gebhart/patrepeval huggingface dataset:
Expanding Mouse-Adapted Yamagata-like Influenza B Viruses in Eggs Enhances In Vivo Lethality in BALB/c Mice (2022)

Despite the yearly global impact of influenza B viruses (IBVs), limited host range has been a hurdle to developing a readily accessible small animal disease model for vaccine studies. Mouse-adapting IBV can produce highly pathogenic viruses through serial lung passaging in mice. Previous studies have highlighted amino acid changes throughout the viral genome correlating with increased pathogenicity, but no consensus mutations have been determined. We aimed to show that growth system can play a role in mouse-adapted IBV lethality. Two Yamagata-lineage IBVs were serially passaged 10 times in mouse lungs before expansion in embryonated eggs or Madin-Darby canine kidney cells (London line) for use in challenge studies. We observed that virus grown in embryonated eggs was significantly more lethal in mice than the same virus grown in cell culture. Ten additional serial lung passages of one strain again showed virus grown in eggs was more lethal than virus grown in cells. Additionally, no mutations in the surface glycoprotein amino acid sequences correlated to differences in lethality. Our results suggest growth system can influence lethality of mouse-adapted IBVs after serial lung passaging. Further research can highlight improved mechanisms for developing animal disease models for IBV vaccine research.
Teleoperation of a Mobile Robot Using a Force-Reflection Joystick With Sensing Mechanism of Rotating Magnetic Field (2009)

Operators' intelligent and skillful decisions are necessary for the teleoperation of a mobile robot when there are many scattered obstacles. Among the sensors used for environment recognition, the camera is the most popular and powerful. However, there are several limitations in the camera-based teleoperation of a mobile robot. For example, shadowed and curved areas cannot be viewed using a narrow view-angle camera, especially in an environment with bad illumination and several obstacles. Therefore, it is necessary to have other sensory information for reliable teleoperations. In this study, 16 ultrasonic sensors are attached around a mobile robot in a ring pattern to measure the distances to the obstacles and a collision vector is introduced as a new tool for obstacle avoidance, which is defined as the normal vector from an obstacle to the mobile robot. Based on this collision vector, a virtual reflection force is generated to avoid the obstacles and then the reflection force is transferred to the operator who is holding the joystick used to control the mobile robot. Based on this reflection force, the operator can control the mobile robot more smoothly and safely. For this bidirectional teleoperation, a master joystick system using a two-axis hall sensor was designed to eliminate the nonlinear region, which exists in a general joystick with two motors and potentiometers. The effectiveness of the collision vector and force-reflection joystick is verified by comparing two vision-based teleoperation experiments, with and without force reflection.
The effect of growth temperature, on big-vein symptom and serological detection of Mirafiori lettuce virus and Lettuce big-vein virus in lettuce. (2004)

From lettuce (Lactuca sativa) leaves with big-vein symptoms, two viruses associated with lettuce big-vein, Mirafiori lettuce virus (MiLV) and Lettuce big-vein virus (LBVV), were isolated. To make clear which virus is really associated with big-vein symptoms expression, the effect of the growth temperature for lettuce, on the serological detection of the two viruses and symptom expression was analyzed. At 27°C, LBVV was detected in the leaves, but neither the big-vein symptoms nor MiLV were observed. When the growth temperature was decreased to 18°C, big-vein symptoms appeared and MiLV was detected in the leaves.
Effect of centbucridine & lignocaine on biochemical changes in isoproterenol induced ischemia in rats. (1991)

Effect of lignocaine and centbucridine against isoproterenol-induced biochemical changes was studied in the rat. Isoproterenol (40 mg/kg twice) increased the heart weight, level of manolaldehyde (MDA) and activity of acid phosphatase, but decreased the myocardial phospholipid content at 48 h. In addition, increase in plasma triglyceride, cholesterol, MDA and creatine phosphokinase activity was observed. Pretreatment of the animals with lignocaine (10 mg/kg) or centbucridine (1, 3 and 10 mg/kg) protected the animals against these biochemical changes. However, increase in heart weight consequent to isoproterenol treatment could not be prevented. Total protection against creatine phosphokinase release in the blood was also not observed. The results suggest that the two drugs inhibit lipolysis. They may also inhibit phospholipases leading to protection against ischemia-induced changes in the rat.
Modulation of Cysteine Biosynthesis in Chloroplasts of Transgenic Tobacco Overexpressing Cysteine Synthase [O-Acetylserine(thiol)-Iyase] (1994)

