gebhart/patrepeval huggingface dataset:
Improving Automated Email Tagging with Implicit Feedback (2015)

Tagging email is an important tactic for managing information overload. Machine learning methods can help the user with this task by predicting tags for incoming email messages. The natural user interface displays the predicted tags on the email message, and the user doesn't need to do anything unless those predictions are wrong (in which case, the user can delete the incorrect tags and add the missing tags). From a machine learning perspective, this means that the learning algorithm never receives confirmation that its predictions are correct---it only receives feedback when it makes a mistake. This can lead to slower learning, particularly when the predictions were not very confident, and hence, the learning algorithm would benefit from positive feedback. One could assume that if the user never changes any tag, then the predictions are correct, but users sometimes forget to correct the tags, presumably because they are focused on the content of the email messages and fail to notice incorrect and missing tags. The aim of this paper is to determine whether implicit feedback can provide useful additional training examples to the email prediction subsystem of TaskTracer, known as EP2 (Email Predictor 2). Our hypothesis is that the more time a user spends working on an email message, the more likely it is that the user will notice tag errors and correct them. If no corrections are made, then perhaps it is safe for the learning system to treat the predicted tags as being correct and train accordingly. This paper proposes three algorithms (and two baselines) for incorporating implicit feedback into the EP2 tag predictor. These algorithms are then evaluated using email interaction and tag correction events collected from 14 user-study participants as they performed email-directed tasks while using TaskTracer EP2. The results show that implicit feedback produces important increases in training feedback, and hence, significant reductions in subsequent prediction errors despite the fact that the implicit feedback is not perfect. We conclude that implicit feedback mechanisms can provide a useful performance boost for email tagging systems.
Structural and Functional Characterization of a Lytic Polysaccharide Monooxygenase with Broad Substrate Specificity (2015)

The recently discovered lytic polysaccharide monooxygenases (LPMOs) carry out oxidative cleavage of polysaccharides and are of major importance for efficient processing of biomass. NcLPMO9C from Neurospora crassa acts both on cellulose and on non-cellulose β-glucans, including cellodextrins and xyloglucan. The crystal structure of the catalytic domain of NcLPMO9C revealed an extended, highly polar substrate-binding surface well suited to interact with a variety of sugar substrates. The ability of NcLPMO9C to act on soluble substrates was exploited to study enzyme-substrate interactions. EPR studies demonstrated that the Cu2+ center environment is altered upon substrate binding, whereas isothermal titration calorimetry studies revealed binding affinities in the low micromolar range for polymeric substrates that are due in part to the presence of a carbohydrate-binding module (CBM1). Importantly, the novel structure of NcLPMO9C enabled a comparative study, revealing that the oxidative regioselectivity of LPMO9s (C1, C4, or both) correlates with distinct structural features of the copper coordination sphere. In strictly C1-oxidizing LPMO9s, access to the solvent-facing axial coordination position is restricted by a conserved tyrosine residue, whereas access to this same position seems unrestricted in C4-oxidizing LPMO9s. LPMO9s known to produce a mixture of C1- and C4-oxidized products show an intermediate situation.
Discrimination of Human Astrocytoma Subtypes by Lipid Analysis Using Desorption Electrospray Ionization Imaging Mass Spectrometry (2010)

Differentiation of human brain astrocytic tumor grades can be achieved by direct lipid analysis using desorption electrospray ionization mass spectrometry (DESI-MS). Distinctive lipid profiles are associated with the degree of malignancy, grades II, III, and IV (see picture). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Length scale of Leidenfrost ratchet switches droplet directionality (2014)

Arrays of tilted pillars with characteristic heights spanning from hundreds of nanometers to tens of micrometers were created using wafer level processing and used as Leidenfrost ratchets to control droplet directionality. Dynamic Leidenfrost droplets on the ratchets with nanoscale features were found to move in the direction of the pillar tilt while the opposite directionality was observed on the microscale ratchets. This remarkable switch in the droplet directionality can be explained by varying contributions from the two distinct mechanisms controlling droplet motion on Leidenfrost ratchets with nanoscale and microscale features. In particular, asymmetric wettability of dynamic Leidenfrost droplets upon initial impact appears to be the dominant mechanism determining their directionality on tilted nanoscale pillar arrays. By contrast, asymmetric wetting does not provide a strong enough driving force compared to the forces induced by asymmetric vapour flow on arrays of much taller tilted microscale pillars. Furthermore, asymmetric wetting plays a role only in the dynamic Leidenfrost regime, for instance when droplets repeatedly jump after their initial impact. The point of crossover between the two mechanisms coincides with the pillar heights comparable to the values of the thinnest vapor layers still capable of cushioning Leidenfrost droplets upon their initial impact. The proposed model of the length scale dependent interplay between the two mechanisms points to the previously unexplored ability to bias movement of dynamic Leidenfrost droplets and even switch their directionality.
Complement inhibitors: a resurgent concept in anti-inflammatory therapeutics (2000)

