gebhart/patrepeval huggingface dataset:
The malignant phenotype in breast cancer is driven by eIF4A1-mediated changes in the translational landscape (2015)

Human mRNA DeXD/H-box helicases are ubiquitous molecular motors that are required for the majority of cellular processes that involve RNA metabolism. One of the most abundant is eIF4A, which is required during the initiation phase of protein synthesis to unwind regions of highly structured mRNA that would otherwise impede the scanning ribosome. Dysregulation of protein synthesis is associated with tumorigenesis, but little is known about the detailed relationships between RNA helicase function and the malignant phenotype in solid malignancies. Therefore, immunohistochemical analysis was performed on over 3000 breast tumors to investigate the relationship among expression of eIF4A1, the helicase-modulating proteins eIF4B, eIF4E and PDCD4, and clinical outcome. We found eIF4A1, eIF4B and eIF4E to be independent predictors of poor outcome in ER-negative disease, while in contrast, the eIF4A1 inhibitor PDCD4 was related to improved outcome in ER-positive breast cancer. Consistent with these data, modulation of eIF4A1, eIF4B and PCDC4 expression in cultured MCF7 cells all restricted breast cancer cell growth and cycling. The eIF4A1-dependent translatome of MCF7 cells was defined by polysome profiling, and was shown to be highly enriched for several classes of oncogenic genes, including G-protein constituents, cyclins and protein kinases, and for mRNAs with G/C-rich 5'UTRs with potential to form G-quadruplexes and with 3'UTRs containing microRNA target sites. Overall, our data show that dysregulation of mRNA unwinding contributes to the malignant phenotype in breast cancer via preferential translation of a class of genes involved in pro-oncogenic signaling at numerous levels. Furthermore, immunohistochemical tests are promising biomarkers for tumors sensitive to anti-helicase therapies.
Decision Support System for Alarm Rationalization using Risk Assessment Matrix (2010)

In this paper, a Decision Support System for Alarm Rationalization using Risk Assessment Matrix (ARRAM) is proposed. When performing alarms review and classifying alarms priority, the ARRAM prototype would be used by process engineers after taking into consideration the safety impact, environmental impact and economic consequences of the hazards. The ARRAM prototype pre-determines the response time available to plant operators before the hazards occur. The objectives of this paper are two-fold: (1) To configure the alarms by using Risk Assessment Matrix and (2) To develop a prototype for classifying the alarms in oil refinery focusing on Crude Distillation Unit. The proposed ARRAM model provides a user-friendly interface for decision maker in making accurate and timely decision when rationalizing random alarms data. Preliminary results show that ARRAM is a useful tool for training new process engineers in familiarizing with alarm management system in oil refinery.
Intracavernous application of SIN-I in rabbit and man: functional and toxicological results. (1993)

The mode of action of the active metabolite SIN-I of the vasodilator prodrug molsidomine was studied in vitro and in vivo in corpus cavernosum of rabbit and man. SIN-I produces a dose-dependent relaxation of isolated human cavernous smooth muscle strips. In the rabbit, the intracavernous application of SIN-I increased the intracavernous pressure to a full erection (approximately 100 cm H2O). This response was highly reproductible. SIN-I was also injected intracavernously 6 times in five rabbits over 2 weeks; no inflammatory or fibrotic reactions were found on histology. SIN-I may be a reliable drug for the treatment of impotence without side-effects.
<title>Image Quality Enhancements For Raster Scan Lithography</title> (1988)

