gebhart/patrepeval huggingface dataset:
Transcranial focused ultrasound neuromodulation of the human primary motor cortex (2018)

Transcranial focused ultrasound is an emerging form of non-invasive neuromodulation that uses acoustic energy to affect neuronal excitability. The effect of ultrasound on human motor cortical excitability and behavior is currently unknown. We apply ultrasound to the primary motor cortex in humans using a novel simultaneous transcranial ultrasound and magnetic stimulation paradigm that allows for concurrent and concentric ultrasound stimulation with transcranial magnetic stimulation (TMS). This allows for non-invasive inspection of the effect of ultrasound on motor neuronal excitability using the motor evoked potential (MEP). We test the effect of ultrasound on single pulse MEP recruitment curves and paired pulse protocols including short interval intracortical inhibition (SICI) and intracortical facilitation (ICF). In addition, we test the effect of ultrasound to motor cortex on a stimulus response reaction time task. Results show ultrasound inhibits the amplitude of single-pulse MEPs and attenuates intracortical facilitation but does not affect intracortical inhibition. Ultrasound also reduces reaction time on a simple stimulus response task. This is the first report of the effect of ultrasound on human motor cortical excitability and motor behavior and confirms previous results in the somatosensory cortex that ultrasound results in effective neuronal inhibition that confers a performance advantage.
Eukaryotic mRNAs encoding abundant and scarce proteins are statistically dissimilar in many structural features (1998)

It is well known that non-coding mRNA sequences are dissimilar in many structural features. For individual mRNAs correlations were found for some of these features and their translational efficiency. However, no systematic statistical analysis was undertaken to relate protein abundance and structural characteristics of mRNA encoding the given protein. We have demonstrated that structural and contextual features of eukaryotic mRNAs encoding high- and low-abundant proteins differ in the 5' untranslated regions (UTR). Statistically, 5' UTRs of low-expression mRNAs are longer, their guanine plus cytosine content is higher, they have a less optimal context of the translation initiation codons of the main open reading frames and contain more frequently upstream AUG than 5' UTRs of high-expression mRNAs. Apart from the differences in 5' UTRs, high-expression mRNAs contain stronger termination signals. Structural features of low- and high-expression mRNAs are likely to contribute to the yield of their protein products.
A Reverse Genetics Approach for Recovery of Recombinant Influenza B Viruses Entirely from cDNA (2002)

The recovery of recombinant influenza A virus entirely from cDNA was recently described (9, 19). We adapted the technique for engineering influenza B virus and generated a mutant bearing an amino acid change E116G in the viral neuraminidase which was resistant in vitro to the neuraminidase inhibitor zanamivir. The method also facilitates rapid isolation of single-gene reassortants suitable as vaccine seeds and will aid further investigations of unique features of influenza B virus.
Structure linkage, and sequence of the two genes encoding the delta and gamma subunits of the nicotinic acetylcholine receptor. (1984)

We have cloned and sequenced a fragment of the chicken genome approximately 9 kilobases in length that comprises the genes encoding the delta and gamma subunits of the nicotinic acetylcholine receptor. The two genes are homologous and have identical structures: both consist of 12 exons, some of which precisely correspond to predicted structural domains of the receptor subunits. The delta and gamma subunit genes are encoded by the same DNA strand and are very closely linked, there being only 740 base pairs between the last codon of delta and the initiator codon of gamma. Blot analysis demonstrates that the genes we describe are unique in the genome. Comparison of the predicted protein sequence for the corresponding subunits of chicken and of the elasmobranch Torpedo reveals a high degree of conservation in some but not all of the protein domains.
Identification of Myoglobin in Human Smooth Muscle (1998)

