gebhart/patrepeval huggingface dataset:
Anesthesia-induced atelectasis assessed by lung sonography (2014)

Background Atelectasis and poorly ventilated lung areas are negative consequences of general anesthesia observed in adult as well as in children. The reported incidence of this anesthesia-induced atelectasis in children is high and comes from 83 % to almost 100 %. The diagnosis of this entity is difficult to do at the bedside; they are commonly small and mostly invisible to standard chest X-ray images. More complex diagnosing techniques like CT scan or magnetic resonance imaging (MRI) can easily diagnose atelectasis although they are strategically impractical. Ultrasound is a bedside, rapid, noninvasive and radiation-free technique. Lung ultrasound (LUS) has an important role for diagnosing pulmonary diseases in children although it role for detecting anesthesia-induced atelectasis has not been determined yet.
Large-Scale Mapping of Transposable Element Insertion Sites Using Digital Encoding of Sample Identity (2013)

Determining the genomic locations of transposable elements is a common experimental goal. When mapping large collections of transposon insertions, individualized amplification and sequencing is both time consuming and costly. We describe an approach in which large numbers of insertion lines can be simultaneously mapped in a single DNA sequencing reaction by using digital error-correcting codes to encode line identity in a unique set of barcoded pools.
Quantitative measurement of ultrasonic pressure field using combination of optical phase contrast and nonlinear acoustic holography methods (2018)

Ultrasound has been widely used in medicine for both diagnosis and therapeutics. To assure its safety and efficacy, it is necessary to establish a fast and accurate method of measuring an ultrasonic field. Hydrophone scanning, which is a standard method for pressure measurement, requires a long measurement time and may disturb the field. In this study, an optical phase contrast method is combined with an acoustic holography method with nonlinear propagation simulation. The nonaxisymmetric pressure field of pulse ultrasound upstream of the focus was measured by the optical phase contrast method combined with a computed tomography (CT) algorithm, and the entire three-dimensional pressure field was reconstructed by acoustic holography. The result obtained by the proposed method agreed well with that by the hydrophone measurement without absolute pressure calibration and confirmed the markedly reduced required measurement time.
Early Expression of the Calmodulin Gene, Which Precedes Appressorium Formation in Magnaporthe grisea , Is Inhibited by Self-Inhibitors and Requires Surface Attachment (1999)

Fungal conidia contain chemicals that inhibit germination and appressorium formation until they are well dispersed in a favorable environment. Recently, such self-inhibitors were found to be present on the conidia of Magnaporthe grisea, and plant surface waxes were found to relieve this self-inhibition. To determine whether the self-inhibitors suppress the expression of early genes involved in the germination and differentiation of conidia, the calmodulin gene was chosen as a representative early gene, because it was found to be expressed early in Colletotrichum gloeosporioides and Colletotrichum trifolii differentiation. After calmodulin cDNA and genomic DNA from M. grisea were cloned, the promoter of the calmodulin gene was fused to a reporter gene, that for green fluorescent protein (GFP), and transformed into the M. grisea genome. Confocal microscopic examination and quantitation of expression of GFP green fluorescence showed (i) that the expression of the calmodulin gene decreased significantly when self-inhibition of M. grisea appressorium formation occurred because of high conidial density or addition of exogenous self-inhibitors and (ii) that the expression level of this gene was restored when self-inhibition was relieved by the addition of plant surface waxes. The increase in fluorescence correlated with the percentage of conidia that formed appressoria. The induction of calmodulin was also confirmed by RNA blotting. Concanavalin A inhibited surface attachment of conidia, GFP expression, and appressorium formation without affecting germination. The high correlation between GFP expression and appressorium formation strongly suggests that calmodulin gene expression and appressorium formation require surface attachment.
Binding Sites for Epidermal Growth Factor in Human Uterine Tissues and Leiomyomas (1984)