Raster scan lithography systems, such as scanned-laser and most E-beam mask writers, produce images through a mosaic of discrete picture elements (pixels). Image qualities of the printed mask (or wafer) are governed by the interplay of several printing variables, including size and shape of the writing spot, pitch and orientation of the pixel grid, relative intensities of pixels, and exposure characteristics of the resist. We will review the theoretical foundations of raster imaging and show how these variables affect several key measures of lithographic image quality, including minimum feature size, edge placement resolution and accuracy, dimensional uniformity, and edge roughness. We will present three quality enhancement techniques and compare their performances to that provided by a basic raster printing scheme where pixels of binary (on or off) values are printed on a cartesian grid. The first technique involves rotating the printing grid 45 degrees to the main axis of the data coordinate system. We will demonstrate that, for lithographic images where most edges are parallel to the data axes, this grid provides 41% more addressable edge positions than a non-rotated grid with the same pixel density. The second technique, adapted from computer-graphics "antialiasing" applications, involves modulating the intensity of pixels along the edges of features to finely control the shape of the aerial image. This provides a vernier mechanism for the placement of exposed edges between grid locations and results in finer effective addressability and smoother edges. Third, we will review how multiple pass printing (a.k.a. vote-taking) reduces random errors, and show how it also reduces systematic errors when certain printing parameters are alternated between passes. Finally, we will present a single printing strategy in which all three techniques are combined to yield high accuracy, high-resolution images with economic use of printing pixels.
Hereditary Spastic Paraplegia (2004)

A founder SPG4 mutation N386S was identified in the families with ADHSP originating from southern Scotland. Clinical investigation showed intrafamilial and interfamilial phenotypic variations. The genetic study demonstrated evidence of further genetic heterogeneity in ADHSP.
Bcr and Abl interaction: oncogenic activation of c-Abl by sequestering Bcr. (2003)

c-Abl tyrosine kinase is under rigorous control because of an unknown cellular inhibitor that maintains c-Abl in a relatively inactive state. Because SH2 domains are positive regulators of the nonreceptor tyrosine kinases, we tested whether this putative inhibitor would bind to an Abl SH2 protein construct and thus activate the c-Abl tyrosine kinase. Expression of a Mr 10,000 Abl SH2 protein in COS-1 and Rat-1 cells activated the tyrosine kinase activity of p145 ABL and induced both morphological transformation and foci formation in Rat-1 cells. Importantly, the R to L mutant of the FLVRES sequence of the Abl SH2 protein also activated the c-Abl tyrosine kinase and induced oncogenic transformation. Addition of the Abl kinase inhibitor STI-571 to ABL SH2-transformed Rat-1 cells inhibited tyrosine phosphorylation of p145 ABL. Overexpression of Bcr has been shown to inhibit the Bcr-Abl oncoprotein, and the endogenous Bcr protein forms a complex with c-Abl in hematopoietic cells and insect cells. Therefore, we determined whether Bcr is the putative c-Abl inhibitor that interacts with the Mr 10,000 Abl SH2 protein. Bcr expression in Rat-1 cells transformed by the Mr 10,000 Abl SH2 protein reduced the activated c-Abl tyrosine kinase activity to near normal levels and reversed the oncogenic effects (morphology changes and foci formation) seen in the Abl SH2-treated cells. We additionally demonstrated that Bcr and the Mr 10,000 Abl SH2 protein are present in a complex. We conclude from these studies that Bcr is a major tyrosine kinase inhibitor of cytoplasmic c-Abl and that procedures that sequester Bcr will release the c-Abl protein from the Bcr/c-Abl complex, which leads to c-Abl oncogenic activation.
Calvin: Deterministic or not? Free will to choose (2011)

Most shared memory systems maximize performance by unpredictably resolving memory races. Unpredictable memory races can lead to nondeterminism in parallel programs, which can suffer from hard-to-reproduce hiesenbugs. We introduce Calvin, a shared memory model capable of executing in a conventional nondeterministic mode when performance is paramount and a deterministic mode when execution repeatability is important. Unlike prior hardware proposals for deterministic execution, Calvin exploits the flexibility of a memory consistency model weaker than sequential consistency. Specifically, Calvin logically orders memory operations into strata that are compatible with the Total Store Order (TSO). Calvin is also designed with the needs of future power-aware processors in mind, and does not require any speculation support. We develop a Calvin-MIST implementation that uses an unordered coalescing write cache, multiple-write coherence protocol, and delayed (timebomb) invalidations while maintaining TSO compatibility. Results show that Calvin-MIST can execute workloads in conventional mode at speeds comparable to a conventional system (providing compatibility) or execute deterministically for a modest average slowdown of less than 20% (when determinism is valued).
Characteristics of a New Series-Resonant Converter with a Parallel Resonant Circuit (1987)

