gebhart/patrepeval huggingface dataset:
Identification of immunogenic LY6K long peptide encompassing both CD4+and CD8+T-cell epitopes and eliciting CD4+T-cell immunity in patients with malignant disease (2014)

Identification of peptides that activate both tumor-specific helper T (Th) cells and cytotoxic T lymphocytes (CTLs) are important for the induction of effective antitumor immune responses. We focused on a long peptide (LP) derived from lymphocyte antigen 6 complex locus K (LY6K) encompassing both candidate Th epitopes and a known CTL epitope. Using IFNγ ELISPOT assays as a marker of activated T cells, we studied the immunogenicity and cross-priming potential of LY6K-LP, assaying human immune cell responses in vitro and immunologic activities in HLA-A24 transgenic mice in vivo. We identified LY6K<sub>172-191</sub>-LP as an effective immunogen spanning naturally processed epitopes recognized by T helper type 1 (Th1) cells and CTLs. LY6K-specific CTLs were induced through cross-presentation of LY6K<sub>172-191</sub>-LP in vitro and in vivo. In addition, LY6K<sub>172-191</sub>-LP enhanced induction of LY6K-specific CTLs among the peripheral blood mononuclear cells (PBMCs) of head-and-neck malignant tumor (HNMT) patients. LY6K<sub>172-191</sub>-LP-specific Th1 immunologic response following 1 week in vitro stimulation of PBMCs with LY6K<sub>172-191</sub>-LP were detected in 16 of 21 HNMT patients (76%) vaccinated with CTL-epitope peptides and 1 of 11 HNMT patients (9%) prior to vaccination, but not in 9 healthy donors. Our results are the first to demonstrate the presence of LY6K-specific Th1 cell responses in HNMT patients and underscore the possible utility of LY6K<sub>172-191</sub>-LP for the induction and propagation of both LY6K-specific Th1 cells and CTLs.
Bias Voltage Dependence of GMR in Insulating Granular Thin Films (1998)

The bias voltage (Vb) dependence of tunnel-type GMR was investigated in Co-Al-O insulating granular thin films. The electrical resistivity (ρ) and MR were measured in the current-perpendicular-to-plane (CPP) geometry for 1-μm-thick Co-Al-O films sandwiched between Au-Cr or Nb-Ti electrodes. The MR was found to remain constant until Vb reached a threshold voltage, whereas ρ decreased rapidly with Vb. The MR started to decrease when Vb exceeded the threshold voltage. This behavior is discussed in terms of the inelastic tunneling process with magnon excitations, which causes the decrease in MR.
Three-dimensional Morphology of the Knee Reveals Ethnic Differences (2011)

We identified differences in three-dimensional knee morphology among Caucasian, African American, and East Asian populations. Clinical studies will be required to determine whether these differences are important for implant design.
Effect of ouabain on Na,K-ATPase and electrolyte transport in the dog ileum in vivo. (1979)

It is currently believed that the rate and direction of sodium transport in the small intestine may be regulated by the activity of Na,K-ATPase in the basolateral cell membrane. We tested this hypothesis by selectively infusing ouabain, a known inhibitor of Na,K-ATPase, into the mesenteric artery supplying a perfused loop of ileum in 18 dogs. Before ouabain infusion there were significant correlations between the activity of Na,K-ATPase and net and lumen to plasma fluxes of sodium and chloride. After ouabain, there was no significant change in sodium and chloride transport, unidirectional fluxes or transmucosal potential difference, despite a 50% reduction in Na,K-ATPase activity. Furthermore, there was no significant correlation between Na,K-ATPase activity and sodium or chloride transport after ouabain. The only statistically significant effect of ouabain infusion was a reduction in the rate of bicarbonate secretion. Thus, the results of our experiments suggest that mucosal Na,K-ATPase is not a rate-limiting step in the absorption of sodium and chloride in the dog ileum, though it may be an important facilitative factor.
Mechanical properties of currently available left atrial appendage occlusion devices: A bench‐testing analysis (2018)

