gebhart/patrepeval huggingface dataset:
Stepwise Charge Separation from a Ruthenium−Tyrosine Complex to a Nanocrystalline TiO<sub>2</sub> Film (2004)

A supramolecular complex composed of Ru(II) tris-bipyridine, tyrosine, and dipicolylamine was synthesized and characterized. This complex was attached to TiO2 nanocrystalline films via ester groups at the Ru(II) chromophore, and photoinduced multistep electron transfer was investigated by laser flash photolysis and electron paramagnetic resonance techniques. Following ultrafast electron injection from the metal−ligand charge transfer excited states of Ru(II) to the conduction band of TiO2, fast intramolecular electron transfer from the tyrosine moiety to the photogenerated Ru(III) was observed, characterized by a rate constant of ∼2 × 106 s-1. By comparison of recovery kinetics at the isosbestic point with that of the reference compound lacking the tyrosine, it was found that the intramolecular electron-transfer efficiency is 90%. A hydrogen-bond-promoted electron-transfer mechanism is proposed.
Resolving Users' Behavior Modeling Ambiguities in Fuzzy-Timed Smart Homes Using Only RFIDs (2006)

Summary Context aware systems successfully exploit the knowledge of the users’ actions—presumably in concordance with the environmental parameters of the smart space that they dwell in such as, their location inside the smart space, current time, etc—in providing ambient-intelligent services like automatic, reactive lighting-appliance control and proactive temperature control. In the past, this kind of intelligence has been realized using high-end sensing technologies like video cameras, microphones and environmental sensors such as pressure sensing pads, ambient light-level sensors, temperature sensors, etc. In this paper, we attempt to realize location, time and behavior aware smart spaces using only Radio Frequency Identification Device (RFID) Technology. RFIDs have been effective in object and people tracking, but using RFIDs results in ambiguities in inferring users’ activities accurately. We propose to resolve this ambiguity using Bayesian Belief Networks (BBNs). We employ a learning system that models time as fuzzy slots to assist users’ location prediction. Our system uses an unobtrusive, negative reinforcement learning (NRL) technique that learns users’ behaviors without querying the users of their actions—as typically been done in previous implementations to improve prediction accuracy. The key contributions of our work are that we have proposed a novel method for modeling users’ behaviors using RFID technology and shown the experimental results of the same.
Susceptibilities of Antiviral-Resistant Influenza Viruses to Novel Neuraminidase Inhibitors (2005)

The susceptibilities of five zanamivir-resistant and six oseltamivir-resistant influenza viruses were assessed against four neuraminidase (NA) inhibitors, including peramivir and A-315675, by a fluorometric NA activity inhibition assay. The enzyme activity of a majority of the variants was effectively inhibited by either A-315675 or both peramivir and A-315675 (50% inhibitory concentration, <10 nM). A novel oseltamivir-resistant influenza virus B variant carrying substitution at residue 198 (Asp-->Asn) (N2 numbering) retained susceptibility to peramivir and A-315675. In vivo, the Asn198 variant showed no apparent fitness impairment as judged by its recovery on day 5 from the nasal washes of ferrets coinfected with equal doses of the wild-type virus and the Asn198 variant. Based on the sequence analysis of the virus in the nasal washes, oseltamivir treatment (5 mg/kg twice daily for 5 days) did not provide growth advantage to the Asn198 variant. Nevertheless, treatment with A-315675 (prodrug A-322278) reduced the number of the animals (two of seven) shedding the Asn198 variant. These studies indicate that different patterns of susceptibility and cross-resistance between NA inhibitors may prove important if antiviral resistance to zanamivir and oseltamivir were to emerge.
The Role of Tissue Macrophage-Mediated Inflammation on NAFLD Pathogenesis and Its Clinical Implications (2017)

