gebhart/patrepeval huggingface dataset:
An enzyme regulating triacylglycerol composition is encoded by the ROD1 gene of Arabidopsis (2009)

The polyunsaturated fatty acids (PUFAs) linoleic acid (18:2) and alpha-linolenic acid (18:3) in triacylglycerols (TAG) are major factors affecting the quality of plant oils for human health, as well as for biofuels and other renewable applications. These PUFAs are essential fatty acids for animals and plants, but also are the source of unhealthy trans fats during the processing of many foodstuffs. PUFAs 18:2 and 18:3 are synthesized in developing seeds by the desaturation of oleic acid (18:1) esterified on the membrane lipid phosphatidylcholine (PC) on the endoplasmic reticulum. The reactions and fluxes involved in this metabolism are incompletely understood, however. Here we show that a previously unrecognized enzyme, phosphatidylcholine:diacylglycerol cholinephosphotransferase (PDCT), encoded by the Arabidopsis ROD1 gene, is a major reaction for the transfer of 18:1 into PC for desaturation and also for the reverse transfer of 18:2 and 18:3 into the TAG synthesis pathway. The PDCT enzyme catalyzes transfer of the phosphocholine headgroup from PC to diacylglycerol, and mutation of rod1 reduces 18:2 and 18:3 accumulation in seed TAG by 40%. Our discovery of PDCT is important for understanding glycerolipid metabolism in plants and other organisms, and provides tools to modify the fatty acid compositions of plant oils for improved nutrition, biofuel, and other purposes.
An overview of the PARCTAB ubiquitous computing experiment (1995)

The PARCTAB system integrates a palm-sized mobile computer into an office network. The PARCTAB project serves as a preliminary testbed for ubiquitous computing, a philosophy originating at Xerox PARC that aims to enrich our computing environment by emphasizing context sensitivity, casual interaction and the spatial arrangement of computers. This article describes the ubiquitous computing philosophy, the PARCTAB system, user interface issues for small devices, and our experience in developing and testing a variety of mobile applications.
Gap Junction–Mediated Intercellular Communication in A Long–Term Primary Mouse Hepatocyte Culture System (2003)

Gap junction-mediated intercellular communication (GJIC) is critical for maintaining integral cellular processes including differentiation and growth control. The disruption of GJIC has been correlated with aberrant function in many cell types, including hepatocytes in vivo; therefore it is imperative that cellular model systems support intercellular communication to simulate normal cellular functions. Functional GJIC has been shown in long-term primary rat hepatocyte cultures, which have been implemented widely to study various aspects of hepatocellular function; however, the onset of transgenic technology in murine species has necessitated the development of a primary mouse hepatocyte system. In this report, we analyze GJIC in a dimethylsulfoxide (DMSO)-containing long-term primary mouse hepatocyte culture system. The cells retain morphologic and biochemical characteristics of differentiated hepatocytes through day 30 post plating, including liver-specific gene expression. We further show that connexin32 and connexin26 expression and gap junction plaque formation increase over time in culture concomitant with an increase in GJIC between adjoining primary mouse hepatocytes. In conclusion, the findings described in this study make it possible to maintain differentiated primary mouse hepatocytes that also show GJIC in long-term culture for 30 days. In addition, this system has the potential to be extended to study primary mouse hepatocytes isolated from genetically engineered mice.
ELECTRICAL SWITCHING IN CHALCOGENIDE GLASSES- SOME NEWER INSIGHTS (2001)

The recent studies on the switching. behavior of several chalcogenide semiconductors indicate that there exists a close relation between the electrical switching and structural effects in these materials; the two network topological Thresholds, namely the Rigidity Percolation and the Chemical Threshold are found to influence considerably the composition dependence of the switching voltages/fields of many memory and threshold switching glasses. Further, changes in the coordination of constituent atoms are found to effect a change in the switching behavior (memory to threshold), Also, an interesting relation has been established between the type of switching exhibited and the thermal diffusivity of the material.
Fast multiresolution image querying (1995)