Endoluminal left atrial appendage occlusion is an emerging therapy to treat patients suffering from atrial fibrillation with contraindications against oral anticoagulation. Different occlusion devices have been introduced into the clinical setting while comparative studies between the devices are sparse. This in vitro study compares several endoluminal left atrial appendage occlusion systems regarding 2 mechanical properties: radial (RF) and tug force (TF). Seven different occluder systems of various sizes (24 in total) underwent testing throughout their recommended sizing range. RF was measured in a commercial RF tester. TF was assessed according to a recently published bench test. RF increased with compression of the devices: The LAmbre 2228 device exerted the highest RF (8.6 N) at maximum compression of 16 mm. The lowest RF of 0.1 N was exhibited by the 27 mm Occlutech occluder at minimal compression. The highest TFs were exerted by the WaveCrest devices at maximum compression with 4.6 and 3.6 N for the 22 mm and the 27 mm device, respectively. The lowest TFs were measured for the first-generation Occlutech devices, particularly for the 24 mm device with 1.1 N at maximum compression and 0.4 N at minimum compression. A strong positive correlation was found between the number of hooks per millimeter circumference of an occluder and its tug force (r = 0.87, P < 0.01). The analysis revealed device stability to be more dependent on anchoring structures than on RF. The wide range of mechanical properties makes comparison of current LAA occluders difficult and emphasizes the need for standardized preclinical testing to prompt clinical compatibility.
Stimulated Brillouin Scattering and Its Dependences on Temperature and Strain in a High-Delta Optical Fiber with F-Doped Depressed Inner-Cladding (2006)

Stimulated Brillouin scattering in a high-delta fiber with F-doped depressed inner-cladding is investigated. Its dependences on temperature and strain are measured and compared for each acoustic mode. The 4th-order scattering shows different behaviors from the others.
<title>Effect of vector quantization on ultrasound tissue characterization</title> (1992)

This paper presents a case study of the effects of compression error on computerized tissue characterization of normal and fatty ultrasound liver images. Two compression techniques were studied, pruned-tree structured vectored quantization (PTSVQ) and PTSVQ with splitting. Vector quantization is a technique for representing a block of image values, or vector, by the vector in a codebook that is closest to the original vector. Splitting is a technique for decomposing image pixel values into the high and low values. The high values are compressed reversibly while the low values are compressed via PTSVQ. Tissue characterization was accomplished by extracting features from a region of interest (ROI). These features included measuring fractal dimension and statistics concerning run length and co-occurrence probabilities of pixels separated by a given direction and distance. The results were: (1) PTSVQ with splitting produced less image distortion at moderate bit rates than PTSVQ as measured by mean square error; (2) PTSVQ with splitting produced more degradation of the tissue characterizer; and (3) Rotation of the ROIs greatly reduced the degradation of the tissue characterizer for both types of compression. This type of rotation uses interpolation to derive pixel values for rotated lattice points that fall between original lattice points. A possible explanation for these results is that PTSVQ caused irregular distortions at edges depending upon the amount of region information included in the design of the codebook. The interpolation during rotation reduces these irregularities.
Resistance Mechanism Against Fluoroquinolones in Mycoplasma hyopneumoniae Field Isolates (2007)

The quinolone resistance-determining regions (QRDR) of gyrA, gyrB, parC, and parE of ten Mycoplasma hyopneumoniae field isolates that were either sensitive (5) or resistant (5) to the fluoroquinolones flumequine and enrofloxacin were characterized. In all five resistant isolates, one point mutation (C --> A) in parC was found, resulting in an amino acid change from serine to tyrosine at position 80 (Escherichia coli numbering). For four of these isolates, this was the only mutation found. These isolates had a minimum inhibitory concentration (MIC) of enrofloxacin of 0.5 microg/ml, whereas for sensitive isolates the MIC of enrofloxacin was < or =0.06 microg/ml. One resistant isolate (Mh 20) had an extra mutation (C --> T) in gyrA resulting in an amino acid change from alanine to valine at position 83 (E. coli numbering), leading to a further increase in the MIC of enrofloxacin (>1 microg/ml). No mutations resulting in an amino acid change were detected in the QRDR of the gyrB and parE genes of the selected isolates. This is the first description of the mechanism of stepwise resistance against fluoroquinolones in M. hyopneumoniae.
Lake Weir Eutrophication Study: Final Report for Phases I and II (1987)