Myoglobin (Mb) has been believed to be absent generally from mammalian smooth muscle tissue. Examination of human rectal, uterine, bladder, colon, small intestine, arterial, and venous smooth muscle by immunohistochemical techniques shows that each of these tissues is immunopositive for both smooth muscle myosin and human Mb. Mb-specific primers were used for the polymerase chain reaction to generate cDNA from smooth muscle tissues. Southern hybridization with a Mb-specific probe gave a very strong signal with the cDNA from rectum, weaker signals from small intestine and uterus, a faint signal from colon, and no signal from bladder tissue. High performance liquid chromatography analysis coupled with sequence determination has shown that contaminating heme-binding serum albumin as well as hemoglobin in extracts of smooth muscle seriously compromise any heme-based or spectrophotometric assay of Mb. Combined affinity and size exclusion chromatography, however, provide the necessary resolution. The cDNA-derived amino acid sequence of human smooth muscle Mb was found to be identical to that of Mb from striated muscle.
Targeted delivery of oligodeoxynucleotides to parenchymal liver cells in vivo (1999)

Anti-sense oligodeoxynucleotides (ODNs) hold great promise for correcting the biosynthesis of clinically relevant proteins. The potential of ODNs for modulating liver-specific genes might be increased by preventing untimely elimination and by improving the local bioavailability of ODNs in the target tissue. In the present study we have assessed whether the local ODN concentration can be enhanced by the targeted delivery of ODNs through conjugation to a ligand for the parenchymal liver cell-specific asialoglycoprotein receptor. A capped ODN (miscellaneous 20-mer sequence) was derivatized with a ligand with high affinity for this receptor, N2-[N2-(N2,N6-bis{N-[p-(beta-d-galactopyranosyloxy) anilino] thiocarbamyl}-L-lysyl)-N6-(N-{p-[beta-D -galactopyranosyloxy] anilino} thiocarbamyl)-L-lysyl]-N6-[N- (p-{beta-D-galactopyranosyloxy}anilino)thiocarbamyl]-L-lysine (L3G4) (Kd 6.5+/-0.2 nM, mean+/-S.D.). Both the uptake studies in vitro and the confocal laser scan microscopy studies demonstrated that L3G4-ODN was far more efficiently bound to and taken up by parenchymal liver cells than underivatized ODN. Studies in vivo in rats showed that hepatic uptake could be greatly enhanced from 19+/-1% to 77+/-6% of the injected dose after glycoconjugation. Importantly, specific ODN accumulation of ODN into parenchymal liver cells was improved almost 60-fold after derivatization with L3G4, and could be attributed to the asialoglycoprotein receptor. In conclusion, the scavenger receptor-mediated elimination pathway for miscellaneous ODN sequences can be circumvented by direct conjugation to a synthetic tag for the asialoglycoprotein receptor. In this manner a crucial requisite is met towards the application of ODNs in vivo to modulate the biosynthesis of parenchymal liver cell-specific genes such as those for apolipoprotein (a), cholesterol ester transfer protein and viral proteins.
Two burgeoning families of platelet factor 4-related proteins: mediators of the inflammatory response. (1990)

The inflammatory response involves the recruitment and activation of various types of cells from the systemic circulation and from local tissues. One important component of the inflammatory response is the activation of platelets at sites of tissue injury and inflammation. In particular, activated platelets release large amounts of two proteins, platelet factor 4 (PF4) and beta-thromboglobulin (beta TG), which mediate several inflammatory processes. Recently, many novel proteins that are structurally related to PF4 and beta TG have been identified. The PF4-related proteins are secreted by white blood cells, endothelial cells, and fibroblasts in response to various inflammatory and mitogenic stimuli. Like PF4, these proteins appear to be inflammatory response mediators; several of them are potent chemoattractants, activating agents, or mitogens for specific cell types that are involved in the inflammatory response. The study of PF4-related proteins provides new insight into the mechanisms of the immune response, and may result in the development of new therapeutic agents.
Therapies Based on Nanoparticles for Eye Drug Delivery (2020)

Eye drug delivery, particularly to the retina, is a technical hurdle that needs to be solved and represents an ongoing current important medical field. Posterior segment eye diseases are a major cause of visual impairment worldwide. Age-related macular degeneration, glaucoma, and diabetic retinopathy are the major causes of blindness. To achieve efficient drug delivery and drug retention time in the posterior segment of the eye, novel delivery systems based on nanoparticles have been developed in the last few years. Nowadays, liposomes represent the most utilized nanoparticles for eye drug delivery and, recently, a broad spectrum of diverse nanoparticles continue to emerge with special characteristics representing ideal candidates for eye drug delivery.
Detection of tissue kallikrein in the bronchoalveolar lavage fluid of asthmatic subjects. (1987)