Cysteine synthase [O-acetyl-L-serine(thiol)-lyase, EC 4.2.99.8] (CSase), which is responsible for the terminal step of cysteine biosynthesis, catalyzes the formation of L-cysteine from O-acetyl-L-serine (OAS) and hydrogen sulfide. Three T-DNA vectors carrying a spinach (Spinacia oleracea) cytoplasmic CSase A cDNA (K. Saito, N. Miura, M. Yamazaki, H. Horano, I. Murakoshi [1992] Proc Natl Acad Sci USA 89: 8078-8082) were constructed as follows: pCSK3F, cDNA driven by the cauliflower mosaic virus (CaMV) 35S RNA promoter with a sense orientation; pCSK3R, cDNA driven by the CaMV 355 promoter with an antisense orientation; pCSK4F, cDNA fused with the sequence for chloroplast-targeting transit peptide of pea ribulose-1,5-biphosphate carboxylase small subunit driven by the CaMV 35S promoter with a sense orientation. These chimeric genes were transferred into tobacco (Nicotiana tabacum) with Agrobacterium-mediated transformation, and self-fertilized progeny were obtained. CSase activities in cell-free extracts of pCSK3F and pCSK4F transformants were 2- to 3-fold higher than those of control and pCSK3R plants. CSase activities in chloroplasts of pCSK4F transformants were severalfold higher than those of control and pCSK3F plants, indicating that the foreign CSase protein is transported and accumulated in a functionally active form in chloroplasts of pCSK4F plants. Isolated chloroplasts of a pCSK4F transformant had a more pronounced ability to form cysteine in response to addition of OAS and sulfur compounds than those of a control plant. In particular, feeding of OAS and sulfite resulted in enhanced cysteine formation, which required photoreduction of sulfite in chloroplasts. The enhanced cysteine formation in a pCSK4F plant responding to sulfite was also observed in leaf discs. In addition, these leaf discs were partially resistant to sulfite toxicity, possibly due to metabolic detoxification of sulfite by fixing into cysteine. These results suggested that overaccumulated foreign CSase in chloroplasts could modulate biosynthetic flow of cysteine in response to sulfur stress.
[Gray platelet syndrome, an example of myelofibrosis of megakaryocytic origin]. (1991)

In this study, the clinical history of two patients with the gray platelet syndrome, a rare congenital disorder associating thrombopathia and myelofibrosis is recalled. Complementary studies on platelets and megakaryocytes were performed, mainly with an immunocytochemical approach. In gray platelets, a general decrease of alpha-granule proteins, including PF4, beta tg and PDGF was observed. The decrease in platelet mitogenic activity (PDGF) was confirmed by biological and radio-immunological measurements. An abnormally high level of these compounds was also found in the plasma. In megakaryocytes cultured from the bone marrow of these patients, alpha-granule proteins were normally expressed in early maturation stages, whereas they were found to be absent in the mature megakaryocytes. An alpha-granule membrane glycoprotein, GMP 140 has been studied in resting and thrombin stimulated gray platelets and was found to be normally expressed at the surface of stimulated platelets. GMP140 was studied in resting platelets by immunoelectron microscopy and found to be present in vacuole probably corresponding to empty granules. This observation allows to conclude that alpha-granule membrane is formed in the gray platelet syndrome, but that there is a storage defect of alpha-granule soluble proteins, possibly due to an abnormal targetting of these proteins to the alpha-granule. Synthesis and subsequent release of these proteins, namely of the mitogenic factors, which can induce myelofibrosis and lung fibrosis by abnormal fibroblast stimulation, is discussed.
Branched-chain alpha-ketoacid dehydrogenase kinase. Molecular cloning, expression, and sequence similarity with histidine protein kinases. (1992)