Conventional series-resonant converters suffer from wide variations in conversion frequency during constant voltage regulation, resulting in audible noise under light-load conditions. A new series-resonant converter has been developed in order to eliminate this problem. The converter uses a parallel resonant circuit with a resonant frequency of over 20 kHz installed in series with the load circuit. The output voltage is thus regulated by varying the conversion frequency in a higher area than that of a conventional series-resonant converter. An efficient, lightweight small-sized rectifier is developed using this new series-resonant converter. The rectifier unit can convert 200-volt AC to 48-volt DC and is capable of supplying an output current of 30 amps. Efficiency for 50 to 100% output current is 92%. The new rectifier is also free from any audible noise.
Antiulcerogenic effect of some plants extracts (2005)

Methanol extracts were prepared from aerial parts of 8 medicinal plants and evaluated for their potential antiulcerogenic effects using ethanol and Aspirin-induced gastric ulcerations in rats. Oral administration of the methanol extract (400 mg/kg) of Bidens bipinnata Linn., Zygophyllum album Linn. f., Plantago major Linn. (leaves) and Schouwia thebaica Webb. significantly (P< 0.01) decreased the average ulcer index with a curative ratio ranged from 100% for B. bipinnata to 58.3% for S. thebaica in the ethanol-induced gastric ulceration. Mentha microphylla C. Koch., Conyza linifolia Willd., C. dioscoridis (Linn.) Desf., Cynanchum acutum Linn. and P. major (seeds) decreased the ulcer index, however, their curative ratios were below 50% but higher than the reference drug Ranitidine (curative ratio 38.9%). B. bipinnata, Z. album and P. major (leaves) in a dose of 400 mg/kg significantly decreased the number of gastric ulcer and decreased total protein in gastric juice in aspirininduced gastric ulceration. The total acidity was significantly (P < 0.01) decreased by all tested plant extracts. Based on the decreased ulcer index, increased curative ratio, decreased number of gastric ulcers and decreased total protein and total acidity, B. bipinnata, Z. album and P. major leaves in a dose of 400 mg/kg produced a potent antiulcerogenic effect against alcoholand aspirin-induced gastric ulcer. Moderate effect was produced by S. thebaica.
Stability Study of Unmodified siRNA and Relevance to Clinical Use (2008)

RNA interference offers enormous potential to develop therapeutic agents for a variety of diseases. To assess the stability of siRNAs under conditions relevant to clinical use with particular emphasis on topical delivery considerations, a study of three different unmodified siRNAs was performed. The results indicate that neither repeated freeze/thaw cycles, extended incubations (over 1 year at 21 degrees C), nor shorter incubations at high temperatures (up to 95 degrees C) have any effect on siRNA integrity as measured by nondenaturing polyacrylamide gel electrophoresis and functional activity assays. Degradation was also not observed following exposure to hair or skin at 37 degrees C. However, incubation in fetal bovine or human sera at 37 degrees C led to degradation and loss of activity. Therefore, siRNA in the bloodstream is likely inactivated, thereby limiting systemic exposure. Interestingly, partial degradation (observed by gel electrophoresis) did not always correlate with loss of activity, suggesting that partially degraded siRNAs retain full functional activity. To demonstrate the functional activity of unmodified siRNA, EGFP-specific inhibitors were injected into footpads and shown to inhibit preexisting EGFP expression in a transgenic reporter mouse model. Taken together, these data indicate that unmodified siRNAs are viable therapeutic candidates.
Concurrent Inference Graphs (2013)

Since their popularity began to rise in the mid-2000s there has been significant growth in the number of multi-core and multi-processor computers available. Knowledge representation systems using logical inference have been slow to embrace this new technology. We present the concept of inference graphs, a natural deduction inference system which scales well on multi-core and multi-processor machines. Inference graphs enhance propositional graphs by treating propositional nodes as tasks which can be scheduled to operate upon messages sent between nodes via the arcs that already exist as part of the propositional graph representation. The use of scheduling heuristics within a prioritized message passing architecture allows inference graphs to perform very well in forward, backward, bi-directional, and focused reasoning. Tests demonstrate the usefulness of our scheduling heuristics, and show significant speedup in both best case and worst case inference scenarios as the number of processors increases.
Reduction of aromatic nitro-compounds to amines with sodium borohydride–copper(<scp>II</scp>) acetylacetonate (1979)