Kininogenase activity was detected by cleavage of radiolabeled substrate (125I-high molecular weight kininogen [HMWK]) in 22 of 24 bronchoalveolar lavage (BAL) fluid samples from 17 asthmatics who either responded to aerosolized allergen challenge or had symptoms of active asthma. In contrast, six of seven normal controls lacked enzymatic activity. Levels of free immunoreactive kinin found in BAL fluid correlated with the presence of kininogenase activity (P = 0.002). The cleavage pattern of 125I-HMWK by the BAL fluid kininogenase (a dominant 65,000-mol wt fragment), and synthetic inhibitor profile (phe-phe-arg-CH2Cl and phenylmethylsulfonyl fluoride) were compatible with a tissue kallikrein. Peak kininogenase activity eluted at an apparent molecular weight of 20,000-34,000 by HPLC gel filtration. Its antigenic identity was established by immunoblotting with anti-human urinary kallikrein antibody and its activity was inhibited by this antibody. Lysylbradykinin was generated during incubation of fractionated BAL fluid and purified HMWK, the characteristic cleavage product of the tissue kallikreins. We conclude that elevated amounts of tissue kallikrein and kinin are present in the bronchoalveolar spaces of asthmatic subjects. Kinin generation may contribute to the asthmatic response directly through edema formation and smooth muscle contraction and by augmenting release and/or production of preformed (histamine) and secondary mediators such as leukotrienes and platelet-activating factor.
Induction of adult levels of -globin in human erythroid cells that intrinsically express embryonic or fetal globin by transduction with KLF1 and BCL11A-XL (2014)

A major barrier to the clinical use of erythrocytes generated in vitro from pluripotent stem cells or cord blood progenitors is failure of these erythrocytes to express adult hemoglobin. The key regulators of globin switching KLF1 and BCL11A are absent or at a lower level than in adult cells in K562 and erythroid cells differentiated in vitro from induced pluripotent stem cells and cord blood progenitors. Transfection or transduction of K562 and cord blood erythroid cells with either KLF1 or BCL11A-XL had little effect on β-globin expression. In contrast, transduction with both transcription factors stimulated β-globin expression. Similarly, increasing the level of BCL11A-XL in the induced pluripotent stem cell-derived erythroid cell line HiDEP-1, which has levels of endogenous KLF1 similar to adult cells but lacks BCL11A, resulted in levels of β-globin equivalent to that of adult erythroid cells. Interestingly, this increase in β-globin was coincident with a decrease in ε- and ζ-, but not γ-globin, implicating BCL11A in repression of embryonic globin expression. The data show that KLF1 and BCL11A-XL together are required, but sufficient to induce adult levels of β-globin in induced pluripotent stem cell and cord blood-derived erythroid cells that intrinsically express embryonic or fetal globin.
Slant from texture and disparity cues: Optimal cue combination (2004)

How does the visual system combine information from different depth cues to estimate three-dimensional scene parameters? We tested a maximum-likelihood estimation (MLE) model of cue combination for perspective (texture) and binocular disparity cues to surface slant. By factoring the reliability of each cue into the combination process, MLE provides more reliable estimates of slant than would be available from either cue alone. We measured the reliability of each cue in isolation across a range of slants and distances using a slant-discrimination task. The reliability of the texture cue increases as |slant| increases and does not change with distance. The reliability of the disparity cue decreases as distance increases and varies with slant in a way that also depends on viewing distance. The trends in the single-cue data can be understood in terms of the information available in the retinal images and issues related to solving the binocular correspondence problem. To test the MLE model, we measured perceived slant of two-cue stimuli when disparity and texture were in conflict and the reliability of slant estimation when both cues were available. Results from the two-cue study indicate, consistent with the MLE model, that observers weight each cue according to its relative reliability: Disparity weight decreased as distance and |slant| increased. We also observed the expected improvement in slant estimation when both cues were available. With few discrepancies, our data indicate that observers combine cues in a statistically optimal fashion and thereby reduce the variance of slant estimates below that which could be achieved from either cue alone. These results are consistent with other studies that quantitatively examined the MLE model of cue combination. Thus, there is a growing empirical consensus that MLE provides a good quantitative account of cue combination and that sensory information is used in a manner that maximizes the precision of perceptual estimates.
Histopathologic Characteristics of Choroidal Melanoma in Eyes Enucleated After Iodine 125 Brachytherapy in the Collaborative Ocular Melanoma Study (2008)