A cDNA for branched-chain alpha-ketoacid dehydrogenase kinase was cloned from a rat heart cDNA library. The cDNA had an open reading frame encoding a protein of 382 amino acid residues with a calculated molecular weight of 43,280. The clone codes for the branched-chain alpha-ketoacid dehydrogenase kinase based on the following: 1) the deduced amino acid sequence contained the partial sequence of the kinase determined by direct sequencing; 2) expression of the cDNA in Escherichia coli resulted in synthesis of a 43,000-Da protein that was recognized specifically by kinase antibodies; and 3) enzyme activity that phosphorylated and inactivated the branched-chain alpha-ketoacid dehydrogenase complex was found in extracts of E. coli expressing the protein. Northern blot analysis indicated the mRNA for the branched-chain alpha-ketoacid dehydrogenase kinase was more abundant in rat heart than in rat liver, as expected from the relative amounts of kinase activity expressed in these tissues. The deduced sequence of the kinase aligned with a high degree of similarity within subdomains characteristic of procaryotic histidine protein kinases. This first mitochondrial protein kinase to be cloned appears more closely related in sequence to procaryotic histidine protein kinases than to eucaryotic serine/threonine protein kinases.
Low-pressure chemical vapor deposition for very large-scale integration processing&#8212;A review (1979)

An overview is presented of low-pressure chemical vapor deposition and its applicability to VLSI processing for depositing thin films of insulators, semiconductors, and metals. The major contributions of low-pressure chemical vapor deposition to VLSI technology are its capability for economically producing films with superior uniformity, high purity, and excellent step coverage-factors essential for achieving the very high device reliability and high product yield required in the manufacturing of VLSI devices. Specific examples from the recent literature are reviewed to exemplify how the technique has been utilized to date in solid-state device technology. Applications of films produced by low-pressure reactive plasma chemical vapor deposition are also included.
Quantization and erasures in frame representations (2006)

Frame representations, which correspond to overcomplete generalizations to basis expansions, are often used in signal processing to provide robustness to errors. In this thesis robustness is provided through the use of projections to compensate for errors in the representation coefficients, with specific focus on quantization and erasure errors. The projections are implemented by modifying the unaffected coefficients using an additive term, which is linear in the error. This low-complexity implementation only assumes linear reconstruction using a pre-determined synthesis frame, and makes no assumption on how the representation coefficients are generated. 
In the context of quantization, the limits of scalar quantization of frame representations are first examined, assuming the analysis is using inner products with the frame vectors. Bounds on the error and the bit-efficiency are derived, demonstrating that scalar quantization of the coefficients is suboptimal. As an alternative to scalar quantization, a generalization of Sigma-Delta noise shaping to arbitrary frame representations is developed by reformulating noise shaping as a sequence of compensations for the quantization error using projections. The total error is quantified using both the additive noise model of quantization, and a deterministic upper bound based on the triangle inequality. It is thus shown that the average and the worst-case error is reduced compared to scalar quantization of the coefficients. 
The projection principle is also used to provide robustness to erasures. Specifically, the case of a transmitter that is aware of the erasure occurrence is considered, which compensates for the erasure error by projecting it to the subsequent frame vectors. It is further demonstrated that the transmitter can be split to a transmitter/receiver combination that performs the same compensation, but in which only the receiver is aware of the erasure occurrence. Furthermore, an algorithm to puncture dense representations in order to produce sparse approximate ones is introduced. In this algorithm the error due to the puncturing is also projected to the span of the remaining coefficients. The algorithm can be combined with quantization to produce quantized sparse representations approximating the original dense representation. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
Continuous measurement with traveling-wave probes (2003)

We consider the use of a traveling-wave probe to continuously measure the quantum state of an atom in free space. Unlike the more familiar cavity QED geometry, the traveling wave is intrinsically a multimode problem. Using an appropriate modal decomposition, we determine the effective measurement strength for different atom-field interactions and different initial states of the field. These include the interaction of a coherent-state pulse with an atom, the interaction of a Fock-state pulse with an atom, and the use of Faraday rotation of a polarized laser probe to perform a quantum nondemolition measurement on an atomic spin.
Silver Enhances Antibiotic Activity Against Gram-Negative Bacteria (2013)