The obese phenotype is characterized by a state of chronic low-grade systemic inflammation that contributes to the development of comorbidities, including nonalcoholic fatty liver disease (NAFLD). In fact, NAFLD is often associated with adipocyte enlargement and consequent macrophage recruitment and inflammation. Macrophage polarization is often associated with the proinflammatory state in adipose tissue. In particular, an increase of M1 macrophages number or of M1/M2 ratio triggers the production and secretion of various proinflammatory signals (i.e., adipocytokines). Next, these inflammatory factors may reach the liver leading to local M1/M2 macrophage polarization and consequent onset of the histological damage characteristic of NAFLD. Thus, the role of macrophage polarization and inflammatory signals appears to be central for pathogenesis and progression of NAFLD, even if the heterogeneity of macrophages and molecular mechanisms that govern their phenotype switch remain incompletely understood. In this review, we discuss the role of adipose and liver tissue macrophage-mediated inflammation in experimental and human NAFLD. This focus is relevant because it may help researchers that approach clinical and experimental studies on this disease advancing the knowledge of mechanisms that could be targeted in order to revert NAFLD-related fibrosis.
Development of the Conscious Sedation Scale: Establishing Content Validity and Reliability (1997)

The purpose of this study was to determine content validity and reliability of the Consciousness Sedation Scale (CSS), an instrument developed as a documentation tool for patient response during invasive procedures using intravenous conscious sedation. Instrument items were developed to reflect goals of conscious sedation recommended by the Association of Operating Room Nurses. Content validity of the parameters and grades was established at Content Validity Index (CVI) .875. Cronbach's coefficient alpha of .69 indicated insufficient reliability of discriminatory items between grades. Further refinement of the tool was indicated.
MobiPack: optimal hitless SONET defragmentation in near-optimal cost (2004)

We study the problem of bandwidth fragmentation in links that comprise rings and meshes in SONET networks. Fragmentation is a serious challenge for network operators since it creates "holes" in the transport pipe causing new demands to be rejected, in spite of sufficient bandwidth being available. Unlike the well-studied, general fragmentation problem, link defragmentation is "hard" and novel due to some unique constraints imposed by the SONET standard. Since a defragmentation operation typically occurs on a network carrying live traffic, in addition to the "quality" of the output, any link defragmentation algorithm has to avoid traffic hit and also optimize the "cost" of reorganizing circuits. We propose an algorithm called mobipack that is optimal in its defragmentation quality. Moreover, we demonstrate via extensive simulations, that it also achieves its goal in a hitless manner with only marginal additional cost over the optimal, making it extremely attractive to use in practice
IgG subclass profiles in normal human sera of antibodies specific to five kinds of microbial antigens (2013)

The levels of subclass-specific immunoglobulin G (IgG) antibodies to five microbial antigens in normal human sera were measured by enzyme-linked immunosorbent assays (ELISA). The aim was to compare the IgG subclass profiles of specific antibodies to diverse antigens originating from virus, intra- and extracellular bacteria. Serum samples from 162 Danish women were analyzed for IgG1, IgG2, IgG3, and IgG4 antibodies against a peptide of the major outer membrane protein (MOMP) of Chlamydia trachomatis, the native outer membrane proteins of Chlamydia pneumoniae, recombinant membrane proteins of Mycoplasma pneumoniae, recombinant parvovirus B19 capsomers (VP1 and VP2) and C-polysaccharide of Streptococcus pneumoniae (pneumococcus). Antibodies specific for viral and bacterial protein antigens belonged mainly to the subclasses IgG1 and IgG3 while the antibody profile specific for pneumococcal C-polysaccharide was dominated by the subclass IgG2. Antibodies to virus, intra- and extracellular bacteria entering the body via the respiratory tract were found primarily to elicit an IgG1 response. In contrast, antibodies specific for MOMP from C. trachomatis, which infects the urogenital tract, were predominantly IgG3. Our results show that the nature of the antigen and/or the site of colonization or infection have impact on which type of IgG subclass a microorganism elicits.
The role of deoxyuridine triphosphate nucleotidohydrolase, uracil-DNA glycosylase, and DNA polymerase alpha in the metabolism of FUdR in human tumor cells. (1980)