We present a method for searching in an image database using a query image that is similar to the intended target. The query image may be a hand-drawn sketch or a (potentially low-quality) scan of the image to be retrieved. Our searching algorithm makes use of multiresolution wavelet decompositions of the query and database images. The coefficients of these decompositions are distilled into small "signatures" for each image. We introduce an "image querying metric" that operates on these signatures. This metric essentially compares how many significant wavelet coefficients the query has in common with potential targets. The metric includes parameters that can be tuned, using a statistical analysis, to accommodate the kinds of image distortions found in different types of image queries. The resulting algorithm is simple, requires very little storage overhead for the database of signatures, and is fast enough to be performed on a database of 20,000 images at interactive rates (on standard desktop machines) as a query is sketched. Our experiments with hundreds of queries in databases of 1000 and 20,000 images show dramatic improvement, in both speed and success rate, over using a conventional L 1 , L 2 , or color histogram norm.
Cyclohexanyl Peptide Nucleic Acids (chPNAs) for Preferential RNA Binding:  Effective Tuning of Dihedral Angle β in PNAs for DNA/RNA Discrimination (2005)

[structures: see text] A serious drawback of peptide nucleic acids (PNAs) from an application perspective that has not been adequately dealt with is nondiscrimination of identical DNA and RNA sequences. An analysis of the available X-ray and NMR solution structures of PNA complexes with DNA and RNA suggested that it might be possible to rationally impart DNA/RNA duplex binding selectivity by tuning the dihedral angle beta of the flexible ethylenediamine part of the PNA backbone (II) via suitable chemical modifications. Cyclohexanyl PNAs (chPNAs) with beta approximately = 65 degrees were designed on the basis of this rationale. The chPNAs introduced remarkable differences in duplex stabilities among their DNA and RNA complexes, with melting temperatures (deltaTm(RNA-DNA) = +16-50 degrees C) depending on the number of modifications and the stereochemistry. This is a highly significant, exceptional binding selectivity of a mix sequence of PNA to RNA over the same DNA sequence as that seen to date. In contrast, cyclopentanyl PNAs (cpPNAs) with beta approximately = 25 degrees hybridize to DNA/RNA strongly without discrimination because of the ring puckering of the cyclopentane ring. The high affinity of chPNAs to bind to RNA without losing base specificity will have immediate implications in designing improved PNAs for therapeutic and diagnostic applications.
Data compression of moving images using geometric transformations (1992)

A new compression technique is presented which can be used to considerably reduce the amount of data that are required to digitally transmit or store a sequence of images. The method used to compress the data is based on image resampling, and describes the new frame as a set of geometric transformations of parts of the previous frame. A modular image processing system is also described which can be used to implement the encoder and decoder for this compression technique.
Noise reduction and targeted exploration in imitation learning for Abstract Meaning Representation parsing (2016)

Semantic parsers map natural language statements into meaning representations, and must abstract over syntactic phenomena, resolve anaphora, and identify word senses to eliminate ambiguous interpretations. Abstract meaning representation (AMR) is a recent example of one such semantic formalism which, similar to a dependency parse, utilizes a graph to represent relationships between concepts As with dependency parsing, transition-based approaches are a common approach to this problem. However, when trained in the traditional manner these systems are susceptible to the accumulation of errors when they find undesirable states during greedy decoding. Imitation learning algorithms have been shown to help these systems recover from such errors. To effectively use these methods for AMR parsing we find it highly beneficial to introduce two novel extensions: noise reduction and targeted exploration. The former mitigates the noise in the feature representation, a result of the complexity of the task. The latter targets the exploration steps of imitation learning towards areas which are likely to provide the most information in the context of a large action-space. We achieve state-ofthe art results, and improve upon standard transition-based parsing by 4.7 F 1 points.
Causal inference in statistics: An overview (2009)

This review presents empirical researchers with recent advances in causal inference, and stresses the paradigmatic shifts that must be undertaken in moving from traditional statistical analysis to causal analysis of multivariate data. Special emphasis is placed on the assumptions that underly all causal inferences, the languages used in formulating those assumptions, the conditional nature of all causal and counterfactual claims, and the methods that have been developed for the assessment of such claims. These advances are illustrated using a general theory of causation based on the Structural Causal Model (SCM) described in Pearl (2000a), which subsumes and unifies other approaches to causation, and provides a coherent mathematical foundation for the analysis of causes and counterfactuals. In particular, the paper surveys the development of mathematical tools for inferring (from a combination of data and assumptions) answers to three types of causal queries: (1) queries about the effects of potential interventions, (also called “causal effects” or “policy evaluation”) (2) queries about probabilities of counterfactuals, (including assessment of “regret,” “attribution” or “causes of effects”) and (3) queries about direct and indirect effects (also known as “mediation”). Finally, the paper defines the formal and conceptual relationships between the structural and potential-outcome frameworks and presents tools for a symbiotic analysis that uses the strong features of both.
Decrease of sympathetic cardiovascular modulation after temporal lobe epilepsy surgery (2002)