In addition to its essential role in immune defense, the complement system contributes to tissue damage in many clinical conditions. Thus, there is a pressing need to develop therapeutically effective complement inhibitors to prevent these adverse effects. This concept, though old, received little scientific attention until recently. Data from animal models of diseases that have been produced using complement-deficient, knockout, and transgenic animals, as well as data demonstrating that complement proteins are produced in many important tissue sites (including the brain) have attracted the interest of many basic research scientists and applied scientists from the biotechnology field and larger pharmaceutical firms. This resurgence of interest has generated a wealth of new information in the field of complement inhibition. In this article, we comprehensively review up-to-date information in the field of complement inhibitors.
Whole-Genome Analysis of the SHORT-ROOT Developmental Pathway in \n<em>Arabidopsis</em> (2016)

&lt;div&gt;&lt;p&gt;Stem cell function during organogenesis is a key issue in developmental biology. The transcription factor SHORT-ROOT (SHR) is a critical component in a developmental pathway regulating both the specification of the root stem cell niche and the differentiation potential of a subset of stem cells in the &lt;em&gt;Arabidopsis&lt;/em&gt; root. To obtain a comprehensive view of the SHR pathway, we used a statistical method called meta-analysis to combine the results of several microarray experiments measuring the changes in global expression profiles after modulating SHR activity. Meta-analysis was first used to identify the direct targets of SHR by combining results from an inducible form of SHR driven by its endogenous promoter, ectopic expression, followed by cell sorting and comparisons of mutant to wild-type roots. Eight putative direct targets of SHR were identified, all with expression patterns encompassing subsets of the native SHR expression domain. Further evidence for direct regulation by SHR came from binding of SHR in vivo to the promoter regions of four of the eight putative targets. A new role for SHR in the vascular cylinder was predicted from the expression pattern of several direct targets and confirmed with independent markers. The meta-analysis approach was then used to perform a global survey of the SHR indirect targets. Our analysis suggests that the SHR pathway regulates root development not only through a large transcription regulatory network but also through hormonal pathways and signaling pathways using receptor-like kinases. Taken together, our results not only identify the first nodes in the SHR pathway and a new function for SHR in the development of the vascular tissue but also reveal the global architecture of this developmental pathway. &lt;/p&gt; &lt;/div&gt;
Tertiary Motifs in RNA Structure and Folding (1999)

Specific tertiary structural motifs determine the complete architecture of RNA molecules (see picture for examples). Within the last few years a number of high-resolution crystal structures of complex RNAs have led to new insights into the mechanisms by which these complex folds are attained. In this review the structures of these tertiary motifs and how they influence the folding pathway of biological RNAs are discussed, as well as new developments in modeling RNA structure based upon these findings.
Fatty-acid composition in serum phospholipids and risk of breast cancer: An incident case-control study in Sweden (1999)

The study of the relationship between dietary intake of fatty acids and the risk of breast cancer has not yielded definite conclusions with respect to causality, possibly because of methodological issues inherent to nutritional epidemiology. To evaluate the hypothesis of possible protection of n-3 polyunsaturated fatty acids (PUFA) against breast cancer in women, we examined the fatty-acid composition of phospholipids in pre-diagnostic sera of 196 women who developed breast cancer, and of 388 controls matched for age at recruitment and duration of follow-up, in a prospective cohort study in Umeâ, northern Sweden. Individual fatty acids were measured as a percentage of total fatty acids, using capillary gas chromatography. Conditional logistic-regression models showed no significant association between n-3 PUFA and breast-cancer risk. In contrast, women in the highest quartile of stearic acid had a relative risk of 0.49 (95% confidence interval, 0.22-1.08) compared with women in the lowest quartile (trend p = 0.047), suggesting a protective role of stearic acid in breast-cancer risk. Besides stearic acid, women in the highest quartile of the 18:0/18:1 n-9c ratio had a relative risk of 0.50 (95% confidence interval, 0.23-1.10) compared with women in the lowest quartile (trend p = 0.064), suggesting a decrease in breast-cancer risk in women with low activity of the enzyme delta 9-desaturase (stearoyl CoA desaturase), which may reflect an underlying metabolic profile characterized by insulin resistance and chronic hyper-insulinemia.
Bilirubin: an endogenous scavenger of nitric oxide and reactive nitrogen species (2006)