The lack of evidence demonstrating FdUMP residues in DNA or FdUTP in cells after exposure to FUdR could be due either to the breakdown of FdUTP by dUTP nucleotidohydrolase (dUTPase) precluding incorporation of FdUTP into DNA via DNA polymerase or to the action of uracil-DNA glycosylase which would remove fluorouracil from DNA. Evidence presented indicates that the human cell has the capacity to form FdUTP and that FdUTP, once formed, will act as a substrate for dUTPase as well as α DNA polymerase. In addition, if FdUTP escapes hydrolysis and is incorporated into DNA, uracil-DNA glycosylase is capable of removing the FU moiety from DNA, creating an apyrimidinic site which conceivably would undergo repair synthesis. Various cultured cell lines and cells obtained from patients with different forms of leukemia were analyzed for dUTPase and glycosylase activity. The specific activity for dUTPase ranged from 0.5 to 14 nmol dUMP formed/min/mg protein. For the glycosylase, the activity ranged from 0.3 to 42 nmol uracil released/min/mg protein. Cytosols prepared from cultured HeLa S3 and KB cells were used to show that FdUTP can be formed, however, only in the presence of high concentrations of dUTP (1 mM), which presumably slows down the hydrolysis of FdUTP by dUTPase. Enzymatic studies utilizing partially purified nucleoside monophosphate kinase and highly purified thymidylate kinase illustrate that both of these enzyme species have the capability of phosphorylating FdUMP to FdUDP. NDP kinase is in turn responsible for the conversion of FdUDP to FdUTP. The Km value of FdUMP for the partially purified HeLa S3 CMP kinase (species having a pI value of 4.8) is 4 mM. The Km value of FdUMP for the highly purified TMP kinase is 225 µM. FdUTP is a substrate for the purified human dUTPase (Km of 1.2 µM) which catalyzes the conversion of FdUTP to FdUMP. Purified HeLa α DNA polymerase will catalyze the incorporation of FdUTP into DNA. The Km of FdUTP for α DNA polymerase is 4.8 µM. In turn the incorporated fluorouracil will act as a substrate for uracil-DNA glycosylase, having a Km value of 1.4 µM.
Theranostic applications of antibodies in oncology (2014)

Targeted therapies, including antibodies, are becoming increasingly important in cancer therapy. Important limitations, however, are that not every patient benefits from a specific antibody therapy and that responses could be short-lived due to acquired resistance. In addition, targeted therapies are quite expensive and are not completely devoid of side-effects. This urges the need for accurate patient selection and response monitoring. An important step towards personalizing antibody treatment could be the implementation of theranostics. Antibody theranostics combine the diagnostic and therapeutic potential of an antibody, thereby selecting those patients who are most likely to benefit from antibody treatment. This review focuses on the clinical application of theranostic antibodies in oncology. It provides detailed information concerning the suitability of antibodies for theranostics, the different types of theranostic tests available and summarizes the efficacy of theranostic antibodies used in current clinical practice. Advanced theranostic applications, including radiolabeled antibodies for non-invasive functional imagining, are also addressed. Finally, we discuss the importance of theranostics in the emerging field of personalized medicine and critically evaluate recent data to determine the best way to apply antibody theranostics in the future.
Molecular regulation of sinapate ester metabolism in<i>Brassica napus</i>: expression of genes, properties of the encoded proteins and correlation of enzyme activities with metabolite accumulation (2004)

Members of the Brassicaceae family accumulate specific sinapate esters, i.e. sinapoylcholine (sinapine), which is considered as a major antinutritive compound in seeds of important crop plants like Brassica napus, and sinapoylmalate, which is implicated in UV-B tolerance in leaves. We have studied the molecular regulation of the sinapate ester metabolism in B. napus, and we describe expression of genes, some properties of the encoded proteins and profiles of the metabolites and enzyme activities. The cloned cDNAs encoding the key enzymes of sinapine biosynthesis, UDP-glucose (UDP-Glc):B. napus sinapate glucosyltransferase (BnSGT1) and sinapoylglucose:B. napus choline sinapoyltransferase (BnSCT), were functionally expressed. BnSGT1 belongs to a subgroup of plant GTs catalysing the formation of 1-O-hydroxycinnamoyl-beta-d-glucoses. BnSCT is another member of serine carboxypeptidase-like (SCPL) family of acyltransferases. The B. napus genome contains at least two SGT and SCT genes, each derived from its progenitors B. oleracea and B. rapa. BnSGT1 and BnSCT activities are subjected to pronounced transcriptional regulation. BnSGT1 transcript level increases throughout early stages of seed development until the early cotyledonary stage, and stays constant in later stages. The highest level of BnSGT1 transcripts is reached in 2-day-old seedlings followed by a dramatic decrease. In contrast, expression of BnSCT is restricted to developing seeds. Regulation of gene expression at the transcript level seems to be responsible for changes of BnSGT1 and BnSCT activities during seed and seedling development of B. napus. Together with sinapine esterase (SCE) and sinapoylglucose:malate sinapoyltransferase (SMT), activities of BnSGT1 and BnSCT show a close correlation with the accumulation kinetics of the corresponding metabolites.
Robust unsupervised detection of human screams in noisy acoustic environments (2015)