A declining pipeline of clinically useful antibiotics has made it imperative to develop more effective antimicrobial therapies, particularly against difficult-to-treat Gram-negative pathogens. Silver has been used as an antimicrobial since antiquity, yet its mechanism of action remains unclear. We show that silver disrupts multiple bacterial cellular processes, including disulfide bond formation, metabolism, and iron homeostasis. These changes lead to increased production of reactive oxygen species and increased membrane permeability of Gram-negative bacteria that can potentiate the activity of a broad range of antibiotics against Gram-negative bacteria in different metabolic states, as well as restore antibiotic susceptibility to a resistant bacterial strain. We show both in vitro and in a mouse model of urinary tract infection that the ability of silver to induce oxidative stress can be harnessed to potentiate antibiotic activity. Additionally, we demonstrate in vitro and in two different mouse models of peritonitis that silver sensitizes Gram-negative bacteria to the Gram-positive-specific antibiotic vancomycin, thereby expanding the antibacterial spectrum of this drug. Finally, we used silver and antibiotic combinations in vitro to eradicate bacterial persister cells, and show both in vitro and in a mouse biofilm infection model that silver can enhance antibacterial action against bacteria that produce biofilms. This work shows that silver can be used to enhance the action of existing antibiotics against Gram-negative bacteria, thus strengthening the antibiotic arsenal for fighting bacterial infections.
Guest EditorialAWPL Special Cluster on “Impact of User-Related Randomness on Antennas and Channels” (2017)

The papers in this special issue focus on the impact of user-related randomness on antennas and channels. In the early days of telecommunications, most antennas were considered as fixed installations, and their performance was determined in terms of their directivity and radiations patterns when the polarizations of the antennas on the transmitting and receiving sides were aligned. With the birth of satellite communications, there soon became a need for reusing the frequencies by polarization multiplexing, resulting in dual polarized systems with an even stricter requirement to alignment in order to avoid interference between the two communication channels. Furthermore, mobile communications resulted in random channels owing to both fast Rayleigh fading and slow shadow fading. Nowadays, wireless devices and base stations/access points are used more and more in hugely differing contexts and environments for terminals. The papers in this issue have been prepared in this context, the aim being to help make better known the issues raised above from the antennas and propagation community and to contribute to foster research and development in this area.
Complex Transmission Dynamics of Clonally Related VirulentMycobacterium tuberculosisAssociated with Barhopping by Predominantly Human Immunodeficiency Virus–Positive Gay Men (1999)

Limited data suggest that measures to reduce tuberculosis transmission should be based on locations rather than on personal contacts. Molecular epidemiologic methods (analysis of IS6110 patterns, spoligotypes, variable numbers of tandem DNA repeats, and automated DNA sequence data) identified a cohort of 48 persons who were infected with progeny of the same Mycobacterium tuberculosis strain. Epidemiologic investigation documented that a large proportion of the patients were gay white human immunodeficiency virus-positive men. Most practiced barhopping, an activity that involved patronizing many bars in the same neighborhood each night. Few subjects were directly linked to more than 1 or 2 other persons by conventional investigation methods, which shows that the transmission dynamics were unusually complex compared with most previously described episodes of strain spread. The data support the concept that identification of locations where pathogen dissemination likely occurs may provide additional strategies for targeted tuberculosis control.
Full three-dimensional approach to the design and simulation of a radio-frequency quadrupole (2013)

