gebhart/patrepeval huggingface dataset:
Interaction Properties of Human Mannan-Binding Lectin (MBL)-Associated Serine Proteases-1 and -2, MBL-Associated Protein 19, and MBL (2001)

The mannan-binding lectin (MBL) activation pathway of complement plays an important role in the innate immune defense against pathogenic microorganisms. In human serum, two MBL-associated serine proteases (MASP-1, MASP-2) and MBL-associated protein 19 (MAp19) were found to be associated with MBL. With a view to investigate the interaction properties of these proteins, human MASP-1, MASP-2, MAp19, as well as the N-terminal complement subcomponents C1r/C1s, Uegf, and bone morphogenetic protein-1-epidermal growth factor (CUB-EGF) segments of MASP-1 and MASP-2, were expressed in insect or human kidney cells, and MBL was isolated from human serum. Sedimentation velocity analysis indicated that the MASP-1 and MASP-2 CUB-EGF segments and the homologous protein MAp19 all behaved as homodimers (2.8-3.2 S) in the presence of Ca(2+). Although the latter two dimers were not dissociated by EDTA, their physical properties were affected. In contrast, the MASP-1 CUB-EGF homodimer was not sensitive to EDTA. The three proteins and full-length MASP-1 and MASP-2 showed no interaction with each other as judged by gel filtration and surface plasmon resonance spectroscopy. Using the latter technique, MASP-1, MASP-2, their CUB-EGF segments, and MAp19 were each shown to bind to immobilized MBL, with K:(D) values of 0.8 nM (MASP-2), 1.4 nM (MASP-1), 13.0 nM (MAp19 and MASP-2 CUB-EGF), and 25.7 nM (MASP-1 CUB-EGF). The binding was Ca(2+)-dependent and fully sensitive to EDTA in all cases. These data indicate that MASP-1, MASP-2, and MAp19 each associate as homodimers, and individually form Ca(2+)-dependent complexes with MBL through the CUB-EGF pair of each protein. This suggests that distinct MBL/MASP complexes may be involved in the activation or regulation of the MBL pathway.
Towards Respiration Rate Monitoring Using an In-Ear Headphone Inertial Measurement Unit (2019)

State-of-the-art respiration tracking devices require specialized equipment, making them impractical for every day at-home respiration sensing. In this paper, we present the first system for sensing respiratory rates using in-ear headphone inertial measurement units (IMU). The approach is based on technology already available in commodity devices: the eSense headphones. Our processing pipeline combines several existing approaches to clean noisy data and calculate respiratory rates on 20-second windows. In a study with twelve participants, we compare accelerometer and gyroscope based sensing and employ pressure-based measurement with nasal cannulas as ground truth. Our results indicate a mean absolute error of 2.62 CPM (acc) and 2.55 CPM (gyro). This overall accuracy is comparable to previous approaches using accelerometer-based sensing, but we observe a higher relative error for the gyroscope. In contrast to related work using other sensor positions, we can not report significant differences between the two modalities or the three postures standing, sitting, and lying on the back (supine). However, in general, performance varies drastically between participants.
Quantum information processing using quasiclassical electromagnetic interactions between qubits and electrical resonators (2013)

Electrical resonators are widely used in quantum information processing, by engineering an electromagnetic interaction with qubits based on real or virtual exchange of microwave photons. This interaction relies on strong coupling between the qubits' transition dipole moments and the vacuum fluctuations of the resonator in the same manner as cavity QED, and has consequently come to be called "circuit QED" (cQED). Great strides in the control of quantum information have already been made experimentally using this idea. However, the central role played by photon exchange induced by quantum fluctuations in cQED does result in some characteristic limitations. In this paper, we discuss an alternative method for coupling qubits electromagnetically via a resonator, in which no photons are exchanged, and where the resonator need not have strong quantum fluctuations. Instead, the interaction can be viewed in terms of classical, effective "forces" exerted by the qubits on the resonator, and the resulting resonator dynamics used to produce qubit entanglement are purely classical in nature. We show how this type of interaction is similar to that encountered in the manipulation of atomic ion qubits, and we exploit this analogy to construct two-qubit entangling operations that are largely insensitive to thermal or other noise in the resonator, and to its quality factor. These operations are also extensible to larger numbers of qubits, allowing interactions to be selectively generated among any desired subset of those coupled to a single resonator. Our proposal is potentially applicable to a variety of physical qubit modalities, including superconducting and semiconducting solid-state qubits, trapped molecular ions, and possibly even electron spins in solids.
Critical Comparison of 31 Commercially Available Digital Slide Systems in Pathology (2006)

