humans. To determine whether or not serotonin concentration increases across the coronary bed in patients with severe, limiting angina, we measured central aortic and coronary sinus serotonin concentrations by a sensitive radioenzymatic assay in 39 patients with coronary artery disease and 13 patients with minimal or no coronary artery lesions as detected by arteriography. Although no difference existed in the mean aortic or coronary sinus serotonin concentrations between these two groups, elevated coronary sinus serotonin concentrations were detected in 23% of those with coronary artery disease. The coronary sinus and aortic serotonin concentration difference was greater in patients with significant coronary artery disease (0.6 +/- 6.62 ng/ml) compared with patients without significant coronary artery disease (-5.6 +/- 10.32 ng/ml) (mean +/- SD) (p less than 0.05). Further analysis revealed that patients with eccentric, irregular coronary artery lesions or intraluminal filling defects had a significantly elevated coronary sinus and aortic serotonin difference (3.1 +/- 5.54 ng/ml) compared with those with smooth concentric lesions (-1.9 +/- 6.61 ng/ml) (p less than 0.02). These data suggest that serotonin is released into the coronary circulation of some patients with coronary artery disease, especially those with frequent angina and complex coronary lesions. Although serotonin may be released in some patients with coronary artery disease, the specific pathophysiologic role of serotonin in the development or perpetuation of certain coronary syndromes in humans remains to be determined.
Lentivirus-based genetic manipulations of cortical neurons and their optical and electrophysiological monitoring in vivo (2004)

It is becoming increasingly clear that single cortical neurons encode complex and behaviorally relevant signals, but efficient means to study gene functions in small networks and single neurons in vivo are still lacking. Here, we establish a method for genetic manipulation and subsequent phenotypic analysis of individual cortical neurons in vivo. First, lentiviral vectors are used for neuron-specific gene delivery from alpha-calcium/calmodulin-dependent protein kinase II or Synapsin I promoters, optionally in combination with gene knockdown by means of U6 promoter-driven expression of short-interfering RNAs. Second, the phenotypic analysis at the level of single cortical cells is carried out by using two-photon microscopy-based techniques: high-resolution two-photon time-lapse imaging is used to monitor structural dynamics of dendritic spines and axonal projections, whereas cellular response properties are analyzed electrophysiologically by two-photon microscopy directed whole-cell recordings. This approach is ideally suited for analysis of gene functions in individual neurons in the intact brain.