gebhart/patrepeval huggingface dataset:
Characterization of CD8 T Cell-Mediated Mutations in the Immunodominant Epitope GP33-41 of Lymphocytic Choriomeningitis Virus (2021)

Cytotoxic T lymphocytes (CTLs) represent key immune effectors of the host response against chronic viruses, due to their cytotoxic response to virus-infected cells. In response to this selection pressure, viruses may accumulate escape mutations that evade CTL-mediated control. To study the emergence of CTL escape mutations, we employed the murine chronic infection model of lymphocytic choriomeningitis virus (LCMV). We developed an amplicon-based next-generation sequencing pipeline to detect low frequency mutations in the viral genome and identified non-synonymous mutations in the immunodominant LCMV CTL epitope, GP33-41, in infected wildtype mice. Infected Rag2-deficient mice lacking CTLs did not contain such viral mutations. By using transgenic mice with T cell receptors specific to GP33-41, we characterized the emergence of viral mutations in this epitope under varying selection pressure. We investigated the two most abundant viral mutations by employing reverse genetically engineered viral mutants encoding the respective mutations. These experiments provided evidence that these mutations prevent activation and expansion of epitope-specific CD8 T cells. Our findings on the mutational dynamics of CTL escape mutations in a widely-studied viral infection model contributes to our understanding of how chronic viruses interact with their host and evade the immune response. This may guide the development of future treatments and vaccines against chronic infections.
Combination induction therapy with monoclonal antibodies specific for CD80, CD86, and CD154 in nonhuman primate renal transplantation (2002)

These data suggest that a synergy exists between these agents, particularly with regard to T-dependent B-cell responses, but that they fail to induce durable tolerance in nonhuman primates.
<i>Fusarium</i>mycotoxins: a trans-disciplinary overview (2018)

Due to health risks and economic losses associated with mycotoxins produced by Fusarium species, there is a compelling need for an improved understanding of these fungi from across diverse perspectives and disciplinary approaches. In this article, we provide a transdisciplinary overview of: (i) Fusarium phylogenetics; (ii) linkages between mycotoxin biosynthetic gene clusters and chemical structures; (iii) biotransformation of mycotoxins to reduce toxicity; (iv) Fusarium population biology; (v) genomics of secondary metabolite production; and (vi) mycotoxigenic fusaria in a phytobiomes context. Phylogenetic studies have made tremendous progress in delineating the species that comprise the genus Fusarium, many of which are morphologically cryptic. Accurate species identification and a thorough understanding of the distribution of mycotoxin biosynthetic genes among those species will facilitate control of mycotoxin contamination. The biochemical pathways leading to the formation of several Fusarium mycotoxins have been elegantly linked with the genes responsible for each chemical transformation during synthesis, and for most structural differences among chemotypes. Screens for the biotransformation of mycotoxins have led to the description of chemical modifications that impact bioactivity and have implications for monitoring and testing of the food supply. Population biology studies have revealed the potential for introductions of foreign genotypes to alter regional populations of mycotoxigenic fusaria. Genomic analyses have begun to reveal the complex evolutionary history of the genes responsible for mycotoxin production, both across and within lineages. Improved understanding of how climate variability impacts plant–Fusarium interactions and mycotoxin accumulation is necessary for effective plant resistance. Additionally, improved understanding of interactions between Fusarium and other members of crop microbiomes is expected to produce novel strategies for limiting disease and mycotoxin accumulation.
Functional Divergence of a Syntenic Invertase Gene Family in Tomato, Potato, and Arabidopsis (2003)