Eyes with secondary enucleation after brachytherapy differ histopathologically from eyes with primary enucleation for uveal melanoma. These histopathologic differences may be due to the effects of radiation, tissue conditions related to plaque failure, and, in some cases, tumor growth. In 40% of eyes enucleated because of suspected failure of local control, increased tumor size could not be histologically confirmed.
High performance 0.25 mu m p-MOSFETs with silicon-germanium channels for 300 K and 77 K operation (2002)

Quarter-micron Si/sub 1-x/Ge/sub x/ p-MOS devices with either thermal or PECVD oxides have been fabricated using an integrable process module (LOCOS isolation, threshold and deep well implants, p/sup +/ polysilicon gates, and TiSi/sub 2/) compatible with conventional 0.25 mu m CMOS with the Si/sub 1-x/Ge/sub x/ channel and Si cap deposited by selective UHV-CVD. Improvements in mobility and transconductance over deep submicron (0.25 mu m channel length) state-of-the-art Si p-MOSFETs were demonstrated by using silicon-germanium channels with low (10-25%) germanium content, both at room temperature (300 K) and low temperature (82 K). The use of Si/sub 1-x/Ge/sub x/ channels can provide better device performance in the same technology generation (same lithography, junction depth, etc.) and also help compensate for the external parasitic resistance penalty.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Calcifediol in chronic renal insufficiency. Skeletal response. (1976)

Quantitative histology of thin, nondecalcified sections was performed on sequential bone biopsy specimens from five patients undergoing long-term hemodialysis and treated with calcifediol (25-hydroxycholecalciferol) for periods of three to nine months. With increase of intestinal absorption of calcium and decline of circulating immunoreactive parathyroid hormone and alkaline phosphatase, the bones of each patient exhibited striking histological improvement. The group as a whole showed statistically significant decreases in osteoclast number and in the percentages of osteoid surface covered by active osteoblasts. Marrow fibrosis was either eliminated or strikingly decreased in each patient. Osteoid volume significantly declined in four of five patients. In patients with osteitis fibrosa as the predominant histological lesion, calcifediol therapy resulted in decreased calcification front activity. Increased activity was the result when osteomalacia predominated.
In vitro migratory capacity of CD34+ cells is related to hematopoietic recovery after autologous stem cell transplantation (2001)

To investigate whether the migratory ability of peripheral blood-derived CD34+ cells of patients undergoing autologous peripheral blood stem cell transplantation is related to the homing efficiency of these cells, the migration in vitro of these cells was determined and correlated with in vivo hematopoietic recovery. Large inter-individual differences of the in vitro migratory ability of the CD34+ cells were observed, ranging from 1.1% to 16.4% for spontaneous migration and 6.2% to 40.8% for SDF-1-induced (100 ng/mL) migration. Significantly faster hematologic recovery was observed in those patients who received transplanted CD34+ cells that showed high spontaneous and SDF-1-induced migration in vitro (P <.05). Moreover, CD34+ cells from healthy G-CSF-mobilized donors exhibited significantly higher spontaneous and SDF-1-induced (P <.01) migration than CD34+ cells from patients mobilized with chemotherapy and G-CSF. The lower migratory capacity in vitro of patient-derived CD34+ cells was not due to lower expression of CXCR-4 but probably reflected decreased motogenic behavior of the cells. These results indicate that the migratory capacity of the cells is important for hematopoietic recovery. The data suggest that the engraftment potential of autologous stem cells is more or less impaired by treatment before or during the mobilization procedure and might possibly be restored by in vitro manipulation of the cells. In addition, an exponential relation between CXCR-4 expression and number of CD34+ cells that mobilized to the peripheral blood was found (P <.001), suggesting that CXCR-4 expression plays a role in the mobilization of CD34+ cells.
Flow compensation in MRI using a phase‐corrected real reconstruction (1993)