Advances in new technologies for complete slide digitization in pathology have allowed the appearance of a wide spectrum of technologic solutions for whole-slide scanning, which have been classified into motorized microscopes and scanners. This article describes technical aspects of 31 different digital microscopy systems. The most relevant characteristics of the scanning devices are described, including the cameras used, the speed of digitization, and the image quality. Other aspects, such as the file format, the compression techniques, and the solutions for visualization of digital slides, (including diagnosis-aided tools) are also considered. Most of the systems evaluated allow a high-resolution digitization of the whole slide within about 1 hour using a x40 objective. The image quality of the current virtual microscopy systems is suitable for clinical, educational, and research purposes. The efficient use of digital microscopy by means of image analysis systems can offer important benefits to pathology departments.
Joint Variant and De Novo Mutation Identification on Pedigrees from High-Throughput Sequencing Data (2014)

The analysis of whole-genome or exome sequencing data from trios and pedigrees has been successfully applied to the identification of disease-causing mutations. However, most methods used to identify and genotype genetic variants from next-generation sequencing data ignore the relationships between samples, resulting in significant Mendelian errors, false positives and negatives. Here we present a Bayesian network framework that jointly analyzes data from all members of a pedigree simultaneously using Mendelian segregation priors, yet providing the ability to detect de novo mutations in offspring, and is scalable to large pedigrees. We evaluated our method by simulations and analysis of whole-genome sequencing (WGS) data from a 17-individual, 3-generation CEPH pedigree sequenced to 50× average depth. Compared with singleton calling, our family caller produced more high-quality variants and eliminated spurious calls as judged by common quality metrics such as Ti/Tv, Het/Hom ratios, and dbSNP/SNP array data concordance, and by comparing to ground truth variant sets available for this sample. We identify all previously validated de novo mutations in NA12878, concurrent with a 7× precision improvement. Our results show that our method is scalable to large genomics and human disease studies.
Spontaneous and evoked ectopic discharges recorded from single human axons (1998)

A quantitative assessment was made of the firing characteristics of repetitive axonal discharges encountered during microneurographic recordings from human peripheral nerves. Spontaneous activity was recorded from 16 single axons using tungsten microelectrodes inserted percutaneously into fascicles of the median or peroneal nerves in normal subjects. These discharges typically consisted of brief bursts of 2-5 spikes occurring at a frequency of 7-10 Hz. Peak instantaneous frequencies usually exceeded 300 Hz. Based on their similarity with spontaneous high-frequency discharges recorded from single axons following nerve damage, ischemia, prolonged electrical stimulation, or hyperventilation, it is concluded that they are generated ectopically at the site of a previous impalement of a nerve fiber. It is suggested that short-term damage to the nerve fiber caused by the microelectrode may allow accumulation of K+ underneath the myelin, triggering an inward flow of K+ and regenerative depolarizations. Alternatively, internodal channels may be exposed following damage to the myelin, resulting in the generation of spontaneous pacemaker potentials and repetitive discharges.
Promoter elements of rice susceptibility genes are bound and activated by specific TAL effectors from the bacterial blight pathogen, Xanthomonas oryzae pv. oryzae (2010)