This study is focused on an unsupervised approach for detection of human scream vocalizations from continuous recordings in noisy acoustic environments. The proposed detection solution is based on compound segmentation, which employs weighted mean distance, T <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> -statistics and Bayesian Information Criteria for detection of screams. This solution also employs an unsupervised threshold optimized Combo-SAD for removal of non-vocal noisy segments in the preliminary stage. A total of five noisy environments were simulated for noise levels ranging from -20dB to +20dB for five different noisy environments. Performance of proposed system was compared using two alternative acoustic front-end features (i) Mel-frequency cepstral coefficients (MFCC) and (ii) perceptual minimum variance distortionless response (PMVDR). Evaluation results show that the new scream detection solution works well for clean, +20, +10 dB SNR levels, with performance declining as SNR decreases to -20dB across a number of the noise sources considered.
STRATIGRAPHIC PROCESSING OF 3D SEISMIC BY CONCURRENT ANALYSIS OF SURFACE AND BOREHOLE DATA (1989)

When seismic data is available in production areas, it is often desirable to use it for stratigraphic interpretation, to estimate the extent of existing reservoirs. 3D seismic data, which contains the producing wells within its volume, is particularly suitable for such an exercise. We present an interpretive processing procedure, supported by a case study, where surface and borehole data are used in cooperation to achieve maximum reliability of the final surface seismic inversion.
Performance Implications of Packet Filtering with Linux eBPF (2018)

Firewall capabilities of operating systems are traditionally provided by inflexible filter routines or hooks in the kernel. These require privileged access to be configured and are not easily extensible for custom low-level actions. Since Linux 3.0, the Berkeley Packet Filter (BPF) allows user-written extensions in the kernel processing path. The successor, extended BPF (eBPF), improves flexibility and is realized via a virtual machine featuring both a just-in-time (JIT) compiler and an interpreter running in the kernel. It executes custom eBPF programs supplied by the user, effectively moving kernel functionality into user space. We present two case studies on the usage of Linux eBPF. First, we analyze the performance of the eXpress Data Path (XDP). XDP uses eBPF to process ingress traffic before the allocation of kernel data structures which comes along with performance benefits. In the second case study, eBPF is used to install application-specific packet filtering configurations acting on the socket level. Our case studies focus on performance aspects and discuss benefits and drawbacks.
Enabling hardware-software multitasking on a reconfigurable computing platform for networked portable multimedia appliances (2002)

This paper describes a user scenario that motivates the introduction of reconfigurable hardware into portable devices together with a vision on the platform that should be built to support reconfigurable computing. Solutions for both the hardware and software problems are presented. Finally, a first demonstrator is depicted
DFineNet: Ego-Motion Estimation and Depth Refinement from Sparse, Noisy Depth Input with RGB Guidance (2019)

Depth estimation is an important capability for autonomous vehicles to understand and reconstruct 3D environments as well as avoid obstacles during the execution. Accurate depth sensors such as LiDARs are often heavy, expensive and can only provide sparse depth while lighter depth sensors such as stereo cameras are noiser in comparison. We propose an end-to-end learning algorithm that is capable of using sparse, noisy input depth for refinement and depth completion. Our model also produces the camera pose as a byproduct, making it a great solution for autonomous systems. We evaluate our approach on both indoor and outdoor datasets. Empirical results show that our method performs well on the KITTI~\cite{kitti_geiger2012we} dataset when compared to other competing methods, while having superior performance in dealing with sparse, noisy input depth on the TUM~\cite{sturm12iros} dataset.
Different Effects of sgRNA Length on CRISPR-mediated Gene Knockout Efficiency (2016)