We have developed a new full 3D approach for the electromagnetic and beam dynamics design and simulation of a radio-frequency quadrupole (RFQ). A detailed full 3D model including vane modulation was simulated, which was made possible by the ever advancing computing capabilities. The electromagnetic (EM) design approach was first validated using experimental measurements on an existing prototype RFQ and more recently on the actual full size RFQ. Two design options have been studied, the original with standard sinusoidal modulation over the full length of the RFQ; in the second design, a trapezoidal modulation was used in the accelerating section of the RFQ to achieve a higher energy gain for the same power and length. A detailed comparison of both options is presented supporting our decision to select the trapezoidal design. The trapezoidal modulation increased the shunt impedance of the RFQ by 34%, the output energy by 15% with a similar increase in the peak surface electric field, but practically no change in the dynamics of the accelerated beam. The beam dynamics simulations were performed using three different field methods. The first uses the standard eight-term potential to derive the fields, the second uses 3D fields from individual cell-by-cell models, and the third uses the 3D fields for the whole RFQ as a single cavity. A detailed comparison of the results from TRACK shows a very good agreement, validating the 3D fields approach used for the beam dynamics studies. The EM simulations were mainly performed using the CST Microwave-Studio with the final results verified using other software. Detailed segment-by-segment and full RFQ frequency calculations were performed and compared to the measured data. The maximum frequency deviation is about 100 kHz. The frequencies of higher-order modes have also been calculated and finally the modulation and tuners effects on both the frequency and field flatness have been studied. We believe that with this new full 3D approach, the enhanced computing capabilities and the calculation precision the electromagnetic design software offer, we may be able to skip the prototyping phase and build the final product at once, although we recognize that prototyping is still needed to establish and validate the fabrication procedure.
Radikal‐Stabilisierungsenergie – das MMEVBH‐Kraftfeld (1995)

Radical‐Stabilization‐Energy – the MMEVBH Force Field Making use of the VB method of Malrieu et al. [6–10] a force field has been developped, which allows to calculate heats of formation of hydrocarbons (conjugated and non‐conjugated olefins, radicals, and diradicals) with high accuracy. With this method radical stabilization energies (RSE) for a great number of delocalized radicals are calculated and compared with experimental values, derived from shock‐tube measurements of dissociation energies or from rotational barriers of substituted olefins. A detailed analysis of the RSE with respect to structure, substituents, strain, and aromaticity is presented.
Improving the definition of high-risk patients for tumor recurrence from clear cell renal cell carcinoma: The U-CISS classification. (2019)

629 Background: Thirty percent of patients with localized clear cell renal cell carcinoma (ccRCC) will ultimately develop recurrence (local or metastatic) after nephrectomy. Current risk stratification systems still misclassify patients. A better stratification is needed to select high-risk patients who may benefit from adjuvant therapy. We sought to improve the existing UISS by the addition of genetic information in a new UCLA cytogenetic integrated staging system (U-CISS). Methods: A total of 240 patients from UCLA with localized ccRCC and cytogenetic analysis on tumor specimen were included in the study. In a continuation of our previous research, cytogenetic (combined loss 3p-14q) and a pathological high-risk feature, microvascular invasion (MVI) were implemented in the UISS. Association with recurrence free survival (RFS) was analyzed in a uni- and multivariable fashion; prognostic accuracy was tested with the c-index. All tumors that had either MVI, combined loss 3p/14q or both in the UISS low-risk group were placed into the U-CISS intermediate group. Tumors with one or both risk factors in the UISS intermediate group were placed into the new U-CISS high-risk group. Results: Fifty patients developed tumor recurrence. On multivariate analysis, combined loss 3p-14q, and MVI were independent prognostic factors. The U-CISS placed significantly better prognosticated RFS in the high-risk group (7/50 (14%) with UISS vs. 23/50 (46%) with U-CISS) and thus, was more accurate in prognosticating RFS. The c-index for recurrence prognostication was improved in the U-CISS (0.70 vs. 0.65 for the UISS). Furthermore, the U-CISS was a better prognostication tool when the intermediate and high-risk group were combined (prognostication of 74% with U-CISS vs. 68% UISS). Conclusions: The use of U-CISS, which integrates genomic alterations with clinical and pathologic features, allowed a re-allocation of patients to create a better stratification of recurrence risk. This new definition of high-risk of recurrence could significantly improve selection of patients who are in greatest need of closer surveillance and/or adjuvant treatment. C.L. and N.K. contributed equally to first authorship.