There is no published data regarding whether human uterine tissues and leiomyomas contain binding sites for epidermal growth factor (EGF). The present study was undertaken with 33 myometria, 13 leiomyomas, and 4 endometria. All myometria (fundus) and leiomyomas and 3 of 4 endometria specifically bound 125I-labeled mouse EGF (myometria: mean, 1.1; range, 0.1-3.9 fmol/mg protein; leiomyomas: mean, 1.1; range, 0.2-2.6 fmol/mg protein; endometria: mean, 1.0; range, 0.0-3.1 fmol/mg protein). [125I]EGF binding to myometrium was ligand specific in that only unlabeled EGF, but not unlabeled insulin, hCG, human PRL, prostaglandin E1, or prostaglandin F2 alpha, competed with [125I]EGF for binding. The apparent dissociation constants and specific binding capacities for myometrium and leiomyoma were: 0.7 nM, 1.9 fmol/mg protein; and 0.1 and 3.7 nM, 0.1 and 4.4 fmol/mg protein, respectively. While smooth muscle content decreased from the fundus to the cervical end of uteri, [125I]EGF binding did not correspondingly decrease (r = 0.5; n = 4). The binding of [125I]EGF to myometrium did not vary with the phase of the menstrual cycle or the patients' diagnosis before hysterectomy (P greater than 0.1). In summary, these results demonstrate that human uteri and leiomyomas contain specific, high affinity binding sites for EGF, but the binding neither exhibited topographical changes nor varied with the phase of the menstrual cycle or benign pathological state of the tissue.
Kohlendioxid als Rohstoff am Beispiel der Synthese von Ameisensäure und ihren Derivaten (1995)

Abstract Kohlendioxid als Rohstoff für chemische Synthesen ist ökologisch und ökonomisch eine interessante Ergänzung zu den derzeit genutzten Kohlenstoffquellen. Um das thermodynamisch stabile und vergleichsweise reaktionsträge CO 2 effizient in das jeweils gewünschte Produkt umwandeln zu können, müssen geeignete Reaktionsbedingungen und Aktivierungsmechanismen gefunden werden. Die katalytische Reduktion von CO 2 zu Ameisensäure und ihren Derivaten ist in diesem Zusammenhang in den letzten Jahren intensiv untersucht worden. Eine Reihe der methodischen Ansätze zur Ameisensäuresynthese aus CO 2 sind inzwischen soweit ausgereift, daß eine Weiterentwicklung zu deren technischer Anwendung in naher Zukunft möglich erscheint. Dies ist nicht zuletzt auf die fruchtbare Wechselwirkung zwischen mechanistischen Untersuchungen und Katalysatorentwicklungen zurückzuführen.
Some ASOs that bind in the coding region of mRNAs and induce RNase H1 cleavage can cause increases in the pre-mRNAs that may blunt total activity (2020)

Antisense oligonucleotide (ASO) drugs that trigger RNase H1 cleavage of target RNAs have been developed to treat various diseases. Basic pharmacological principles suggest that the development of tolerance is a common response to pharmacological interventions. In this manuscript, for the first time we report a molecular mechanism of tolerance that occurs with some ASOs. Two observations stimulated our interest: some RNA targets are difficult to reduce with RNase H1 activating ASOs and some ASOs display a shorter duration of activity than the prolonged target reduction typically observed. We found that certain ASOs targeting the coding region of some mRNAs that initially reduce target mRNAs can surprisingly increase the levels of the corresponding pre-mRNAs. The increase in pre-mRNA is delayed and due to enhanced transcription and likely also slower processing. This process requires that the ASOs bind in the coding region and reduce the target mRNA by RNase H1 while the mRNA resides in the ribosomes. The pre-mRNA increase is dependent on UPF3A and independent of the NMD pathway or the XRN1-CNOT pathway. The response is consistent in multiple cell lines and independent of the methods used to introduce ASOs into cells.
Compatibilizing effect of poly(styrene)-block-poly(isoprene) copolymers in heterogeneous poly(styrene)/natural rubber blends (2001)

Compatibility of poly(styrene) (PS)/natural rubber (NR) blend is improved by the addition of diblock copolymer of poly(styrene) and cis-poly(isoprene) (PS-b-PI). The compatibilizing effect has been investigated as a function of block copolymer molecular weight, composition and concentration. The effect of homopolymer molecular weight, processing conditions and mode of addition on the morphology of the dispersed phase have also been investigated by means of optical microscopy and scanning electron microscopy. A sharp decrease in phase dimensions is observed with the addition of a few percent of block copolymers. The effect levels off at higher concentrations. The leveling off could be an indication of interfacial saturation. For concentrations below the critical value, the particle size reduction is linear with copolymer volume fraction and agrees well with the prediction of Noolandi and Hong. The addition of the block copolymer improves the mechanical properties of the blend. An attempt is made to correlate the mechanical properties with the morphology of the blends. © 2001 Society of Chemical Industry
Combined prophylactic and therapeutic cancer vaccine: Enhancing CTL responses to HPV16 E2 using a chimeric VLP in HLA‐A2 mice (2006)

