gebhart/patrepeval huggingface dataset:
Kinetic analysis of N-acylphosphatidylserine accumulation and implications for membrane assembly in Rhodopseudomonas sphaeroides (1982)

The accumulation of N-acylphosphatidylserine (NAPS) in response to the inclusion of Tris in the growth medium of Rhodopseudomonas sphaeroides strain M29-5 has been examined. In the accompanying paper (Donohue et al., J. Bacteriol. 152:000--000, 1982), we show that in response to Tris, NAPS accumulated to as much as 40% of the total cellular phospholipid content. NAPS accumulation began immediately upon addition of Tris and was reflected as an abrupt 12-fold increase in the apparent rate of NAPS accumulation. We suggest that Tris altered the flow of metabolites through a preexisting and previously unknown metabolic pathway. NAPS accumulation ceased immediately upon the removal of Tris; however, accumulated NAPS remained largely metabolically stable. Importantly, under conditions in which NAPS was not accumulated, the intracytoplasmic membrane was shown to be virtually devoid of newly synthesized NAPS. The significance of this observation is discussed in terms of its physiological implications on phospholipid transfer and membrane biogenesis in R. sphaeroides.
A Multi-country Evaluation of Neisseria meningitidis Serogroup B Factor H–Binding Proteins and Implications for Vaccine Coverage in Different Age Groups (2013)

These observations highlight a difference in epidemiology of fHBP subfamilies in different age groups, with fHBP subfamily A strains causing more disease in vulnerable populations, such as infants, than in adolescents.
Interferon-Induced Protection against Foot-and-Mouth Disease Virus Infection Correlates with Enhanced Tissue-Specific Innate Immune Cell Infiltration and Interferon-Stimulated Gene Expression (2009)

Previously, we demonstrated that type I interferon (IFN-alpha/beta) or a combination of IFN-alpha/beta and type II IFN (IFN-gamma) delivered by a replication-defective human adenovirus 5 (Ad5) vector protected swine when challenged 1 day later with foot-and-mouth disease virus (FMDV). To gain a more comprehensive understanding of the mechanism of protection induced by IFNs, we inoculated groups of six swine with Ad5-vectors containing these genes, challenged 1 day later and euthanized 2 animals from each group prior to (1 day postinoculation [dpi]) and at 1 (2 dpi) and 6 days postchallenge (7 dpi). Blood, skin, and lymphoid tissues were examined for IFN-stimulated gene (ISG) induction and infiltration by innate immune cells. All IFN-inoculated animals had delayed and decreased clinical signs and viremia compared to the controls, and one animal in the IFN-alpha treated group did not develop disease. At 1 and 2 dpi the groups inoculated with the IFNs had increased numbers of dendritic cells and natural killer cells in the skin and lymph nodes, respectively, as well as increased levels of several ISGs compared to the controls. In particular, all tissues examined from IFN-treated groups had significant upregulation of the chemokine 10-kDa IFN-gamma-inducible protein 10, and preferential upregulation of 2',5'-oligoadenylate synthetase, Mx1, and indoleamine 2,3-dioxygenase. There was also upregulation of monocyte chemotactic protein 1 and macrophage inflammatory protein 3alpha in the skin. These data suggest that there is a complex interplay between IFN-induced immunomodulatory and antiviral activities in protection of swine against FMDV.
Double strand RNA-mediated RNA interference through feeding in larval gypsy moth, Lymantria dispar (Lepidoptera: Erebidae) (2017)

RNA interference (RNAi) technology uses dsRNAs to silence specific targeted genes by downregulating their expression. It has become a potent tool for functional and regulatory studies of insect genes and has potential to be applied for insect control. Though it has been challenging to generate effective RNAi in lepidopteran insects, in the current study this technology was applied to develop specific RNAi-based molecular tools that could be used to negatively impact the invasive lepidopteran forest pest, gypsy moth (GM). GM midgut-specific genes were selected for dsRNA design from larval transcriptome profiles. Two methods were used to produce specific dsRNAs, bacterial expression and in vitro synthesis, which were then fed per os to GM larvae. Depletion of uncharacterized gene targets known as locus 365 and locus 28365, or their stacked combination, depleted target transcripts in a sequence specific manner and resulted in 60% reduction in body mass. Treated GM females that were able to moult to the adult stage displayed an approximately two-fold reduction in egg masses. These have potential to be developed as molecular biopesticides for GM.
Salt resistant crop plants (2014)