Flow- and motion-related artifacts are problematic in clinical MR imaging. In this paper we discuss the utility of a phase-corrected real reconstruction to reduce flow artifacts. This technique is particularly useful when flow-compensation pulse sequences may not be possible, such as when a very short echo delay or small field-of-view is desired. We will demonstrate that the phase-corrected real reconstruction provides superior results to the magnitude reconstruction either used alone or in conjunction with existing flow-compensation techniques.
Determination of the maximum specific uptake capacities for glucose and oxygen in glucose‐limited fed‐batch cultivations of Escherichia coli (2001)

A simple pulse-based method for the determination of the maximum uptake capacities for glucose and oxygen in glucose limited cultivations of E. coli is presented. The method does not depend on the time-consuming analysis of glucose or acetate, and therefore can be used to control the feed rate in glucose limited cultivations, such as fed-batch processes. The application of this method in fed-batch processes of E. coli showed that the uptake capacity for neither glucose nor oxygen is a constant parameter, as often is assumed in fed-batch models. The glucose uptake capacity decreased significantly when the specific growth rate decreased below 0.15 h(-1) and fell to about 0.6 mmol g(-1) h(-1) (mmol per g cell dry weight and hour) at the end of fed-batch fermentations, where specific growth rate was approximately 0.02 h(-1). The oxygen uptake capacity started to decrease somewhat earlier when specific growth rate declined below 0.25 h(-1) and was 5 mmol g(-1) h(-1) at the end of the fermentations. The behavior of both uptake systems is integrated in a dynamic model which allows a better fitting of experimental values for glucose in fed-batch processes in comparison to generally used unstructured kinetic models.
Isotonic Glycerol and Sodium Hyaluronate Containing Artificial Tear Decreases Conjunctivochalasis after One and Three Months: A Self-Controlled, Unmasked Study (2015)

Controlled-Trials.com ISRCTN81112701 http://www.isrctn.com/ISRCTN81112701.
Pulmonary Large Cell Carcinoma Expressing Neuroendocrine Markers: The Morphological, Biological, and Neuroendocrine Features of Their Cell Lines and Surgical Cases (1992)

A cell line expressing neuroendocrine (NE) markers, designated as KTS9, was established from a human large cell carcinoma of the lung using serum-free medium, ACL-3. KTS9 cells showed morphological characteristics of large cell undifferentiated carcinoma (LCUC) and expressed some general NE markers including neuron-specific enolase (NSE), protein gene product (PGP) 9.5, neural cell adhesion molecule (N-CAM), synaptophysin and neurofilaments (NF) of 200 kd. Some cells of this cell line were positive to chromogranin-A (CG-A), but did not express Leu7 or aromatic L-amino acid decarboxylase (AADC). Such a cell line derived from LCUC with NE properties has not previously been reported. The biological and NE properties of the KTS9 cell line were compared with those of 2 surgical cases of LCUC with NE markers and of the KTA7 cell line previously reported to derive from large cell carcinoma and to possess NE markers such as alpha-hCG, PGP9.5 N-CAM and AADC. Tumor cells of 2 large cell carcinomas expressed NSE, PGP9.5, N-CAM and NF. The KTS9 and KTA7 cell lines and 2 large cell carcinomas were thus considered to be LCUCs with NE differentiation. Both lines had the morphological characteristics of LCUC, relatively short doubling time and discordant expression of NE markers, indicating them to be closely related to the variant type of small cell carcinoma cell lines and thus possibly to represent high-grade malignancy. They may be useful for examining the biological behavior and NE features of large cell-type NE tumors of the lung.
A Neural Attention Model for Sentence Summarization (2015)

Summarization based on text extraction is inherently limited, but generation-style ab-stractive methods have proven challeng-ing to build. In this work, we propose a fully data-driven approach to abstrac-tive sentence summarization. Our method utilizes a local attention-based model that generates each word of the summary con-ditioned on the input sentence. While the model is structurally simple, it can eas-ily be trained end-to-end and scales to a large amount of training data. The model shows significant performance gains on the DUC-2004 shared task compared with several strong baselines. 1