Abstract We identified the strategies to induce a CTL response to human papillomavirus (HPV) 16 E2 in HLA‐A2 transgenic mice (AAD). A chimeric HPV16 virus‐like particle (VLP) that includes full length HPV16 E7 and E2 (VLP‐E7E2) was generated. The combination of E2 and E7 has the advantage that E2 is expressed in early dysplasia and neoplasia lesions, where E7 is expressed in more advance lesions. Since T cell response to E2 is less defined, we first evaluated the strategies to enhancing CD8 + T cell responses to HPV E7, using different combinations of immune‐modulators with VLP‐E7E2. Data showed that the CTL response to E7 could be significantly enhanced by coinjection of GM‐CSF and antiCD40 antibodies with chimeric VLP‐E7E2 without adjuvant. However, using the same combination, a low level of CD8 + T cell response to E2 was detected. To enhance the CD8+ T cell response to E2, we analyzed T cell epitopes from E2 sequence. A heterogonous prime‐boost with chimeric VLP‐E7E2 and E2 peptides was performed. The data showed that the priming with chimeric VLP‐E7E2, followed by boosting with E2 peptides, gave a better CTL response than 2 immunizations with E2 peptides. The enhanced immunity is due to the increase of CD11c + and CD11c + CD40 + double positive dendritic cells in mice that received immune‐modulators, GM‐CSF and antiCD40. Furthermore, the level of anti‐L1 antibodies remains similar in mice immunized with chimeric VLP with/without immune‐modulators. Thus, the data suggested that the chimeric VLP‐E7E2 has a therapeutic potential for the treatment of HPV‐associated CINs and cancer without diminishing VLPs potential as a prophylactic vaccine by inducing anti‐L1 antibodies against free virus. © 2006 Wiley‐Liss, Inc.
Supplementary Figure Legends 1-2 from Cytoglobin, the Newest Member of the Globin Family, Functions as a Tumor Suppressor Gene (2023)

Supplementary Figure Legends 1-2 from Cytoglobin, the Newest Member of the Globin Family, Functions as a Tumor Suppressor Gene
Development of a clinical intravascular dual-modality optical coherence tomography and near-infrared autofluorescence/fluorescence imaging platform (2021)

We present our next generation clinical dual-modality OCT and near infrared autofluorescence/fluorescence (NIRAF/NIRF) imaging platform. This platform allows combined tissue microstructure visualization (OCT) and obtaining molecular information either by intrinsic tissue near infrared autofluorescence (NIRAF) or by exogenous near infrared fluorescence contrast agents (NIRF). Components of this platform, OCT-NIRAF/NIRF imaging system, rotary junction and catheters, were developed using an industry standard design control processes to enable quality clinical translation. We have identified sources of image degradation in dual-modality catheter-based imaging (e.g. core-cladding crosstalk in OCT, background noise in fluorescence) and present methods to mitigate their effects. We also show catheter fabrication and validation, as well as automated fluorescence sensitivity and distance calibration methods that ensure robust and repeatable system performance.
Creation of colour centres in diamond by collimated ion‐implantation through nano‐channels in mica (2011)

Abstract The fabrication of scalable quantum devices in diamond relies on the ability to produce optical centres with a high spatial resolution. Ion implantation is the most powerful technique for placing impurity atoms in a diamond matrix. Even though shallow optical centres can be produced with a resolution below 20 nm, deep centres may be preferred for generally better overall properties. However, the focusing of ion beams in the MeV range can hardly be achieved below 1 µm. We present here a novel approach by implanting ions through a mask with high‐aspect‐ratio nano‐channels and improve the collimation to below 50 nm. The mask contains parallel oriented channels of a few tens of nanometres in diameter. They are produced by exposing mica sheets to GeV heavy ion projectiles and subsequent track etching. We demonstrate the high‐resolution creation of deep nitrogen‐vacancy (NV) centres in diamond by implanting nitrogen ions through the nano‐channels. Transmission rates and energy distribution of the nitrogen ions transmitted through the nano‐channels were also analysed.
High-Latitude Galactic Dust Emission in the BOOMERANG Maps (2001)