Soil salinity is a major constraint to agriculture. To improve salinity tolerance of crops, various traits can be incorporated, including ion exclusion, osmotic tolerance and tissue tolerance. We review the roles of a range of genes involved in salt tolerance traits. Different tissues and cells are adapted for specific and often diverse function, so it is important to express the genes in specific cell-types and to pyramid a range of traits. Modern biotechnology (marker-assisted selection or genetic engineering) needs to be increasingly used to introduce the correct combination of genes into elite crop cultivars. Importantly, the effects of introduced genes need to be evaluated in the field to determine their effect on salinity tolerance and yield improvement.
Parametric optics with whispering-gallery modes (2003)

We propose to fabricate a dielectric cavity sustaining high-Q whispering gallery modes from a periodically poled material possessing a quadratic nonlinearity to achieve an efficient interaction among the modes. We show that the periodical poling allows for compensation of both the material and the cavity dispersions that prohibits the nonlinear interaction otherwise. Such a cavity might be a basic element of a family of efficient nonlinear devices operating at a broad range of optical wavelengths.
Magneto-optical detection of weak magnetic fields (2005)

Imaging modalities currently available for inexpensive imaging of biomagnetic fields are limited. Magneto-optical films have been used in magnetic field imaging systems with detection floors of 0.1-1 mT. A technique for magneto-optical detection of weak magnetic fields using bismuth-doped yttrium iron garnet (Bi:YIG) thin films is described. Results showing typical detected fields of 10 nT are presented. Such a device has potential clinical applications in MCG imaging and the tracking of magnetic particles.
Combining predictive capabilities of transcranial doppler with electrocardiogram to predict hemorrhagic shock (2009)

Hemorrhagic shock (HS) potentially impacts the chance of survival in most traumatic injuries. Thus, it is highly desirable to maximize the survival rate in cases of blood loss by predicting the occurrence of hemorrhagic shock with biomedical signals. Since analyzing one physiological signal may not enough to accurately predict blood loss severity, two types of physiological signals - Electrocardiography (ECG) and Transcranial Doppler (TCD) - are used to discover the degree of severity. In this study, these degrees are classified as mild, moderate and severe, and also severe and non-severe. The data for this study were generated using the human simulated model of hemorrhage, which is called lower body negative pressure (LBNP). The analysis is done by applying discrete wavelet transformation (DWT). The wavelet-based features are defined using the detail and approximate coefficients and machine learning algorithms are used for classification. The objective of this study is to evaluate the improvement when analyzing ECG and TCD physiological signals together to classify the severity of blood loss. The results of this study show a prediction accuracy of 85.9% achieved by support vector machine in identifying severe/non-severe states.
Comparison of two activity-controlled rate-adaptive pacing principles: acceleration versus vibration. (1992)

Activity-guided rate-adaptive pacing is currently the most widely used principle for rate adaptation. Broad experience has been gathered from several hundred thousand pacemakers that adjust the pacing rate according to vibrational forces detected by a piezosensor bonded to the inner side of the pacemaker can. A new generation of accelerometer-based pacemakers has been introduced into clinical practice. The vibrational type detects vibration, pressure, and shock waves traveling through the body with physical stress and using the pacemaker can as a resonator. In contrast, the accelerometer is insulated from the pacemaker housing and is incorporated into electronic hybrid circuitry. The forces detected by an accelerometer are motion and acceleration of the body in an anterior-posterior direction. Clinical studies conducted to date have shown that the accelerometer to be superior to the conventional vibration activity pacemakers, as far as the discrimination of different workloads and rejection of unwanted environmental noise are concerned.
Removal of Particulate Contamination from Solid Surfaces Using Polymeric Micropillars (2016)