Comparative analysis of complex developmental pathways depends on our ability to resolve the function of members of gene families across taxonomic groups. LIN5, which belongs to a small gene family of apoplastic invertases in tomato (Lycopersicon esculentum), is a quantitative trait locus that modifies fruit sugar composition. We have compared the genomic organization and expression of this gene family in the two distantly related species: tomato and Arabidopsis. Invertase family members reside on segmental duplications in the near-colinear genomes of tomato and potato (Solanum tuberosum). These chromosomal segments are syntenically duplicated in the model plant Arabidopsis. On the basis of phylogenetic analysis of genes in the microsyntenic region, we conclude that these segmental duplications arose independently after the separation of the tomato/potato clade from Arabidopsis. Rapid regulatory divergence is characteristic of the invertase family. Interestingly, although the processes of gene duplication and specialization of expression occurred separately in the two species, synteny-based orthologs from both clades acquired similar organ-specific expression. This similar expression pattern of the genes is evidence of comparable evolutionary constraints (parallel evolution) rather than of functional orthology. The observation that functional orthology cannot be identified through analysis of expression similarity highlights the caution that needs to be exercised in extrapolating developmental networks from a model organism.
A feasibility study of full-bridge type superconducting fault current controller on electric machine power stability (2015)

Recently, because of the advent of Smart Grid and integration of distributed generations, electrical power grids are facing uncountable challenges. Increase of fault current is one of such serious challenges and there are some fault current limiters (FCLs) that can limit the fault current. Existing grid protection FCLs, however, simply limit the fault current passively and can allow the existing protection coordination schemes to fail. This phenomenon leads to catastrophic failure in the complex system and may cause unpredictable power grid operation. Unlike a FCL, a superconducting fault current controller (SFCC) employs a full-bridge thyristor rectifier, a high temperature superconducting (HTS) DC reactor, and an embedded control unit to maintain the fault current level at a proper value by adjusting the phase angle of thyristors. This paper contains experimental and numerical analysis to design and fabricate a SFCC system for protection and stability improvement in power grids. At first, fundamental characteristics of a SFCC system were introduced. System circuit diagram and operational principles were proposed. Secondly, the developed small-scale SFCC system was introduced and verified. A 40 Vrms/30 Arms class prototype SFCC employing HTS DC reactor was fabricated and short circuit tests that simulate various fault conditions were implemented to verify the control performance of the fault current. Finally, the practical feasibility of application of the SFCC system to the power system was studied. The problems caused by three-phase faults from the power grid were surveyed and transient stability analysis of the power system was conducted by simulations. From the experimental and simulation results, we can verify the feasibility of the SFCC in power system.
Sensor Selection and State Estimation for Unobservable and Non-Linear System Models (2021)

To comply with the increasing complexity of new mechatronic systems and stricter safety regulations, advanced estimation algorithms are currently undergoing a transformation towards higher model complexity. However, more complex models often face issues regarding the observability and computational effort needed. Moreover, sensor selection is often still conducted pragmatically based on experience and convenience, whereas a more cost-effective approach would be to evaluate the sensor performance based on its effective estimation performance. In this work, a novel estimation and sensor selection approach is presented that is able to stabilise the estimator Riccati equation for unobservable and non-linear system models. This is possible when estimators only target some specific quantities of interest that do not necessarily depend on all system states. An Extended Kalman Filter-based estimation framework is proposed where the Riccati equation is projected onto an observable subspace based on a Singular Value Decomposition (SVD) of the Kalman observability matrix. Furthermore, a sensor selection methodology is proposed, which ranks the possible sensors according to their estimation performance, as evaluated by the error covariance of the quantities of interest. This allows evaluating the performance of a sensor set without the need for costly test campaigns. Finally, the proposed methods are evaluated on a numerical example, as well as an automotive experimental validation case.
Joint detection CDMA antenna diversity techniques (1997)

In the early 1990s the development of an air interface concept for UMTS and IMT 2000 was started, which is based on a combination of the multiple access methods FDMA, TDMA and CDMA, and in which multiple access interference is combatted by joint detection in the receivers. This air interface concept is termed joint detection (JD)-CDMA. In cellular mobile radio systems the directional inhomogeneity of the radio channels can be exploited to increase the spectral efficiency by antenna diversity techniques. The goal of this paper is to demonstrate the beneficial effects of receiver antenna diversity techniques in the uplink of JD-CDMA air interfaces. By means of computer simulations of realistic scenarios, the spectral efficiencies obtainable by different versions of antenna diversity techniques, namely space diversity, antenna arrays and sets of sector antennas are determined. (7 pages)
A New System for Three-dimensional Clinostat Synchronized X-irradiation with a High-speed Shutter for Space Radiation Research (2016)