Located 57 feet above sea level at 21 01* N-081 55' W, Lake Weir falls within the intermediate zone between warm temperate and subtropical climates (Beaver et al 1981).This 2100 hectare lake system is comprised of three distinct basins: Little Lake Weir, Sunset Harbor, and Lake Weir proper.LakeWeir proper is nearly circular with a diameter of approximately seven kilometers.The lake has a relatively small vegetated littoral none; the sides of the lake basin drop off quickly to a flat bottom ranging from six to eight meters in depth.Lake Weir is a seepage lake with no permanent tributaries.It receives water and nutrients through groundwater seepage, surface runoff, and precipitation (Messer 1975).There is intermittent outflow to the Oklawaha River over a weir structure located on the north shore.The Lake Weir watershed, defined on the basis of topographic highs surrounding the lake, was determined to be 45OO hectares in area (Figure 1-1).Several small enclosed wetlands occupy topographic lows in the upper watershed.Messer (1975) did not include these in his calculations, and hence arrived at a smaller watershed area.E-iecause of the low nutrient affinity of the soils (Messer 1975), nutrient loading from the entire 4500 hectare watershed may impact the lake.
Outcomes and Complications of Lead Removal: Can We Establish a Risk Stratification Schema for a Collaborative and Effective Approach? (2015)

Transvenous lead removal is highly successful, with few serious procedural complications. We propose a risk stratification scheme that may categorize patients as low, moderate, and high risk for lead extraction. Such a strategy may guide which extractions are best performed in the operating room.
Safe current injection strategies for a STATCOM under asymmetrical grid faults (2010)

This paper explores different strategies to set the reference current of a STATCOM under unbalanced grid voltage conditions and determines the maximum deliverable reactive power in each case to guarantee the injected current is permanently within the STATCOM secure operation limits. The paper presents a comprehensive derivation of the proposed STATCOM control strategies to set the reactive current reference under unbalanced grid faults, together with an extensive evaluation using simulation and experimental results from a low-scale laboratory setup in order to verify and validate the dynamic performance achieved by the proposed reactive current limiting algorithms.
Improving mitochondria and ER stability helps eliminate upper motor neuron degeneration that occurs due to mSOD1 toxicity and TDP‐43 pathology (2021)

Mechanism-focused and cell-based drug discovery approaches not only addressed key cellular defects responsible for UMN loss, but also identified NU-9, the first compound to improve the health of diseased UMNs, neurons that degenerate in ALS, HSP, PLS, and ALS/FTLD patients.
Squaric Ester-Based, pH-Degradable Nanogels: Modular Nanocarriers for Safe, Systemic Administration of Toll-like Receptor 7/8 Agonistic Immune Modulators (2021)

Small-molecular Toll-like receptor 7/8 (TLR7/8) agonists hold promise as immune modulators for a variety of immune therapeutic purposes including cancer therapy or vaccination. However, due to their rapid systemic distribution causing difficult-to-control inflammatory off-target effects, their application is still problematic, in particular systemically. To address this problem, we designed and robustly fabricated pH-responsive nanogels serving as versatile immunodrug nanocarriers for safe delivery of TLR7/8-stimulating imidazoquinolines after intravenous administration. To this aim, a primary amine-reactive methacrylamide monomer bearing a pendant squaric ester amide is introduced, which is polymerized under controlled RAFT polymerization conditions. Corresponding PEG-derived squaric ester amide block copolymers self-assemble into precursor micelles in polar protic solvents. Their cores are amine-reactive and can sequentially be transformed by acid-sensitive cross-linkers, dyes, and imidazoquinolines. Remaining squaric ester amides are hydrophilized affording fully hydrophilic nanogels with profound stability in human plasma but stimuli-responsive degradation upon exposure to endolysosomal pH conditions. The immunomodulatory behavior of the imidazoquinolines alone or conjugated to the nanogels was demonstrated by macrophages <i>in vitro</i>. <i>In vivo</i>, however, we observed a remarkable impact of the nanogel: After intravenous injection, a spatially controlled immunostimulatory activity was evident in the spleen, whereas systemic off-target inflammatory responses triggered by the small-molecular imidazoquinoline analogue were absent. These findings underline the potential of squaric ester-based, pH-degradable nanogels as a promising platform to permit intravenous administration routes of small-molecular TLR7/8 agonists and, thus, the opportunity to explore their adjuvant potency for systemic vaccination or cancer immunotherapy purposes.
Soft tissue angiofibroma: Clinicopathologic, immunohistochemical and molecular analysis of 14 cases (2017)