We present millimeter-wave observations obtained by the BOOMERANG (Balloon Observations Of Millimetric Extragalactic Radiation ANd Geophysics) experiment of Galactic emission at intermediate and high (b &lt; -20&lt;degrees&gt;) Galactic latitudes. We find that this emission is well correlated with extrapolated dust maps and is spectrally consistent with thermal emission from interstellar dust (ISD). The ISD brightness in the 410 GHz map has an angular power spectrum c(l) similar to l(-beta) with 2 less than or similar to beta less than or similar to 3. At 150 GHz and at multipoles l similar to 200, the angular power spectrum of the IRAS- correlated dust signal is estimated to be l/(l + 1)c(l)/2 pi = 3.7 +/- 2.9 muK(2). This is negligible with respect to the cosmic microwave background (CMB) signal measured by the same experiment l(l + 1)c(l)/2 pi = 4700 +/- 540 muK(2). For the uncorrelated dust signal, we set an upper limit to the contribution to the CMB power at 150 GHz and of l similar to 200 l(l + l)c(l)/2 pi &lt; 3 &lt;mu&gt;K-2 at 95% CL.
A dual-page programming scheme for high-speed multigigabit-scale NAND flash memories (2001)

To realize a low-cost and high-speed programming NAND flash memory, a new programming scheme, a "dual-page programming scheme," has been proposed. This architecture drastically increases the program throughput without circuit area overhead. In the proposed scheme, two memory cells are programmed at the same time using only one page buffer. Therefore, the page size, i.e., the number of memory cells programmed simultaneously, is doubled and the program speed is improved. As the number of page buffers required in the proposed scheme is the same as that in the conventional one, there is no circuit area increase. This novel operation is made possible by using a bitline as a dynamic latch to temporarily store the program data. As a result, the programming is accelerated by 73% in a 1-Gb generation and 62% in a 4-Gb generation, 18.2-MB/s 1-Gb or 30.7-MB/s 4-Gb NAND flash memory can be realized with this new architecture.
Dose-dependent effects of l-carnosine on the renal sympathetic nerve and blood pressure in urethane-anesthetized rats (2004)

The physiological function of L-carnosine (beta-alanyl-L-histidine) synthesized in mammalian muscles has been unclear. Previously, we observed that intravenous (i.v.) injection of L-carnosine suppressed renal sympathetic nerve activity (RSNA) in urethane-anesthetized rats, and L-carnosine administered via the diet inhibited the elevation of blood pressure (BP) in deoxycorticosterone acetate salt hypertensive rats. To identify the mechanism, we examined effects of i.v. or intralateral cerebral ventricular (l.c.v.) injection of various doses of L-carnosine on RSNA and BP in urethane-anesthetized rats. Lower doses (1 microg i.v.; 0.01 microg l.c.v.) of L-carnosine significantly suppressed RSNA and BP, whereas higher doses (100 microg i.v.; 10 microg l.c.v.) elevated RSNA and BP. Furthermore, we examined effects of antagonists of histaminergic (H1 and H3) receptors on L-carnosine-induced effects. When peripherally and centrally given, thioperamide, an H3 receptor antagonist, blocked RSNA and BP decreases induced by the lower doses of peripheral L-carnosine, whereas diphenhydramine, an H1 receptor antagonist, inhibited increases induced by the higher doses of peripheral L-carnosine. Moreover, bilateral lesions of the hypothalamic suprachiasmatic nucleus eliminated both effects on RSNA and BP induced by the lower (1 microg) and higher (100 microg) doses of peripheral L-carnosine. These findings suggest that low-dose L-carnosine suppresses and high-dose L-carnosine stimulates RSNA and BP, that the suprachiasmatic nucleus and histaminergic nerve are involved in the activities, and that L-carnosine acts in the brain and possibly other organs.
New Insights into the Pathogenesis of Mastocytosis: Emerging Concepts in Diagnosis and Therapy (2022)