The reduction of aromatic nitro-compounds by NaBH4 in ethanol in the presence of various transition metal cetylacetonates has been investigated. Copper(II) acetylacetonate was found to be the most effective catalyst for reduction to the corresponding amines. This reaction appears to proceed through a hydride metal complex.
Cache designs for energy efficiency (2002)

Caches usually consume a significant amount of energy in modern microprocessors (e.g. superpipelined or superscalar processors). In this paper, we examine contemporary cache design techniques and provide an analytical model for estimating cache energy consumption. We also present several novel techniques for designing energy-efficient caches, which include block buffering, cache sub-banking, and Gray code addressing. Experimental results suggest that both the block buffering and Gray code addressing techniques are ideal for instruction cache designs which tend to be accessed in a consecutive sequence. Cache sub-banking is ideal for both instruction and data caches. Overall, these techniques can achieve an order of magnitude energy reduction on caches.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Biochemical and Immunological Effects of <i>Listeria monocytogenes</i> Hemolysin (1970)

The biochemical and immunological effects of Listeria monocytogenes hemolysin in CD-1 mice were studied. Intraperitoneal injection of 256 complete hemolytic units (CHU) caused a twofold increase in plasma beta-glucuronidase levels but was not lethal. In contrast, 256 or more CHU caused 100% lethality in 4 to 5 min when administered intravenously. Intravenous administration of 50 CHU caused a 10- to 11-fold increase in plasma beta-glucuronidase levels and was lethal for a variable percentage of the animals. Carbon clearance experiments showed the phagocytic index to be depressed by relatively small amounts of intravenously administered hemolysin and suggested that hemolysin may function as a leucocidal agressin during listeric infection. Increased plasma levels of ornithine carbamyltransferase after intravenous injection of hemolysin indicated hepatocellular damage. Liver carbohydrate and blood glucose determinations on fasted mice showed a reduced gluconeogenic capability in hemolysin-treated animals. Mice immunized with purified hemolysin or live vaccine were more resistant to several of the toxic parameters studied. The data indicate that hemolysin is produced during listeric infection and is antigenic, but not necessarily a protective immunogen.
Fractal Branching Pattern in the Pial Vasculature in the Cat (2001)

Arborization pattern was studied in pial vascular networks by treating them as fractals. Rather than applying elaborate taxonomy assembled from measures from individual vessel segments and bifurcations arranged in their branching order, the authors' approach captured the structural details at once in high-resolution digital images processed for the skeleton of the networks. The pial networks appear random and at the same time having structural elements similar to each other when viewed at different scales--a property known as self-similarity revealed by the geometry of fractals. Fractal (capacity) dimension, Dcap, was calculated to evaluate the network's spatial complexity by the box counting method (BCM) and its variant, the extended counting method (XCM). Box counting method and XCM were subject to numerical testing on ideal fractals of known D. The authors found that precision of these fractal methods depends on the fractal character (branching, nonbranching) of the structure they evaluate. Dcaps (group mean +/- SD) for the arterial and venous pial networks in the cat (n = 6) are 1.37 +/- 0.04, 1.37 +/- 0.02 by XCM, and 1.30 +/- 0.04, 1.31 +/- 0.03 by BCM, respectively. The arterial and venous systems thus appear to be developed according to the same fractal generation rule in the cat.
Power Density in Theta/Alpha Frequencies of the Waking EEG Progressively Increases During Sustained Wakefulness (1995)

Electroencephalogram (EEG) power density and self-rated fatigue were assessed in nine healthy women during a 40-hour period of sustained wakefulness under constant behavioral and environmental conditions (constant routine protocol). Waking EEG recordings were performed for 4 minutes after 3, 10, 27 and 34 hours of prior wakefulness. EEG power density in the 6.25- to 9.0-Hz frequency range progressively increased across the four recordings, suggesting an endogenous homeostatic component in the regulation of the theta/alpha frequencies under constant conditions. Subjective fatigue also exhibited an increasing component in the course of the constant routine protocol, with a clear circadian modulation. Fatigue ratings and the theta/ alpha power density of the waking EEG recorded at the same four time points during the constant routine protocol correlated significantly. Our data demonstrate the presence of a homeostatic component in the control of EEG power density in the 6.25- to 9.0-Hz range.
Sorption of uranyl ions on phosphorylated lignin (2009)