Bilirubin is the final product of heme metabolism. Until recently, bilirubin was considered as a mere by-product of heme degradation but, in the last 20 years, many papers have appeared in the literature demonstrating that this bile pigment is endowed with a strong antioxidant activity, being able to counteract the cellular damage elicited by reactive oxygen species in many in vitro and in vivo experimental systems. Interestingly, compelling evidence has shown that BR can serve as an endogenous scavenger of both nitric oxide and reactive nitrogen species, thus widening the protective role of bilirubin to other reactive species originating within the cellular milieu. The aim of this paper is to give an overview of the interaction between bilirubin and nitric oxide/reactive nitrogen species; furthermore, the possible pathophysiological and clinical relevance of this interaction will be discussed.
Molecular Cloning of Genes Under Control of the Circadian Clock in Neurospora (1989)

To investigate the regulation of messenger RNA abundance by circadian clocks, genomic and complementary DNA libraries were screened with complementary DNA probes enriched, by means of sequential rounds of subtractive hybridization, for sequences complementary to transcripts specific to either early morning or early evening cultures of Neurospora. Only two morning-specific genes were identified through this protocol. RNA blot analysis verified that the abundance of the transcripts arising from these genes oscillates with a period of 21.5 hours in a clock wild-type strain and 29 hours in the long-period clock mutant strain frq7. Genetic mapping through the use of restriction fragment length polymorphisms shows the two genes, ccg-1 and ccg-2, to be unlinked. These data provide a view of the extent of clock control of gene expression.
TREATMENT OF CEREBRAL INFARCTION WITH DIMETHYL SULFOXIDE IN THE MONGOLIAN GERBIL* (1983)

Dimethyl sulfoxide (DMSO) has been reported to have beneficial effects in the treatment of central nervous system trauma, possibly due to its reported anti-inflammatory, antiedemic, anticoagulate, diuretic, hypothermic, vasodilatory, and respiratory stimulatory effects as well as an ability to correct membrane instability and penetrate the blood-brain barrier. In this paper we discussed these properties, and how they may be of benefit in ischemic cerebral infarction and elevated intracranial pressure. We also described a study we performed to determine if treatment with DMSO would decrease the morbidity and mortality from experimental cerebral infarction.
Side-chain derivatives of biologically active nucleosides. Part 1. Side-chain analogs of 3'-azido-3'-deoxythymidine (AZT) (1992)