In temporal lobe epilepsy (TLE), there is evidence of ictal and interictal autonomic dysregulation, predominantly with sympathetic overactivity. The effects of TLE surgery on autonomic cardiovascular control and on baroreex sensitivity (BRS) have not been studied. To evaluate such effects, we monitored heart rate (HR), systolic blood pressure (BP sys ) and respiration in 18 TLE patients 34 months before and after TLE surgery. We used Blackman-Tukey spectral analysis to assess sympathetic and parasympathetic modulation as powers of HR and BP sys oscillations in the low frequency (LF, 0.040.15 Hz) and high frequency (HF, 0.150.5 Hz) bands. BRS was determined as the LF transfer function gain between BP and HR. After surgery, HR, BP sys , respiration and HF powers remained unchanged, while LF powers of HR (1.57 T 1.54 bpm 2 ) and BP sys (2.19 T 1.34 mmHg 2 ) and BRS (0.68 T 0.31 bpm/mmHg) were smaller than pre-surgical LF powers of HR (3.87 T 3.26 bpm 2 ) and BP sys (4.80 T 3.84 mmHg 2 ) and BRS (1.12 T 0.39 bpm/mmHg; P < 0.05). After TLE surgery, there is a reduction of sympathetic cardiovascular modulation and BRS that might result from decreased inuences of interictal epileptogenic discharges on brain areas involved in cardiovascular autonomic control. TLE surgery seems to stabilize the cardiovascular control in epilepsy patients by reducing the risk of sympathetically mediated tachyarrhythmias and excessive bradycardiac counter-regulation, both of which might be relevant for the pathophysiology of sudden unexpected death in epilepsy patients (SUDEP). Thus, TLE surgery might contribute to reducing the risk of SUDEP.
A new endogenous ATP analog (ApppI) inhibits the mitochondrial adenine nucleotide translocase (ANT) and is responsible for the apoptosis induced by nitrogen‐containing bisphosphonates (2006)

1. Bisphosphonates are currently the most important class of antiresorptive drugs used for the treatment of diseases with excess bone resorption. On the basis of their molecular mechanism of action, bisphosphonates can be divided into two pharmacological classes; nitrogen-containing (N-BPs) and non-nitrogen-containing bisphosphonates (non-N-BP). Both classes induce apoptosis but they evoke it differently; N-BPs by inhibiting the intracellular mevalonate pathway and protein isoprenylation, and non-N-BPs via cytotoxic ATP analog-type metabolites. N-BPs are not metabolized to ATP analogs, but we report here that these bisphosphonates can induce formation of a novel ATP analog (ApppI) as a consequence of the inhibition of the mevalonate pathway in cells. We also investigated whether ApppI is involved in the apoptosis induced by N-BPs. 2. Mass spectrometry and NMR were used to identify ApppI in N-BP treated osteoclasts, macrophages and glioma cells. The potency of different bisphosphonates to promote ApppI production was tested in J774 macrophages. The effects of ApppI on ADP/ATP translocase in isolated mitochondria and its capability to induce apoptosis in osteoclasts were also studied. 3. ApppI production correlated well with the capacity of N-BPs to inhibit mevalonate pathway. ApppI inhibited the mitochondrial ADP/ATP translocase and caused apoptosis in osteoclasts. 4. In conclusion, these findings provide the basis for a new mechanism of action for N-BPs. Some of these very potent bisphosphonates, such as zoledronic acid, represent a third class of bisphosphonates that can act both via the inhibition of the mevalonate pathway and by the blockade of mitochondrial ADP/ATP translocase, which is known to be involved in the induction of apoptosis.
Self-tuned remote execution for pervasive computing (2005)