Considering further human activity in space, it is necessary to study the biological effects of combined microgravity and space radiation; however, many aspects of these combined effects remain unclear. In the field of space biology, it is difficult to investigate relative biological effectiveness (RBE) and combined effects because the ability to conduct and replicate space experiments is restricted. Therefore, a new three-dimensional (3D) clinostat synchronized X-irradiation system with a high-speed shutter was fabricated following the development of a heavy-ion irradiation system. This study showed that the system could simultaneously irradiate rotating samples using the 3D clinostat, with the samples in a horizontal position. The samples were completely irradiated because of the flatness and symmetry of the irradiation fields. Doses were virtually identical under both standing and rotation conditions, with the difference being <1% under the assumption of X-irradiation at a dose of 1 Gy. Our new device could accurately synchronize X-irradiation and simulated microgravity at the ground level. The device is expected to greatly contribute to space radiation research as a valuable platform for studies concerning RBE and the combined effects of radiation under microgravity.
Continuous versus intermittent angiotensin converting enzyme inhibition in renal hypertensive rats. (1993)

Converting enzyme inhibitors impair renal function of the kidney beyond a stenosis of the renal artery in humans and induce histological lesions in the clipped kidney of renal hypertensive rats. In two-kidney, one clip hypertensive rats, we compared the time course and magnitude of the biochemical effects of angiotensin converting enzyme inhibition on the plasma renin-angiotensin system, cardiac hypertrophy, renal lesions, and 24-hour blood pressure decrease induced by either intermittent angiotensin converting enzyme inhibition administration (benazepril PO, 10 mg/kg once a day, n = 93) or continuous administration (benazeprilat, 3 mg/kg per day via osmotic pumps, n = 92). Control rats (n = 91) received the drug vehicle intermittently or continuously. Mortality was significantly reduced by both intermittent (n = 3/93) and continuous (n = 3/92) inhibition compared with controls (n = 18/91) (P < .001). Changes in the plasma renin-angiotensin system and blood pressure were parallel. A continuous suppression of the activity of the plasma renin-angiotensin system was associated with a 24-hour decrease in blood pressure with continuous inhibition, whereas intermittent inhibition induced a similar fall in blood pressure only for the first hours after gavage.(ABSTRACT TRUNCATED AT 250 WORDS)
Plasmonic Directional Photodetectors for Edge Enhancement (2021)

Angle-sensitive plasmonic photodetectors that can perform optical-domain spatial filtering operations are developed. The edge enhancement capabilities of these devices are demonstrated via computational imaging simulations based on their measured angular response.
Long-Term Efficacy of Adalimumab for Treatment of Moderately to Severely Active Ulcerative Colitis (2012)

Purpose: To evaluate long-term efficacy of adalimumab (ADA) for patients with moderately to severely active ulcerative colitis (UC). Methods: The ADA UC development program consists of two trials (ULTRA 1 and ULTRA 2)1, 2 followed by an ongoing multicenter open-label (OL) extension. Patients entering the extension on OL weekly ADA dosing continued on same. Patients entering the extension study from any blinded cohort (ADA or placebo [PBO]) or an OL cohort receiving ADA 40 mg every other week (eow) received OL ADA 40 mg eow. For patients entering from a blinded cohort, increase to 40 mg weekly for flare or non-response was allowed at or after week 12. For patients entering from an OL cohort, increase to 40 mg weekly for flare or non-response was allowed at or after week 12 for patients in clinical response at entry, or week 2 for patients with inadequate response at entry. Adjustments to concomitant medications including corticosteroids were allowed per protocol specifications. Partial Mayo score (PMS, Mayo score without endoscopy subscore) was collected at every study visit during the lead-in trials and the OL extension. Mean PMS over time through 2 years (112 weeks) from first dose of ADA was assessed using observed case method in the “any ADA” population (patients who received at least one dose of ADA in the lead-in or extension trials,) using a data cut off of 31 July 2011. The proportion of patients in clinical remission per PMS (PMS ≤2 with no subscore >1) at week 60 of the OL extension was assessed in the intent-to-treat (ITT) population (patients enrolled in the extension, excluding patients from sites non-compliant with good clinical practices), using the last observation carried forward (LOCF) method to handle missing data. Results: The observed mean PMS at day of first dose of ADA was 5.9 (n=992), and decreased over time through 112 weeks of treatment to 1.8 (N=444, Table). Of the 588 ITT patients from the lead-in studies who enrolled into the OL extension, 351 (59.7%, LOCF) achieved clinical remission per PMS at week 60 of the OL extension. No new safety signals were observed.Table: Mean PMS over time in the “any ADA” population, observedConclusion: The results of the ongoing extension trial support clinically meaningful efficacy of adalimumab for the treatment of moderately to severely active UC, sustained for up to 2 years.
Motion Area Detection Based on Information of Compressed-Domain (2008)