Starting from 3-O-mesyl-1,2-O-isopropylidene-alpha-D-allofuranose (9) the anomeric mixtures of the requisite carbohydrates 1,2-di-O-acetyl-6-O-benzoyl-5-deoxy-3-O-mesyl-D-allofuranoses++ + 17A alpha/beta, 1,2-di-O-acetyl-5,6-di-O-benzoyl-3-O-mesyl-D-allofuranoses 17B alpha/beta, and 1,2-di-O-acetyl-5,6-di-O-benzoyl-3-O-mesyl-L-talofuranoses 17C alpha/beta were synthesized. 1,2-Di-O-acetyl-5-O-benzoyl-6-deoxy-3-O-mesyl-D-allofuranoses++ + 17D alpha/beta and the corresponding L-talofuranoses 17E alpha/beta were obtained from 6-deoxy-3,5-di-O-benzoyl-1,2-O-isopropylidene-alpha-D- allofuranose (12) and the corresponding beta-L-talofuranose 13. Coupling of these sugar derivatives with thymine gave the beta-nucleoside derivatives 18A-E. Treatment of compounds 18A-E with DBU produced the corresponding 2,3'-anhydro nucleosides 19A-E with a free 2'-OH group. After deoxygenation of 2'-O-[[(4-methylphenyl)oxy]thiocarbonyl] compounds 20A-E with tributyltin hydride the 2,3'-anhydro bridge of the 2'-deoxynucleosides 21A-E was opened with LiN3 to produce the protected 3'-azido-2,3'-dideoxynucleoside derivatives 22A-G. Saponification with NaOCH3 gave 1-(3'-azido-2',3',5'-trideoxy-beta-D-allofuranosyl)thymine (2; homo-AZT), the 5'-C-(hydroxymethyl) derivatives of AZT 1-(3'-azido-2',3'- dideoxy-beta-D-allofuranosyl)thymine (3) and 1-(3'-azido-2',3'-dideoxy-alpha-L-talofuranosyl)thymine (4), and the 5'-C-methyl derivatives of AZT 1-(3'-azido-2',3',6'-trideoxy-beta-D-allofuranosyl)thymine (5) and 1-(3'-azido-2',3',6'-trideoxy-alpha-L-talofuranosyl)thymine (6). Compounds 2-6 were evaluated for their inhibitory effect on human immunodeficiency virus type 1 (HIV-1) and type 2 (HIV-2) replication in MT-4 cells and found inactive at subtoxic concentrations. Compounds 2-4 and 6 are not effective against herpes simplex virus type 1 (HSV-1) and type 2 (HIV-2), vaccinia virus (VV), and vesicular stomatitis virus (VSV) at 400 micrograms/mL. 5 is slightly active against HSV-1, HSV-2 and VV at 150, 300, and 300 micrograms/mL, respectively.
Antisense-mediated exon skipping: A versatile tool with therapeutic and research applications (2007)

Antisense-mediated modulation of splicing is one of the few fields where antisense oligonucleotides (AONs) have been able to live up to their expectations. In this approach, AONs are implemented to restore cryptic splicing, to change levels of alternatively spliced genes, or, in case of Duchenne muscular dystrophy (DMD), to skip an exon in order to restore a disrupted reading frame. The latter allows the generation of internally deleted, but largely functional, dystrophin proteins and would convert a severe DMD into a milder Becker muscular dystrophy phenotype. In fact, exon skipping is currently one of the most promising therapeutic tools for DMD, and a successful first-in-man trial has recently been completed. In this review the applicability of exon skipping for DMD and other diseases is described. For DMD AONs have been designed for numerous exons, which has given us insight into their mode of action, splicing in general, and splicing of the DMD gene in particular. In addition, retrospective analysis resulted in guidelines for AON design for DMD and most likely other genes as well. This knowledge allows us to optimize therapeutic exon skipping, but also opens up a range of other applications for the exon skipping approach.
Agreement in Assessing Cup-to-Disc Ratio Measurement Among Stereoscopic Optic Nerve Head Photographs, HRT II, and Stratus OCT (2006)

Although the overall agreement between various methods was good, the mean estimates were statistically different. Additional studies are needed to evaluate the sources of variability, their level of significance, and longitudinal agreement between various methods of the CDR estimation.
Immunotherapeutic Applications of IL-15 (2012)

IL-15 is a member of the IL-2 family of cytokines, which play a fundamental role in innate and adaptive immune responses. IL-15 has pleiotropic immune-enhancing activities, as it stimulates NK, T and NKT cell proliferation, survival and effector functions. In view of these properties, IL-15 is regarded as a good candidate for cancer immunotherapy. This possibility is reinforced by its low toxicity and efficacy in preclinical tumor models. The use of IL-15 to boost the immune response in HIV infection has also been proposed, although further studies are required to establish potential risks and benefits. Clinical trials of IL-15 have been initiated in cancer patients and in HIV vaccination and will elucidate the potential of IL-15-based immunotherapy. The purpose of this review is to provide an update on the potential applications of IL-15 in cancer immunotherapy and HIV infection.
Cloning and nucleotide sequences of genes relevant for biosynthesis of poly(3‐hydroxybutyric acid) in Chromatium vinosum strain D (1992)