Soft tissue angiofibroma is rare and has characteristic histomorphological and genetic features. For diagnostic purposes, there are no specific antibodies available. Fourteen lesions (6 females, 8 males; age range 7-67 years) of the lower extremities (12) and trunk (2) were investigated by immunohistochemistry, including for the first time NCOA2. NCOA2 was also tested in a control group of other spindle cell lesions. The known fusion-genes (AHRR-NCOA2 and GTF2I-NCOA2) were examined using RT-PCR in order to evaluate their diagnostic value. Cases in which no fusion gene was detected were additionally analysed by RNA sequencing. All cases tested showed nuclear expression of NCOA2. However, this was not specific since other spindle cell neoplasms also expressed this marker in a high percentage of cases. Other variably positive markers were EMA, SMA, desmin and CD34. STAT6 was negative in the cases tested. By RT-PCR for the most frequently observed fusions, an AHRR-NCOA2 fusion transcript was found in 9/14 cases. GTF2I-NCOA2 was not detected in the remaining cases (n = 3). RNA sequencing revealed three additional positive cases; two harbored a AHRR-NCOA2 fusion and one case a novel GAB1-ABL1 fusion. Two cases failed molecular analysis due to poor RNA quality. In conclusion, the AHRR-NCOA2 fusion is a frequent finding in soft tissue angiofibroma, while GTF2I-NCOA2 seems to be a rare genetic event. For the first time, we report a GAB1-ABL1 fusion in a soft tissue angiofibroma of a child. Nuclear expression of NCOA2 is not discriminating when compared with other spindle cell neoplasms.
Preparation of 2α,3α-dihydroxy-7-oxa-6-oxo-23,24-dinor-B-homo-5α-cholanic acid, its esters and amides as brassinolide analogues (1986)

Synthesis of brassinosteroids IIb, d, g, i, k, m, o and evaluation of their growth-promoting activity is reported. The acid IIb shows high activity in both the bean first and second internode assay.
Raja -- A Multidisciplinary Artistic Performance (2011)

Motion-based interactive systems have long been utilizedin contemporary dance performances. These performancesbring new insight to sound-action experiences in multidisciplinary art forms. This paper discusses the related technology within the framework of the dance piece, Raja. The performance set up of Raja gives a possibility to use two complementary tracking systems and two alternative choices formotion sensors in real-time audio-visual synthesis.
Primary focal cryosurgery of the prostate: Long-term clinical and biochemical outcomes in a large cohort at a tertiary referral center. (2015)

114 Background: Modern primary focal cryosurgery (PFC) has emerged as a primary therapy option for localized and minimal low-risk prostate cancer (PCa), achieving good local cancer control and survival outcome. The aim of this analysis was to report on the experience of PFC in our tertiary referral center in the management of localized PCa. Methods: We identified a consecutive series of patients that underwent PFC for localized PCa at our institution between 8/2000 and 1/2014. Demographics, PSA levels and Gleason scores before primary treatment and at time of recurrence were assessed; BDFS, OS, and DSS were assessed. BCR was defined by the Phoenix (PD) and Stuttgart Definitions (SD). Results: A total of 126 patients were included in the analysis, with a median follow-up of 40.3 (0.8-116, IQR 41) months. Median age was 73.5 (range 45-92, IQR 9) years. Median initial serum PSA level was 6.0 (1-44.5, IQR 3) ng/ml. Median primary and secondary Gleason score on initial biopsy was 3 (3-5, IQR 1) with a median sum of 6 (6-10, 1), and 15% (2-95%, IQR 0) of biopsy tissue involved with cancer. Median number of biopsy cores was 12 (2-32), with a median of 1 (1-12, IQR 1) core affected by cancer. Median PSA nadir post-treatment was 1.3 (0.1-13.1, IQR 2) ng/ml. According to PD and SD, 24 and 37 patients had BCR after a median of 14.9 (3.4-91.3, IQR 17) and 13.0 (2.9-90.3, IQR 11) months. Overall 4-year-BDFS was 83% and 73% by PD and SD, respectively. 5-year OS and DSS was 95%, and 99.2%. Of patients that met BCR criteria, almost 25% were proven to be negative on biopsy, confirming over-estimation of failures. Patients that recurred had significantly higher initial median PSA levels (8.5 vs. 5.8 ng/ml; p&lt;0.01) and PSA-nadir (2.1 vs. 1.0 ng/ml; p&lt;0.05). Conclusions: Our analysis confirms PFC being a good option with low rate of morbidities for patients with localized PCa, with excellent BDFS and DSS at a long follow-up of 40 months. Controversy exists regarding criteria of BCR-definitions after focal therapies. More stringent definitions, such as the SD, especially in a focal cryosurgery setting, significantly over-estimate failure rates, and prostate biopsy seems to be the only reliable means to assess for recurrence at this point.
2- and 8-alkynyl-9-ethyladenines: Synthesis and biological activity at human and rat adenosine receptors (2005)