A procedure was developed for preparing an effective lignin-based sorbent containing 16.6 wt % phosphorus. The distribution coefficient of uranyl ions with this sorbent is as high as 9680. The physicochemical properties of the sorbent were determined.
Maintenance of Epstein–Barr virus (EBV) <i>oriP</i> -based episomes requires EBV-encoded nuclear antigen-1 chromosome-binding domains, which can be replaced by high-mobility group-I or histone H1 (2001)

EBV-encoded nuclear antigen-1 (EBNA-1) binding to a cis-acting viral DNA element, oriP, enables plasmids to persist in dividing human cells as multicopy episomes that attach to chromosomes during mitosis. In investigating the significance of EBNA-1 binding to mitotic chromosomes, we identified the basic domains of EBNA-1 within amino acids 1-89 and 323-386 as critical for chromosome binding. In contrast, the EBNA-1 C terminus (amino acids 379-641), which includes the nuclear localization signal and DNA-binding domain, does not associate with mitotic chromosomes or retain oriP plasmid DNA in dividing cell nuclei, but does enable the accumulation of replicated oriP-containing plasmid DNA in transient replication assays. The importance of chromosome association in episome maintenance was evaluated by replacing EBNA-1 amino acids 1-378 with cell proteins that have similar chromosome binding characteristics. High-mobility group-I amino acids 1-90 or histone H1-2 could substitute for EBNA-1 amino acids 1-378 in mediating more efficient accumulation of replicated oriP plasmid, association with mitotic chromosomes, nuclear retention, and long-term episome persistence. These data strongly support the hypothesis that mitotic chromosome association is a critical factor for episome maintenance. The replacement of 60% of EBNA-1 with cell protein is a significant step toward eliminating the need for noncellular protein sequences in the maintenance of episomal DNA in human cells.
Learning Semantic Hierarchies: A Continuous Vector Space Approach (2015)

Semantic hierarchy construction aims to build structures of concepts linked by hypernym-hyponym (“is-a”) relations. A major challenge for this task is the automatic discovery of such relations. This paper proposes a novel and effective method for the construction of semantic hierarchies based on continuous vector representation of words, named word embeddings, which can be used to measure the semantic relationship between words. We identify whether a candidate word pair has hypernym-hyponym relation by using the word-embedding-based semantic projections between words and their hypernyms. Our result, an F-score of 73.74%, outperforms the state-of-the-art methods on a manually labeled test dataset. Moreover, combining our method with a previous manually built hierarchy extension method can further improve F-score to 80.29%.
Same day diagnosis of Down's syndrome and sex in single cells using multiplex fluorescent PCR. (1998)

The major reason for prenatal diagnosis lies in the detection of trisomies, particularly trisomy 21 (Down's syndrome). Current techniques require lengthy laboratory procedures and high costs. Furthermore, diagnosis is often not possible if the sample is of small size or is contaminated. An alternative method, quantitative fluorescent polymerase chain reaction (PCR) of short tandem repeats (STRs), can also be used to diagnose trisomies and it has the advantage that a result is obtained within five to eight hours. However, this method is currently limited to relatively large amounts of sample, which restricts diagnostic confidence and value. Recently, genetic diagnosis using fluorescent PCR has been applied at the single cell level but is limited to sex or single gene defect diagnosis. This study, using quantitative multiplex fluorescent PCR, provides for the first time simultaneous diagnosis and confirmation of sex and trisomy in single cells. Two markers for chromosome 21 increase diagnostic confidence, informativeness, and confirmation. This system is rapid (five hours), reliable, and accurate and we believe that it will be more cost effective than alternative methods. The technique has direct application to preimplantation genetic diagnosis, early prenatal diagnosis, and other diagnostic systems where sample size is limited.