Mastocytosis is a heterogeneous group of neoplasms defined by a numerical increase and accumulation of clonal mast cells (MCs) in various organ systems. The disease may present as cutaneous mastocytosis or systemic mastocytosis (SM). On the basis of histopathological and molecular features, clinical variables, and organ involvement, SM is divided into indolent SM, smoldering SM, SM with an associated hematologic neoplasm, aggressive SM, and MC leukemia. Each variant is defined by unique diagnostic criteria and a unique spectrum of clinical presentations. A key driver of MC expansion and disease evolution is the oncogenic machinery triggered by mutant forms of <i>KIT</i>. The genetic background, additional somatic mutations, and comorbidities also contribute to the course and prognosis. Patients with SM may also suffer from mediator-related symptoms or even an MC activation syndrome. This article provides an update of concepts on the genetics, etiology, and pathology of mastocytosis, with emphasis on diagnostic criteria and new treatment concepts.
A Joint Solution for Scheduling and Precoding in Multiuser MISO Downlink Channels (2019)

The average performance of the MISO downlink channel, with a large number of users compared to transmit antennas of the base station, depends on the interference management which necessitates the joint design of scheduling and precoding. Unlike the previous works which do not offer a truly joint design, this paper focuses on formulating a problem amenable for the joint update of scheduling and precoding. Novel optimization formulations are investigated to reveal the hidden difference of convex/ concave structure for three classical criteria (weighted sum rate, max-min signal-to-interference plus noise ratio, and power minimization) and associated constraints are considered. Thereafter, we propose a convex-concave procedure framework based iterative algorithm where scheduling and precoding variables are updated jointly in each iteration. Finally, we show the superiority in performance of joint solution over the state-of-the-art designs through Monte-Carlo simulations.
Adsorption Stnlctures of Benzene and Pyridine on a $Si(5\;5\;12)-2{\times}1$ (2006)

We investigated the adsorption of benzene and pyridine on at 80 K by using variable-low temperature scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. The benzene molecule most strongly binds to two adatoms on the D3 and D2 units in a tilted butterfly configuration, which consists of bonds between C atoms and Si adatoms and two C=C double bonds in the benzene molecule Pyridine molecules interact with adatom(s) on the D2 and D3 units through both Si-N dative bonding and bonds. The dative bonding through the lone pair electrons of N atom produces a vertical configuration (pyridine-like), which is more stable than bonds bonds can be formed either through Si-N1 and Si-C4 or Si-C2 and Si-C5.
Determining optimal community protection strategies for the influenza vaccine (2019)

<b>Introduction</b>: Seasonal influenza poses a major risk to the health of the population. Optimal strategies for influenza vaccination can help to reduce this risk. <b>Areas covered</b>: Systematic evaluations of the burden of influenza are first reviewed. Key meta-analysis, randomized trials, and observational studies are critically reviewed to provide the best estimates of the efficacy of influenza vaccine. The concept of herd effect is first introduced and this is followed by the rationale and the evidence to support herd effect that can be provided with strategic use of influenza vaccination in populations. Challenges including the effect of repeated influenza vaccination and vaccine hesitancy are reviewed. The citations were selected by the authors based on PubMed searches of the literature. <b>Expert opinion</b>: Efforts to develop new vaccines, including a universal vaccine, offer the best prospects for improved herd effect. Increasing uptake in new populations can increase likelihood of a herd effect.
Bandwidth expansion of 12.5-GHz-spaced laser frequency comb in near-infrared region by improving pulse compression magnification (2021)

We have developed a pulse compressor with low input power and a high compression ratio of 90 or more. Finally, we succeeded in producing a broadband LFC from 950 to 1750 nm with 12.5-GHz spacing and high contrast across the whole spectrum.
SIM and PALM: high-resolution microscopy methods and their consequences for cell biology (2010)

The diffraction limit in traditional fluorescence microscopy (approximately 200 and 600 nanometers in lateral and axial directions, respectively) has restricted the applications in bio-medical research. However, over the last 10 years various techniques have emerged to overcome this limit. Each of these techniques has its own characteristics that influence its application in biology. This paper will show how two of the techniques, Structured Illumination Microscopy (SIM) and PhotoActivated Localization Microscopy (PALM), complement each other in imaging of biological samples beyond the resolution of classical widefield fluorescence microscopy. As a reference the properties of two well known standard imaging techniques in this field, confocal Laser Scanning Microscopy (LSM) and Total Internal Reflection (TIRF) microscopy, are compared to the properties of the two high resolution techniques. Combined SIM/PALM imaging allows the extremely accurate localization of individual molecules within the context of various fluorescent structures already resolved in 3D with a resolution of up to 100nm using SIM. Such a combined system provides the biologist with an unprecedented view of the sub-cellular organization of life.