This Research Article describes a novel method for removal of particulate contamination, loosely referred to as dust, from solid surfaces using polymeric micropillars. In this Research Article, we illustrate for the first time that polymeric microfibrils of controlled interfacial and geometrical properties can effectively remove micrometric and submicrometric contaminant particles from a solid surface without damaging the underlying substrate. Once these microfibrils are brought into contact with a contaminated surface, because of their their soft and flexible structure, they develop intimate contact with both the surface contaminants and the substrate. While these intrinsically nonsticky micropillars have minimal interfacial interactions with the substrate, we show that they produce strong interfacial interactions with the contaminant particles, granting the detachment of the particles from the surface upon retraction of the cleaning material. The origin and strength of the interfacial interactions at the interfaces between a contaminant particle and both the substrate and the cleaning materials are thoroughly discussed. Unlike flat substrates of the same material, using microfibrillar structures of controlled interfacial and geometrical properties also allows the elimination of the adsorbed particles from the contact interface. Here we demonstrate that by moving the adsorbed particles from the tip to the side of the fibrils and consequently removing them from the contact interface, polymeric microfibrils can clean all contaminant particles from the surface. The effects of the geometrical and interfacial properties of polymeric micropillars on removing the adsorbed particles from the tips of the pillars are fully discussed. This research is not only important in terms of introducing a novel method which can offer a new paradigm for thorough yet nondestructive cleaning of dust particles from solid surfaces, but also it is of fundamental significance for researchers with interests in exploiting the benefits offered by microstructured surfaces in development of interfacially active materials and devices.
Inversion of the Cis Geometry Requirement for Cytotoxicity in Structurally Novel Platinum(II) Complexes Containing the Bidentate N,O-Donor Pyridin-2-yl-acetate (2000)

Water soluble platinum(II) complexes have been synthesized that contain the N,O-chelate pyridin-2-yl acetate (PyAc) as a novel structural motif in platinum antitumor complexes. The trans-platinum complex trans-[PtCl(PyAc-N,O)(NH3)] (2) (N-donors are trans) and its isomer cis-[PtCl(PyAc-N,O)(NH3)] (4) (N trans to Cl) were prepared from trans-[PtCl2((NH3)(PyAcH)].H2O (1.H2O) and cis-[PtCl2(NH3)(PyAcMe) (3), respectively, employing the bidentate ligand as its methylester (PyAcMe). 2 and 4 are readily formed from the respective dichloro species, even at low pH and in the presence of extra chloride, indicating a high thermodynamic stability of the PyAc chelate ring. 1.H2O and 2-4 were characterized by 1H NMR and IR spectroscopy and elemental analyses. The solid-state structure of 2 was determined: triclinic, P1 (no. 2), with a = 8.170(2) A, b = 9.274(3) A, c = 7.374(2) A, alpha = 108.68(2) degrees, beta = 113.27(2) degrees, gamma = 74.40(2) degrees, V = 479.7(6) A3, Z = 2. The six-membered metallacyclus in 2 adopts a "boat" form, allowing a strainless coordination of platinum. The most promising cytotoxic properties in the above series of compounds have been established for 2 (and 1, which rapidly transforms into 2 at 37 degrees C and neutral pH). Preliminary ID50 values were 0.88 and 1.26 microM, respectively, in cisplatin-sensitive L1210 leukemia. Both compounds proved to be cross-resistant to the clinical drug. Reactions of 2 and 4 with 5'-guanosine monophosphate (5'-GMP) under physiological conditions gave the monofunctional adducts trans- and cis-[Pt(5'-GMP-N7)(PyAc-N,O)(NH3)] (I and II). Chelate-bound carboxylate was not replaced by guanine-N7 when an excess of nucleotide was applied (NMR). In an analogous reaction, 2 reacts with the oligonucleotide d(TCGT) [5'-T(1)-C(2)-G(3)-T(4)-3'] to give the adduct d(TCGT)-N7(3)-Pt(PyAc-O,N)(NH3) (III), which was characterized by a combination of total correlation spectroscopy, double-quantum-filtered correlation spectroscopy, nuclear Overhauser effect spectrometry, and rotating-frame Overhauser enhancement spectroscopy experiments. Binding of the [Pt(PyAc-N,O)(NH3)]+ fragment to N7 of G(3) causes an increase of N-type character of the T(4) and G(3) deoxyribose residues relative to the unplatinated sequence, while those of T(1) and C(2) remain S-type. An internucleotide nuclear Overhauser effect between H6(4) and H2'(3) indicates stacking between guanine and the 3'-thymine base. The most striking feature proved to be the pronounced upfield shift and broadening of the 1H NMR signals assigned to the base protons H5 and H6 in III. Magnetization transfer between H5(2) and H3 of pyridine suggests that this effect is caused by base-base interactions involving the planar ligand on platinum, which must be situated on the 5' face of guanine. Possible implications for the DNA binding and cytotoxic effect of the compounds are discussed.
Sensing and experimental based modeling of direct metal deposition (2006)