Pervasive computing creates environments saturated with computing and communication capability, yet gracefully integrated with human users. Remote execution has a natural role to play, in such environments, since it lets applications simultaneously leverage the mobility of small devices and the greater resources of large devices. In this paper, we describe Spectra, a remote execution system designed for pervasive environments. Spectra monitors resources such as battery, energy and file cache state which are especially important for mobile clients. It also dynamically balances energy use and quality goals with traditional performance concerns to decide where to locate functionality. Finally, Spectra is self-tuning-it does not require applications to explicitly specify intended resource usage. Instead, it monitors application behavior, learns functions predicting their resource usage, and uses the information to anticipate future behavior.
MEKK1/JNK signaling stabilizes and activates p53 (1998)

Activation of the tumor suppressor p53 by stress and damage stimuli often correlates with induction of stress kinases, Jun-NH2 kinase (JNK). As JNK association with p53 plays an important role in p53 stability, in the present study we have elucidated the relationship between the JNK-signaling pathway and p53 stability and activity. Expression of a constitutively active form of JNKK upstream kinase, mitogen-activated protein kinase kinase kinase (DeltaMEKK1), increased the level of the exogenously transfected form of p53 in p53 null (10.1) cells as well as of endogenous p53 in MCF7 breast cancer cells. Increased p53 level by forced expression of DeltaMEKK1 coincided with a decrease in p53 ubiquitination in vivo and with prolonged p53 half-life. Computerized modeling of the JNK-binding site (amino acids 97-116; p7 region) enabled us to design mutations of exposed residues within this region. Respective mutations (p53(101-5-8)) and deletion (p53(Deltap7)) forms of p53 did not exhibit the same increase in p53 levels upon DeltaMEKK1 expression. In vitro phosphorylation of p53 by JNK abolished Mdm2 binding and targeting of p53 ubiquitination. Similarly, DeltaMEKK1 expression increased p53 phosphorylation by immunopurified JNK and dissociated p53-Mdm2 complexes. Transcriptional activity of p53, as measured via mdm2 promoter-driven luciferase, exhibited a substantial increase in DeltaMEKK1-expressing cells. Cotransfection of p53 and DeltaMEKK1 into p53 null cells potentiated p53-dependent apoptosis, suggesting that MEKK1 effectors contribute to the ability of p53 to mediate programmed cell death. Our results point to the role of MEKK1-JNK signaling in p53 stability, transcriptional activities, and apoptotic capacity as part of the cellular response to stress.
Incidence of New-Onset Seizures in Mild to Moderate Alzheimer Disease (2012)

Seizure rates in patients with mild to moderate AD in clinical trials are similar to rates observed in longer observational cohort studies, but they are greater than expected in the general elderly population. Younger age, greater degree of cognitive impairment, and history of antipsychotic use were independent risk factors for new-onset seizures in AD.
Generation of adenovirus by transfection of plasmids (1983)

Biologically active fragments of Adenovirus 5 (Ad5) DNA that span the entire genome have been cloned into plasmids. The covalently attached terminal protein was removed and Eco RI linkers added in a fashion that preserves the Ad5 terminal sequences. When plasmids containing overlapping fragments that represent the entire genome are cotransfected onto 293 cells, infectious virus is obtained. Generation of virus depends upon the release of the 0 or 100 mu Ad5 terminus from pBR322 DNA by Eco RI cleavage. During virus production the modified termini of the transfected fragments are corrected exactly to that of wt viral DNA. The above method for preparing adenovirus recombinants has been used to construct a mutant, Ad5 delta (78.9-84.3), lacking most of the non-essential EIII transcriptional unit. This mutant is phenotypically wild type with respect to burst size and kinetics of growth. Surprisingly, it inhibits wt viral growth upon mixed infections of HeLa or 293 cells, apparently at the level of DNA replication.
Recent studies of the mineral phase in bone and its possible linkage to the organic matrix by protein-bound phosphate bonds (1984)