*Plant pathogenic bacteria of the genus Xanthomonas inject transcription activator-like effector (TALe) proteins that bind to and activate host promoters, thereby promoting disease or inducing plant defense. TALes bind to corresponding UPT (up-regulated by TALe) promoter boxes via tandemly arranged 34/35-amino acid repeats. Recent studies uncovered the TALe code in which two amino acid residues of each repeat define specific pairing to UPT boxes. *Here we employed the TALe code to predict potential UPT boxes in TALe-induced host promoters and analyzed these via beta-glucuronidase (GUS) reporter and electrophoretic mobility shift assays (EMSA). *We demonstrate that the Xa13, OsTFX1 and Os11N3 promoters from rice are induced directly by the Xanthomonas oryzae pv. oryzae TALes PthXo1, PthXo6 and AvrXa7, respectively. We identified and functionally validated a UPT box in the corresponding rice target promoter for each TALe and show that box mutations suppress TALe-mediated promoter activation. Finally, EMSA demonstrate that code-predicted UPT boxes interact specifically with corresponding TALes. *Our findings show that variations in the UPT boxes of different rice accessions correlate with susceptibility or resistance of these accessions to the bacterial blight pathogen.
Inhibitory effect of duramycin on partial reactions catalyzed by sodium-potassium adenosinetriphosphatase from dog kidney (1984)

The polypeptide antibiotic duramycin inhibited the (Na+,K+)-adenosinetriphosphatase purified from dog kidney. An analysis of its mode of action revealed that the formation of phosphoenzyme from Pi but not from ATP was inhibited. The rate of dephosphorylation of the phosphoenzyme formed from ATP was markedly reduced. In contrast to quercetin, duramycin did not inhibit K+-dependent p-nitrophenylphosphatase activity. The effect of duramycin was completely reversed by phospholipids.
CR8, a Novel Inhibitor of CDK, Limits Microglial Activation, Astrocytosis, Neuronal Loss, and Neurologic Dysfunction after Experimental Traumatic Brain Injury (2014)

Central nervous system injury causes a marked increase in the expression of cell cycle-related proteins. In this study, we show that cell cycle activation (CCA) is detected in mature neurons at 24 hours after rat lateral fluid percussion (LFP)-induced traumatic brain injury (TBI), as reflected by increased expression of cyclin G1, phosphorylated retinoblastoma (phospho-Rb), E2F1 and proliferating cell nuclear antigen (PCNA). These changes were associated with progressive cortical, hippocampal, and thalamic neuronal loss and microglial and astrocyte activation. Notably, we detected 5-bromo-2'-deoxyuridine (BrdU)-positive neurons, microglia, and astrocytes at 7 days, but not at 24 hours, suggesting that cell cycle reaches the S phase in these cell types at the latter time point. A delayed systemic post-LFP administration at 3 hours of CR8--a potent second-generation cyclin-dependent kinase (CDK) inhibitor--reduced CCA; cortical, hippocampal, and thalamic neuronal loss; and cortical microglial and astrocyte activation. Furthermore, CR8 treatment attenuated sensorimotor and cognitive deficits, alleviated depressive-like symptoms, and decreased lesion volume. These findings underscore the contribution of CCA to progressive neurodegeneration and chronic neuroinflammation following TBI, and demonstrate the neuroprotective potential of cell cycle inhibition in a clinically relevant experimental TBI model.
Computationally‐Assisted Approach to the Vibrational Spectra of Molecular Crystals: Study of Hydrogen‐Bonding and Pseudo‐Polymorphism (2006)

A new computationally-assisted methodology (PiMM), which accounts for the effects of intermolecular interactions in the crystal, is applied to the complete assignment of the Raman and infrared vibrational spectra of room temperature forms of crystalline caffeine, theobromine, and theophylline. The vibrational shifts due to crystal packing interactions are evaluated from ab initio calculations for a set of suitable molecular pairs, using the B3LYP/6-31G* approach. The proposed methodology provides an answer to the current demand for a reliable assignment of the vibrational spectra of these methyl-xanthines, and clarifies several misleading assignments. The most relevant intermolecular interactions in each system and their effect on the vibrational spectra are considered and discussed. Based on these results, significant insights are obtained for the structure of caffeine in the anhydrous form (stable at room temperature), for which no X-ray structure has been reported. A possible structure based on C((8))--H...N((9)) and C((1,3))--H...O intermolecular interactions is suggested.
Glutathione S-Transferase Pull-Down Assay (2003)