Motion object detection is the basis of video surveillance;the real-time performance and the detection accuracy of the existing algorithms need to be improved.Motion area detection algorithm based on compressed-domain information is proposed in this paper.Motion vector produced in the process of compression is used to be rid of background motion of camera,then information of DCT coefficient and macro-block type are used to wipe off illusive motion block.Morphological post-processing method is introduced to reduce noise and improve detection precision.Testing with standard sequence,this algorithm has the advantage of high-speed,and can detect motion area exactly.
Symbol-Level Multiuser MISO Precoding for Multi-Level Adaptive Modulation (2017)

Symbol-level precoding is a new paradigm for multiuser multiple-antenna downlink systems aimed at creating constructive interference among transmitted data streams. This can be enabled by designing the precoded signal of the multiantenna transmitter on a symbol level, taking into account both channel state information and data symbols. Previous literature has studied this paradigm for Mary phase shift keying modulations by addressing various performance metrics, such as power minimization and maximization of the minimum rate. In this paper, we extend this to generic multi-level modulations, i.e., Mary quadrature amplitude modulation by establishing connection to PHY layer multicasting with phase constraints. Furthermore, we address the adaptive modulation schemes which are crucial in enabling the throughput scaling of symbol-level precoded systems. In this direction, we design the signal processing algorithms for minimizing the required power under per-user signal to interference noise ratio or goodput constraints. Extensive numerical results show that the proposed algorithm provides considerable power and energy efficiency gains, while adapting the employed modulation scheme to match the requested data rate.
Remaining small bowel endoscopic lesions at surgery have no influence on early anastomotic recurrences in Crohn's disease. (1995)

Endoscopic lesions let in place after "curative" surgery have no influence on early endoscopic anastomotic recurrences in CD.
Acetaminophen Induces Apoptosis and Inhibited Growth and MMP Secretion in Human Hepatoma Cell Line SK‐Hep‐1 (2007)

Acetaminophen (APAP), a widely used over‐the‐counter analgesic‐antipyretic agent, causes few adverse effects when taken in the usual therapeutic dose. However, APAP overdose leads to hepatic injury in human and animals, and is often fatal. The aim of the present investigation was to study in vitro the mechanism of APAP toxicity by assessing cellular viability, apoptosis, MMP secretion and morphology in human hepatoma cell line SK‐Hep‐1 exposed to APAP. Human hepatoma cell line SK‐Hep‐1 (ATCC) was grown in MEM medium with 10% FBS and antibiotics in 24‐well tissue culture plates. At near confluence, cells were treated with APAP at 0, 1, 5, 10, 15 and 20 mM, in triplicate at each concentration. Viability was assessed by MTT assay, apoptosis by green caspase detection kit, MMP secretion by zymography and morphology by H&amp;E staining. APAP inhibited the growth of SK‐Hep‐1 cells by 20% of the control at 5–20 mM concentration and induced slight apoptosis at 5 mM, moderate at 10 mM and significant at 15 and 20 mM. Zymography demonstrated two bands corresponding to MMP‐2 and MMP‐9 secretion by SK‐Hep‐1 cells. APAP inhibited secretion of both MMPs in a dose dependent fashion, with virtual total inhibition of MMP‐2 at 5 mM and MMP‐9 at 15 mM concentration. H&amp;E staining showed no morphological changes up to 15 mM concentration. The present study demonstrates that APAP causes toxicity to SK‐Hep‐1 cells by inducing cellular apoptosis and by inhibiting cellular MMP secretion and growth. Research funded by Dr. Rath Health Foundation
Steroidal and Nonsteroidal Anti-inflammatory Agents (1984)