This paper presents an experimental investigation on the process dynamics of direct metal deposition. An optical sensing system, including three couple charged device cameras and a two-color pyrometer, is used to monitor molten pool geometry and pool temperature during the deposition process. Molten pool area size and height are obtained by image processing. Auto regressive exogenous models and state space models are implemented to identify the direct metal deposition process relating laser power to molten pool temperature, as well as traverse speed to molten pool temperature. The models are validated by experimental data.
Development and Microstructure of Cu&ndash;Zr Alloy Wire with Ultimate Tensile Strength of 2.2 GPa (2012)

Round, bar-shaped ingots of hypoeutectic Cu–4- and Cu–5 at%Zr alloys were cast using the copper-mold casting method. The ingots were drawn into wires with a drawing ratio (η) of 5.9 or more. The relationship between the mechanical and electrical properties of these wires as well as their microstructure was investigated. It was found that the Cu–5 at%Zr alloy wire drawn down to 40 µm in diameter with η = 8.6 exhibited an ultimate tensile strength (UTS) of 2234 MPa, 0.2% proof stress of 1873 MPa, total strain to fracture of 4.2%, Young’s modulus of 126 GPa, and electrical conductivity of 16%IACS. As for the Cu–4 at%Zr alloy, it could be wire-drawn down to 27 µm in diameter with η = 9.4.Both UTS and Young’s modulus increase linearly with η. A nanosized lamellar structure was noticed in the α-Cu and Cu9Zr2 intermetallic compound phases. Furthermore, it was observed that a nanosized amorphous phase was formed within the layers of the Cu9Zr2 intermetallic compound phase. The increase in the strength of the wire-drawn Cu–4- and Cu–5 at%Zr alloy is due to the synergistic effects resulting from the development of deformation twins in the α-Cu phase and the formation of the nanosized lamellar structure in the α-Cu and Cu9Zr2 intermetallic compound phases.High electrical conductivity of 16%IACS was obtained for the wire-drawn Cu–5 at%Zr alloy. This high value can be attributed to the low density of dislocations in the α-Cu phase.
Integrating a dynamic lexicon with a dynamic full-text retrieval system (1993)

There has been a great deal of interest within the Information Retrieval community in evaluating the use of linguistic knowledge to improve the indexing and searching of textual databases. Such systems must often employ a lexicon to store information about the words and phrases comprising the application's domain. Unlike a static lexicon, a dynamic lexicon raises practical concerns about the coordination between the state of the lexicon and IR indexing schemes based on lexical knowledge. Additionally, it introduces a host of database management issues, many of which are similar to those found in the text databases as well. In this paper, we explore a range of system design and performance issues that arise when integrating a dynamic lexicon with a dynamic full-text information retrieval system. We observe that the principle of functional isolation argues against the use of language-dependent information in article indexes and favors the use of query-time strategies for applying lexical knowledge. We propose and evaluate a system architecture which embodies this principle. We also show how a storage and retrieval infrastructure based on Burkowski's [BURKOWSKI92] “containment model” abstraction can be employed to implement both the text retrieval and lexicon facilities required in an integrated system.
A Natural Route to Nanowires and Energy Storage (2012)

Organic electronics is a burgeoning area, with a growing range of applications. This new research – in which nanowires are grown naturally rather then synthesized chemically – may provide new methods for biologically-produced or biologically-inspired materials for sustainable nanomanufacturing. Pilin nanofilaments (pili) — known now as microbial nanowires — are a class of fibrous proteins found in the sediment bacteria Geobacter. Temperature studies find metallic characteristics. The conductivity can be modulated by doping or by using an applied voltage in an electrochemical transistor configuration, showing the potential for device applications, including supercapacitors for energy storage.
Analysis of Transmission Schemes for Dual-Antenna Terminals in Massive MIMO Systems (2018)

The overall system performance of massive MIMO is improved by equipping user terminals with multiple antennas. In this paper, we investigate transceiver designs for the case of a single downlink stream and in particular, we study the uplink pilot design. Moreover, we study the consequences of channel estimation errors at the base-station, and to what extent a dual-antenna terminal can get access to relevant channel statistics for optimization of the pilot signal. Gain expressions for comparison of different designs are derived. We verify the analytic results based on antennas integrated into Sony-Xperia handsets measured with the Lund University massive MIMO testbed. The measurements are performed at frequencies <6GHz since this part of the spectrum is a candidate for NR standard according to 3GPP.
Chemoprobe-based assays of histone lysine demethylase 1A target occupation enable in vivo pharmacokinetics and pharmacodynamics studies of KDM1A inhibitors (2019)