The glutathione S-transferase (GST) pull-down assay is a relatively easy, straightforward method to identify potential protein kinase C (PKC)-binding partners. The method is also extensively used to confirm known interactions and to map interaction sites. The pull-down method relies on the immobilization of a GST fusion protein on glutathione sepharose beads that serve as a solid phase. The first step requires the expression of the PKC domain of interest as a fusion protein with the GST moiety. After binding of the GST fusion protein to the glutathione sepharose matrix, the mixture is incubated with whole-cell homogenate or a purified protein. Nonbound material is washed off the column, and subsequently the binding complex is eluted. Upon elution, the mixture is resolved by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and analyzed by Coomassie staining, silver staining, or Western blot. This chapter focuses on the GST tag; however, other tags, such as hexa-Histidine (6xHis) and maltose-binding protein (MBP), are also commonly used and will be mentioned throughout the chapter (see Note 1).
The 3′-untranslated region of CaMKIIα is a cis-acting signal for the localization and translation of mRNA in dendrites (1996)

Neuronal signaling requires that synaptic proteins be appropriately localized within the cell and regulated there. In mammalian neurons, polyribosomes are found not just in the cell body, but also in dendrites where they are concentrated within or beneath the dendritic spine. The alpha subunit of Ca(2+)-calmodulin-dependent protein kinase II (CaMKII alpha) is one of only five mRNAs known to be present within the dendrites, as well as in the soma of neurons. This targeted subcellular localization of the mRNA for CaMKII alpha provides a possible cell biological mechanism both for controlling the distribution of the cognate protein and for regulating independently the level of protein expression in individual dendritic spines. To characterize the cis-acting elements involved in the localization of dendritic mRNA we have produced two lines of transgenic mice in which the CaMKII alpha promoter is used to drive the expression of a lacZ transcript, which either contains or lacks the 3'-untranslated region of the CaMKII alpha gene. Although both lines of mice show expression in forebrain neurons that parallels the expression of the endogenous CaMKII alpha gene, only the lacZ transcripts bearing the 3'-untranslated region are localized to dendrites. The beta-galactosidase protein shows a variable level of expression along the dendritic shaft and within dendritic spines, which suggests that neurons can control the local biochemistry of the dendrite either through differential localization of the mRNA or variations in the translational efficiency at different sites along the dendrite.
Synthesis of 1-Formyl-1,2-dihydroquinoline Derivatives by a Lewis Acid-Catalyzed Cyclization of o-(1-Hydroxy-2-alkenyl)phenyl Isocyanides (1995)

Abstract An efficient route to 1-formyl-1,2-dihydroquinolines 6 is described based on the BF3-catalyzed cyclization of o-(1-hydroxy-2-alkenyl)phenyl isocyanides 4, which can be prepared feasibly by the reaction of N-(o-acylphenyl)formamides 1 with alkenylmagnesium bromides 2 followed by treatment of the resulting hydroxy formamides 3 with phosphorous oxychloride.
A new phagemid vector for positive selection of recombinants based on a conditionally lethal barnase gene (1999)

A new phagemid cloning vector for positive selection of recombinants, pBa-7, was constructed which contains an active barnase gene encoding the cytotoxic ribonuclease from Bacillus amyloliquefaciens, under control of the lac promoter. PBa-7 is a derivative of the high-copy number pBluescript II KS+ phagemid in which the modified barnase killer gene has been fused downstream from the lac promoter of the pBluescript II KS+ multiple restriction site. When a lacIq-negative Escherichia coli strain is transformed by this vector, the active barnase blocks bacterial growth by massive RNA destruction [1]. However, if barnase is inactivated by insertion of a foreign DNA fragment into the multirestriction site of the vector, this recombinant plasmid no longer interferes with the host viability. The positive selection of recombinant clones is highly efficient and bench manipulations are considerably simplified. When E. coli transformants are plated out on rich medium with ampicillin, only cells containing recombinant plasmids give rise to colonies. In a lacIq-positive host, the positive selection is IPTG-dependent. Therefore, pBa-7 phagemid can be amplified and prepared in large quantities from lacIq-positive E. coli hosts. Hence, pBa-7 seems to be suitable for most genetic engineering manipulations.
Circulating Levels of GDF15, MMP7 and miR-200c as a Poor Prognostic Signature in Gastric Cancer (2014)