CRISPR-Cas9 is a powerful genome editing technology, yet with off-target effects. Truncated sgRNAs (17nt) have been found to decrease off-target cleavage without affecting on-target disruption in 293T cells. However, the potency of 17nt sgRNAs relative to the full-length 20nt sgRNAs in stem cells, such as human mesenchymal stem cells (MSCs) and induced pluripotent stem cells (iPSCs), has not been assessed. Using a GFP reporter system, we found that both 17nt and 20nt sgRNAs expressed by lentiviral vectors induce ~95% knockout (KO) in 293T cells, whereas the KO efficiencies are significantly lower in iPSCs (60-70%) and MSCs (65-75%). Furthermore, we observed a decrease of 10-20 percentage points in KO efficiency with 17nt sgRNAs compared to full-length sgRNAs in both iPSCs and MSCs. Off-target cleavage was observed in 17nt sgRNAs with 1-2nt but not 3-4nt mismatches; whereas 20nt sgRNAs with up to 5nt mismatches can still induce off-target mutations. Of interest, we occasionally observed off-target effects induced by the 17nt but not the 20nt sgRNAs. These results indicate the importance of balancing on-target gene cleavage potency with off-target effects: when efficacy is a major concern such as genome editing in stem cells, the use of 20nt sgRNAs is preferable.
Improved multidirectional associative memories for training sets including common terms (2003)

Improved multidirectional associative memories (IMAMs) are proposed and simulated. The IMAM fundamental component is a multilayer neural network. IMAMs can memorize and recall multiple associations even when training sets include common terms, such as the training sets composed of (A,a,1), (A,b,2), (C,b,3). The structure of the proposed IMAMs is represented by mutual connections of multilayer neural networks. The proposed IMAMs require less parameters compared with other associative memories and are capable of automatic recall. Recall performance can be greatly improved by using a priority coefficient.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Isolation and in vitro translation of zein messenger ribonucleic acid (1976)

Zein messenger RNA was isolated from membrane-bound polyribosomes of developing maize kernels by oligo(dT)-cellulose chromatography. Translation of the mRNA in vitro yielded protein similar to native zein in amino acid content, ethanol solubility, and mobility on sodium dodecyl sulfate- polyacrylamide gels. The zein mRNA sedimented as a homogeneous peak on sucrose gradients and contained a poly(A)-rich region based upon hybridization to [3H]poly(U). The mRNA had an apparent molecular weight of 540 000 on agarose-acrylamide gels. It synthesized both 21 800 and 19 000 molecular weight zein components in the wheat-germ cell-free protein synthesis system. The possibility of a polycistronic mRNA or two mRNAs of similar molecular weight is considered.
Encyclopedia of plant pathology (2001)

This is the first truly comprehensive A-Z reference work on the subject, having approximately 2,000 pages in a practical two-volume format. The full-length entries provide detail that glossaries and dictionaries cannot. Over 900 individual entries provide thorough coverage, and a number of biographical entries are included on important plant pathologists and plant scientists.
Molecular analysis of a chromosomal translocation, t(9;14)(p13;q32), in a diffuse large-cell lymphoma cell line expressing the Ki-1 antigen. (1990)

We have studied a translocation, t(9;14)(p13;q32), in a diffuse large-cell lymphoma cell line, KIS-1, that expresses the Ki-1 (CD30) antigen. Molecular cloning of the immunoglobulin heavy-chain locus (IGH) of this cell line revealed an unknown segment linked 5' to IGH. The breakpoint on chromosome 14 was 265 base pairs downstream from the 3' border of the JH6 joining gene segment. Class switch recombination deleted most of the constant genes of IGH (CH) and juxtaposed the C alpha 2 gene downstream of the translocation junction. Analysis of somatic cell hybrids and in situ chromosomal hybridization demonstrated that the translocated segment was normally located at band p13 of chromosome 9. The chromosome 9 sequences were transcriptionally active, giving rise to transcripts of approximately 11 kilobases. The KIS-1 cells seemed to have a small quantity of chimeric transcripts containing both chromosome 9 and C alpha 2 sequences.
Disseminated Phialophora parasitica Infection in Humans: Case Report and Review (1989)

A case of recurrent systemic infection caused by Phialophora parasitica occurred in an elderly woman and over a 4-year period was documented (either clinically or at autopsy) to involve two sites on the chest wall, the hip, the vertebral body, and the aorta. The infection was treated with intravenous amphotericin B and a subsequent course of terbinafine. To our knowledge, this is the first reported case of disseminated infection by P. parasitica with systemic involvement as well as of its treatment with terbinafine. The literature on human infection caused by P. parasitica, which is rare and has occurred in both normal and compromised hosts and with and without antecedent trauma, was reviewed; problems encountered both in the laboratory identification of P. parasitica and in therapy were assessed.