Screening of cellular activity for inhibitors of histone lysine modifiers is most frequently performed indirectly by analyzing changes in the total levels of histone marks targeted by lysine methylases/demethylases. However, inhibition of histone lysine modifiers often leads to local rather than total changes in histone marks. Also, because histone modifications can be modulated by more than one cellular enzyme, it is not always clear whether changes in histone marks are a direct or indirect consequence of the inhibitor treatment applied. Direct assessment of target occupation can provide a useful tool to quantify the fraction of an epigenetic modifier that is bound to a pharmacological inhibitor (target engagement). Here, we developed and used a novel chemoprobe-based immunoassay to quantify target engagement in cells. Quantification of the fraction of free KDM1A was made possible, in an immune-based assay, by coupling a biotinylated chemoprobe to a warhead capable of selectively and irreversibly binding to the free active form of KDM1A. The results obtained confirmed that this approach is able to determine the degree of target engagement in a dose-dependent manner. Furthermore, the assay can be also used on tissue extracts to analyze the <i>in vivo</i> pharmacokinetics and pharmacodynamics relationship of KDM1A inhibitors, as has been exemplified with ORY-1001 (iadademstat), a potent and irreversible inhibitor of KDM1A. The principle of this assay may be applied to other targets, and the KDM1A probe may be employed in chemoproteomic analyses.
Synthesis of Cholesterol Analogues Bearing BODIPY Fluorophores by Suzuki or Liebeskind–Srogl Cross‐Coupling and Evaluation of Their Potential for Visualization of Cholesterol Pools (2014)

We report a synthetic route to BODIPY-cholesterol conjugates in which the key steps were Suzuki or Liebeskind-Srogl cross-coupling of cholesterol phenyl moieties with structurally diverse BODIPY scaffolds. All conjugates feature single-bonded and hydrophobic linkages between the fluorophore and sterol that are devoid of heteroatoms. Using HeLa cells, we show that these BODIPY-cholesterol analogues can be used simultaneously with the parent BODIPY-cholesterol for cell imaging and flow cytometry. The BODIPY-cholesterol analogues exhibit similar cellular localization in HeLa cells and show similar cholesterol efflux properties from THP-1 cells to HDL acceptors. These results demonstrate that the red-shifted BODIPY-cholesterol analogues behave in a manner similar to unlabeled cholesterol and are useful probes for simultaneous visualization of intracellular cholesterol pools and for monitoring cholesterol efflux from cells to extracellular acceptors.
Synthesis of Water-Soluble Poly(<i>p</i>-phenyleneethynylene) in Neat Water under Aerobic Conditions via Suzuki-Miyaura Polycondensation Using a Diborylethyne Synthon (2008)

We report the synthesis, structure, and characterization of a novel ethyne synthon, 1,2-bis(4',4',5',5'-tetramethyl[1',3',2']dioxaborolan-2'-yl)ethyne (B2C2). We demonstrate the utility of B2C2 in the Suzuki-Miyaura polycondensation reaction, synthesizing a water-soluble poly(p-phenyleneethynylene) from [2,5-diiodo-1,4-bis(3-propoxy-sulfonicacid)benzene] sodium salt in neat water under an aerobic atmosphere.
Crawling Back and Forth: Using Back and Out Links to Locate Bilingual Sites (2011)

This paper presents a novel crawling strategy to locate bilingual sites. It does so by focusing on the Web graph neighborhood of these sites and exploring the patterns of the links in this region to guide its visitation policy. A sub-task in the problem of bilingual site discovery is the job of detecting bilingual sites, i.e., given a Web site, verify whether it is bilingual or not. We perform this task by combining supervised learning and language identification. Experimental results demonstrate that our crawler outperforms previous crawling approaches and produces a high-quality collection of bilingual sites, which we evaluate in the context of machine translation in the tourism and hospitality domain. The parallel text obtained using our novel crawling strategy results in a relative improvement of 22 % in BLEU score (English-to-Spanish) over an out-ofdomain seed translation model trained on the European parliamentary proceedings. 1