Aim: To analyze GDF15 and MMP7 serum levels as diagnostic biomarkers in gastric cancer (GC) patients. The prognostic value of GDF15 and MMP7 serum levels in combination with miR-200c blood expression was also analyzed. Patients & methods: Fifty-two GC and 23 control samples were included. Results: GDF15 and MMP7 proved to be powerful tools for GC diagnosis. Increased levels of GDF15 and MMP7 were associated with shorter progression-free survival and overall survival in univariate analysis. In multivariate analysis, the combination of high levels of GDF15, MMP7 and miR-200c was an independent predictor for death (p = 0.033). Conclusion: GDF15 and MMP7 serum levels have diagnostic value for GC. The combination marker formed by GDF15, MMP7 and miR-200c is indicative of adverse evolution in GC patients.
Catalytic Enantioselective Conjugate Reduction of Lactones and Lactams (2003)

A dramatic acceleration of the enantioselective copper-catalyzed conjugate reduction of alpha,beta-unsaturated lactones, lactams, and esters is reported upon addition of alcohol additives. Good to excellent yields and enantioselectivities were realized using a catalyst generated in situ from CuCl(2).H(2)O, t-BuONa, p-tol-BINAP, and PMHS, and this methodology was applied to the synthesis of (-)-Paroxetine.
Contribution to the Theory of Indexing (1973)

An attempt is made to characterize the usefulness of terms occurring in stored documents and user queries as a function of their frequency characteristics across the documents of a collection. It is found that the best terms are those having medium frequency in the collection and skewed frequency distributions. Correspondingly, terms exhibiting either very high or very low document frequency are not as useful. To improve the indexing vocabulary, it becomes necessary to group low frequency terms into classes, and to break up high frequency terms by forming phrases. An indexing theory is described based on term frequency considerations, and a new phrase generation method is introduced. The resulting improvements in the indexing vocabulary are evaluated.
Spatial Heterogeneity in Oligodendrocyte Lineage Maturation and Not Cerebral Blood Flow Predicts Fetal Ovine Periventricular White Matter Injury (2006)

Although periventricular white matter injury (PWMI) is the leading cause of chronic neurological disability and cerebral palsy in survivors of premature birth, the cellular-molecular mechanisms by which ischemia-reperfusion contributes to the pathogenesis of PWMI are not well defined. To define pathophysiologic relationships among ischemia, acute cerebral white matter damage, and vulnerable target populations, we used a global cerebral ischemia-reperfusion model in the instrumented 0.65 gestation fetal sheep. We developed a novel method to make repeated measurements of cerebral blood flow using fluorescently labeled microspheres to resolve the spatial heterogeneity of flow in situ in three-dimensional space. Basal flow in the periventricular white matter (PVWM) was significantly lower than in the cerebral cortex. During global cerebral ischemia induced by carotid occlusion, flow to all regions was reduced by nearly 90%. Ischemia of 30 or 37 min duration generated selective graded injury to frontal and parietal PVWM, two regions of predilection for human PWMI. Injury was proportional to the duration of ischemia and increased markedly with 45 min of ischemia to extensively damage cortical and subcortical gray matter. Surprisingly, the distribution of PVWM damage was not uniform and not explained by heterogeneity in the degree of white matter ischemia. Rather, the extent of white matter damage coincided with the presence of a susceptible population of late oligodendrocyte progenitors. These data support that although ischemia is necessary to generate PWMI, the presence of susceptible populations of oligodendrocyte progenitors underlies regional predilection to injury.
Deficiency of peptidoglycan and lipopolysaccharide components in Rickettsia tsutsugamushi (1987)

Analyses of chemical composition in whole cells of Rickettsia tsutsugamushi were performed and compared with those of the other rickettsiae and gram-negative bacteria. The results indicated that R. tsutsugamushi does not contain detectable amounts of 3-deoxy-D-mannooctulosonic acid, heptose, muramic acid, or glucosamine (less than 2, less than 2, less than 3, and less than 3 nmol/mg, respectively). The microorganism was found to contain four kinds of fatty acids (16:0, 18:0, 18:1, and 18:2), but not hydroxy fatty acids. Furthermore, in analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by silver or Coomassie blue staining, lipopolysaccharide bands were not detected in preparations treated with proteinase K. It is concluded that R. tsutsugamushi has little or no peptidoglycan or lipopolysaccharide.