From a genomic library of Chromatium vinosum strain D in lambda L47, a 16.5-kbp EcoRI-restriction fragment was identified by hybridization with a DNA fragment harboring the operon for Alcaligenes eutrophus poly(3-hydroxyalkanoate) (PHA) synthesis. This fragment and subfragments thereof restored the ability to synthesize and accumulate PHA in PHA-negative mutants of A. eutrophus. A region of 6977 bp was sequenced; seven open reading frames (ORFs) were identified which probably represent coding regions; six of these are most probably relevant for PHA biosynthesis in C. vinosum. The structural genes for biosynthetic acetyl-CoA acyltransferase (beta-ketothiolase; phbACv, 1188 bp) and NADH-dependent acetoacetyl-CoA reductase (phbBCv, 741 bp) were separated by ORF4 (462 bp) and ORF5 (369 bp). Downstream of phbBCv ORF7 (471 pb) was identified which was not completed at the 3' terminus. The functions of ORF4, ORF5, and ORF7 are not known. The amino acid sequences of beta-ketothiolase and acetoacetyl-CoA reductase deduced from phbACv and phbBCv, exhibited a similarity of 68.2% and 56.4% identical amino acids, respectively, to the corresponding enzymes of A. eutrophus. Antilinear to and upstream of the genes mentioned above, two genes were identified which were transcribed from a sigma 70-dependent promoter. This promoter overlapped with and was divergent to the phbACv promoter; the transcriptional start sites were mapped by S1 nuclease protection assays. These genes were ORF2 (1074 bp), whose function is not known but whose presence in Escherichia coli is essential for expression of PHA synthase activity, and the structural gene for a PHA synthase of low M(r) (phbCCv, 1068 bp). The gene products of ORF2 and phbCCv, with M(r) of 40,525 and 39,730, respectively, were expressed in E. coli applying the T7 RNA polymerase/promoter system. Although the amino acid sequence of PHA synthase deduced from phbCCv exhibited only 24.7% overall similarity with the PHA synthase of A. eutrophus, highly conserved regions were identified.
Waveform Design for Sum Rate Optimization in Time-Reversal Multiuser Downlink Systems (2011)

Utilizing channel reciprocity, the traditional time-reversal technique boosts the signal-to-noise ratio at the receiver with very low transmitter complexity. However, the large delay spread gives rise to severe inter-symbol interference (ISI) when the data rate is high, and the performance is further degraded in the multiuser downlink due to the inter-user interference (IUI). In this work, we study the weighted sum rate optimization problem in the time-reversal multiuser downlink using waveform design. By exploiting the relation between the allocated power and the SINR targets, an iterative algorithm is proposed to optimize the waveform design through a new power allocation algorithm. Simulation results are shown to demonstrate the superior performance of the proposed algorithm in comparison with other traditional methods.
Toward a Generalized and High-throughput Enzyme Screening System Based on Artificial Genetic Circuits (2013)

Large-scale screening of enzyme libraries is essential for the development of cost-effective biological processes, which will be indispensable for the production of sustainable biobased chemicals. Here, we introduce a genetic circuit termed the Genetic Enzyme Screening System that is highly useful for high-throughput enzyme screening from diverse microbial metagenomes. The circuit consists of two AND logics. The first AND logic, the two inputs of which are the target enzyme and its substrate, is responsible for the accumulation of a phenol compound in cell. Then, the phenol compound and its inducible transcription factor, whose activation turns on the expression of a reporter gene, interact in the other logic gate. We confirmed that an individual cell harboring this genetic circuit can present approximately a 100-fold higher cellular fluorescence than the negative control and can be easily quantified by flow cytometry depending on the amounts of phenolic derivatives. The high sensitivity of the genetic circuit enables the rapid discovery of novel enzymes from metagenomic libraries, even for genes that show marginal activities in a host system. The crucial feature of this approach is that this single system can be used to screen a variety of enzymes that produce a phenol compound from respective synthetic phenyl-substrates, including cellulase, lipase, alkaline phosphatase, tyrosine phenol-lyase, and methyl parathion hydrolase. Consequently, the highly sensitive and quantitative nature of this genetic circuit along with flow cytometry techniques could provide a widely applicable toolkit for discovering and engineering novel enzymes at a single cell level.
The stereotactic approach for mapping epileptic networks: a prospective study of 200 patients (2014)

Based on these results, SEEG methodology is safe, reliable, and effective. It is associated with minimal morbidity and mortality, and serves as a practical, minimally invasive approach to extraoperative localization of the epileptogenic zone in patients with refractory epilepsy.