Two hundred and eighty-three patients scheduled to undergo extracapsular cataract extraction with intraocular lens implantation were randomized into four treatment groups that received 1% topical indomethacin and 0.1% topical dexamethasone sodium phosphate, either drug and the other drug's placebo, or two placebos. Inflammation was assessed by clinical grading, and the breakdown of the blood-aqueous barrier was evaluated by slit-lamp anterior segment fluorophotometry. Patients who used either or both anti-inflammatory agents had significantly less inflammation or blood-aqueous barrier breakdown than did those who used neither agent. Also, the use of both topical indomethacin and dexamethasone resulted in less fluorescein leakage during the second postoperative week than did the use of dexamethasone alone. Since this difference could not be detected by clinical measurement, we believe that fluorophotometry is a more sensitive quantitative measure. Clinical assessment of inflammation did correlate with fluorophotometric measurements, as patients with clinically unacceptable inflammation had 3.7 times more fluorescein leakage in the surgically treated eye than did patients with clinically acceptable inflammation.
Seroprevalence of Selected Infectious Agents in a Free-Ranging, Low-Density Lion Population in the Central Kalahari Game Reserves in Botswana (2007)

Twenty-one free-ranging Central Kalahari lions (Panthera leo) exhibited a high prevalence rate of feline herpesvirus (100%) and feline immunodeficiency virus (71.4%). Canine distemper virus and feline calicivirus occurred with a low prevalence. All individuals tested negative for feline coronavirus, feline parvovirus, feline leukemia virus, Ehrlichia canis, and Anaplasma phagocytophilum.
Interleukin-13 and Interferon-Gamma Producing Skin Resident CD8+ T Cells: A Vicious Circle of Barrier Disruption of the Skin in Atopic Dermatitis (2008)

MEETING ABSTRACTS: Abstracts from the Fifth Georg Rajka International Symposium of Atopic Dermatitis, Kyoto, Japan, May 11-13, 2008: Part 1: 5. Immunology of Atopy and Atopic Dermatitis
Equilibrium properties of a quadrupolar glass (1994)

We introduce a semimicroscopic discrete-state model appropriate to the orientational glass phase in mixed alkali halide cyanides with 〈111〉 equilibrium orientations of the ${\mathrm{CN}}^{\mathrm{\ensuremath{-}}}$ ions, such as K(CN${)}_{\mathit{x}}$${\mathrm{Br}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$. The order-parameter fields are defined as symmetry adapted combinations of the occupation number operators along the cubic body diagonals, which transform according to the ${\mathit{T}}_{2\mathit{g}}$ representation of the cubic group. These interact via an infinite-range random interaction in the presence of quenched local random strains. We then use the replica formalism to derive a replica-symmetric solution for the components of the orientational-glass order parameter, the linear susceptibilities, and the elastic compliances. The high-temperature orientational-glass phase is characterized by an isotropic order-parameter matrix with only the diagonal elements ${\mathit{q}}_{\mathrm{\ensuremath{\mu}}}$ being nonzero. At high temperatures, the behavior of the order parameter q=${\mathrm{\ensuremath{\Sigma}}}_{\mathrm{\ensuremath{\mu}}}$${\mathit{q}}_{\mathrm{\ensuremath{\mu}}}$/3 is similar to that of an Ising spin glass, however, at intermediate and low temperatures the two models differ significantly. We also derive the instability line ${\mathit{T}}_{\mathit{f}}$(\ensuremath{\Delta}) separating the replica-symmetric isotropic phase from the low-temperature anisotropic orientational glass phase, which is characterized by broken replica symmetry. In contrast to the random-bond--random-field model of an Ising spin glass, the instability temperature increases with random-field variance, implying that in quadrupolar glasses replica-symmetry breaking may be relevant already at relatively high temperatures. Finally, an expression for the distribution of local strains related to the NMR line shape is derived. It is also shown that the quadrupolar glass order parameter can be determined by NMR.