The synthesis of a series of 9-ethyladenine derivatives bearing alkynyl chains in 2- or 8-position was undertaken, based on the observation that replacement of the sugar moiety in adenosine derivatives with alkyl groups led to adenosine receptor antagonists. All the synthesized compounds were tested for their affinity at human and rat A(1), A(2A), and A(3) adenosine receptors in binding assays; the activity at the human A(2B) receptor was determined in adenylyl cyclase experiments. Biological data showed that the 2-alkynyl derivatives possess good affinity and are slightly selective for the human A(2A) receptor. The same compounds tested on the rat A(1) and A(2A) subtypes showed in general lower affinity for both receptors. On the other hand, the affinity of the 8-alkynyl derivatives at the human A(1), A(2A), and A(2B) receptors proved to be lower than that of the corresponding 2-alkynyl derivatives. On the contrary, the affinity of the same compounds for the human A(3) receptor was improved, resulting in A(3) selectivity. As in the case of the 2-alkynyl-substituted compounds, the 8-alkynyl derivatives showed decreased affinity for rat receptors. However, it is worthwhile to note that the 8-phenylethynyl-9-ethyladenine was the most active compound of the two series (K (i) in the nanomolar range) at both the human and rat A(3) subtype. Docking experiments of the 2- and 8-phenylethynyl-9-ethyladenines, at a rhodopsin-based homology model, gave a rational explanation of the preference of the human A(3) receptor for the 8-substituted compound.
Crossability between Transgenic Blue Chrysanthemums and the Wild Chrysanthemum Species <i>Chrysanthemum japonense</i> var. <i>japonense</i> (2020)

Transgenic chrysanthemums (Chrysanthemum morifolium) with blue flower colors have already been created, and are expected to be commercialized. However, cultivated chrysanthemums are known to cross with wild species native to Japan, and careful studies are needed to assess the risk of these transgenes escaping into wild Chrysanthemum populations. We previously reported on the transmission of transgenes from the model cultivar 'Taihei' to interspecific progeny. For this study, we used the recently developed cultivar 'Sei Arabella' and a promising breeding strain (T37) as transgene hosts, and performed crosses between these lines and the wild species Chrysanthemum japonense var. japonense. We found relatively high seed set rates (20.6%-83.4%) after artificial, reciprocal pollinations, and the inheritance and segregation of the transgenes in the hybrid progeny were confirmed by PCR. Some of the transgenic progeny exhibited blue flower colors and contained modified anthocyanins, like their transgenic parents. These results were similar to those obtained with 'Taihei' and thus suggested that the risk of transgenes escaping to wild species could be quite high. Therefore, it will be important to investigate techniques to reduce this risk.
Absorption recovery time reduction in InGaN/GaN quantum well saturable absorbers (2008)

In this work, a simple method to reduce the absorption recovery time of the InGaN/GaN quantum well saturable absorber was demonstrated. The recovery time of the saturable absorber grown by metal organic chemical vapor deposition was effectively controlled by controlling the crystal quality. Transmission electron microscopy results showed that, for saturable absorbers with reduced GaN buffer thicknesses, increased dislocations were introduced into the quantum well regions. The degraded crystal quality would therefore cause an increased density of nonradiative recombination centers, which were responsible for the fast recovery of the absorption. In addition, with the as-grown thin GaN buffers, the severe interference-induced reflectivity fluctuations were successfully suppressed.
Engineered nonlinear materials using gold nanoantenna array (2018)

Gold dipole nanoantennas embedded in an organic molecular film provide strong local electromagnetic fields to enhance both the nonlinear refractive index (n<sub>2</sub>) and two-photon absorption (2PA) of the molecules. An enhancement of 53× for 2PA and 140× for nonlinear refraction is observed for BDPAS (4,4'-bis(diphenylamino)stilbene) at 600 nm with only 3.7% of gold volume fraction. The complex value of the third-order susceptibility enhancement results in a sign change of n<sub>2</sub> for the effective composite material relative to the pure BDPAS film. This complex nature of the enhancement and the tunability of the nanoantenna resonance allow for engineering the effective nonlinear response of the composite film.