The most widely accepted hypothesis to account for maturational changes in the X-ray diffraction characteristics of bone mineral has been the 'amorphous calcium phosphate theory', which postulates that an initial amorphous calcium phosphate solid phase is deposited that gradually converts to poorly crystalline hydroxyapatite. Our studies of bone mineral of different ages by X-ray radial distribution function analysis and 31P n.m.r. have conclusively demonstrated that a solid phase of amorphous calcium phosphate does not exist in bone in any significant amount. 31P n.m.r. studies have detected the presence of acid phosphate groups in a brushite-like configuration. Phosphoproteins containing O-phosphoserine and O-phosphothreonine have been isolated from bone matrix and characterized. Tissue and cell culture have established that they are synthesized in bone, most likely by the osteoblasts. Physiochemical and pathophysiological studies support the thesis that the mineral and organic phases of bone and other vertebrate mineralized tissues are linked by the phosphomonester bonds of O-phosphoserine and O-phosphothreonine, which are constituents of both the structural organic matrix and the inorganic calcium phosphate crystals.
Expression Profiling of Nuclear Receptors in Human and Mouse Embryonic Stem Cells (2009)

Nuclear receptors (NRs) regulate gene expression in essential biological processes including differentiation and development. Here we report the systematic profiling of NRs in human and mouse embryonic stem cell (ESC) lines and during their early differentiation into embryoid bodies. Expression of the 48 human and mouse NRs was assessed by quantitative real-time PCR. In general, expression of NRs between the two human cell lines was highly concordant, whereas in contrast, expression of NRs between human and mouse ESCs differed significantly. In particular, a number of NRs that have been implicated previously as crucial regulators of mouse ESC biology, including ERRbeta, DAX-1, and LRH-1, exhibited diametric patterns of expression, suggesting they may have distinct species-specific functions. Taken together, these results highlight the complexity of the transcriptional hierarchy that exists between species and governs early development. These data should provide a unique resource for further exploration of the species-specific roles of NRs in ESC self-renewal and differentiation.
Regulation and Tissue-Specific Distribution of mRNAs for Three Extracellular Invertase Isoenzymes of Tomato Suggests an Important Function in Establishing and Maintaining Sink Metabolism (1997)

The aim of the present study was to gain insight into the contribution of extracellular invertases for sink metabolism in tomato (Lycopersicon esculentum L.). The present study shows that extracellular invertase isoenzymes are encoded by a gene family comprising four members: Lin5, Lin6, Lin7, and Lin8. The regulation of mRNA levels by internal and external signals and the distribution in sink and source tissues has been determined and compared with mRNA levels of the intracellular sucrose (Suc)-cleaving enzymes Suc synthase and vacuolar invertase. The specific regulation of Lin5, Lin6, and Lin7 suggests an important function of apoplastic cleavage of Suc by cell wall-bound invertase in establishing and maintaining sink metabolism. Lin6 is expressed under conditions that require a high carbohydrate supply. The corresponding mRNA shows a sink tissue-specific distribution and the concentration is elevated by stress-related stimuli, by the growth-promoting phytohormone zeatin, and in response to the induction of heterotrophic metabolism. The expression of Lin5 and Lin7 in gynoecia and stamens, respectively, suggests an important function in supplying carbohydrates to these flower organs, whereas the Lin7 mRNA was found to be present exclusively in this specific sink organ.
Cardiac Ion Channel Expression and Contractile Function in Mice with Deletion of Thyroid Hormone Receptor or (2001)

Cardiac myocytes express the two thyroid hormone receptors (T3Rs), T3Rα and T3Rβ. However, which isoform contributes to specific, T3-induced alterations of cardiac function remains unclear. Here, we used individual T3R isoform knockout (KO) mice to study the effects of T3Rα and T3Rβ in the heart. Our findings indicate that potassium channel genes that code for K+ channels involved in action potential repolarization, like KV 4.2 and minK, are T3Rα targets. Both are markedly regulated by thyroid status. The recently identified cyclic nucleotide-gated channels, HCN2 and HCN4, are targets of T3Rα and are unchanged in a euthyroid T3Rβ KO. However, these transcripts respond markedly to altered T3 signaling concomitant with bradycardia in T3Rα KO and hypothyroid animals, as well as tachycardia in hyperthyroid T3Rβ KO mice. SERCA2a and myosins are T3 regulated and were also targets of T3Rα, and the papillary muscles of αKO animals showed a slowed rate of force development. Because of the absence of significant cardiac effects in euthyroid T3Rβ KO mice, we determined messenger RNA levels for both T3Rα and T3Rβ in the heart. We found that T3Rβ is present at a 1:3 ratio to T3Rα1. We conclude that the cardiac phenotype regulated by T3 is predominantly mediated by T3Rα and that the lack of T3Rα cannot be compensated by T3Rβ in the heart.