gebhart/patrepeval huggingface dataset:
Production and Transplantation of Retinal Cells from Human and Mouse Embryonic Stem Cells (2012)

Over the last few years, numerous studies have introduced strategies for the generation of neuronal populations from embryonic stem cells. These techniques are valuable both in the study of early neurogenesis and in the generation of an unlimited source of donor cells for replacement therapies. We have developed a protocol to direct mouse and human embryonic stem cells to retinal fates by using the current model of eye specification. Our method is a multistep protocol in which the cultures are treated with IGF1 and a combination of BMP and Wnt inhibitors to promote the expression of key retinal progenitor genes, as assayed by RT-PCR and immunofluorescence microscopy. The retinal progenitor population spontaneously undergoes differentiation towards various types of retinal neurons, including photoreceptors.
Early termination of coding unit splitting for HEVC (2012)

The emerging high-efficiency video coding (HEVC) standard employs a new coding structure characterized by coding unit (CU), prediction unit (PU) and transform unit (TU). It improves the coding efficiency significantly, but also introduces great computation complexity on the decision of optimal CU, PU and TU sizes. To reduce the encoding complexity, we propose a CU splitting early termination scheme for inter frame coding. In the proposed scheme, the characteristics of prediction residuals are utilized to early terminate the CU splitting. Specifically, the Mean Square Error (MSE) between the prediction block and the origin block for each CU level is obtained and then compared with an adaptive threshold. The recursive CU splitting process is early terminated according to the threshold. Experimental results demonstrate that, the proposed algorithm achieves up to 34.83% total encoding time reduction with less than 0.25% BD-rate increase on average.
Monocyte Chemoattractant Protein-1 (1999)

The ploidy of smooth muscle cells (SMCs) enzymatically isolated from the aorta and superior mesenteric artery (elastic arteries), caudal artery (small muscular artery) and the small mesenteric arteries and arterioles (mesenteric resistance vessels) of the spontaneously hypertensive (SHR) and Wistar-Kyoto (WKY) rats at ages 12, 26, 32 and 40 weeks was determined by flow cytometric DNA analysis and Feulgen-DNA photometric measurements. Frequency of polyploid cells in the aorta and superior mesenteric artery of the SHR increased from 4.43 ± 1.35 and 7.58 ± 1.69%, respectively, at 12 weeks to 31.26 ± 3.00 and 14.13 ± 1.30% at 40 weeks. There was a smaller increase in the percentage of polyploid cells in these two vessels of the WKY from 4.73 ± 0.74 and 5.82 ± 0.33%, respectively, at 12 weeks to 10.64 ± 0.17 and 7.68 ± 0.64% at 40 weeks. The caudal artery and mesenteric resistance vessels showed no significant increase in the percentage of 4N (tetraploid) cells in the SHR from 12 weeks (6.80 ± 0.92 and 6.10 ± 0.75%) to 40 weeks (7.83 ± 0.67 and 7.57 ± 0.07%). Similarly, there was no significant change in ploidy in these arteries of the WKY. Hence, while polyploidy of SMCs increases in the aorta and superior mesenteric artery of the rat with increasing age and with duration of hypertension, there is no significant change in the number of polyploid cells in smaller vessels such as the caudal artery or mesenteric resistance vessels. Since it is the resistance vessels that are involved in the development and maintenance of hypertension, polyploidy of SMCs in the blood vessel wall appears to hold little relevance to the etiology of this disease. As well, increased incidence of polyploidy is not directly attributable to increases in blood pressure as the caudal artery has a high systolic pressure in the SHR yet the incidence of polyploid cells in this artery does not differ from
Free and complexed prostate-specific antigen (PSA): in vitro stability, epitope map, and development of immunofluorometric assays for specific and sensitive detection of free PSA and PSA-alpha 1-antichymotrypsin complex (1995)

Generation of 15 monoclonal antibodies (MAbs) allowed construction of epitope maps and specific two-site immunofluorometric assays for free prostate-specific antigen (PSA) and PSA complexed with alpha 1-antichymotrypsin (ACT). Close correlation of PSA concentrations obtained with the use of different assays of free PSA suggested extensive similarity in immunodetection of free PSA in serum. Assays of the PSA-ACT complex overestimated the concentration of PSA-ACT in serum because of nonspecific adsorbance of ACT or cathepsin G-complexed ACT to the solid phase. This interference was substantially decreased in the presence of heparin. In studying the stability of purified PSA and PSA-ACT complexes formed in vitro, we found that the free PSA was stable during storage for 4 weeks at 35 degrees C, whereas PSA-ACT complexes largely dissociated in these conditions. The instability of PSA-ACT complexes was counteracted by storage at low temperatures, by adjusting the pH of the storage buffer between 6.8 and 7.4, and through addition of 100-1000-fold molar excess of native ACT. The ease of calibration and the accuracy of free PSA assays in comparison with assays of the PSA-ACT complex suggest that measurements of free to total PSA most accurately reflect the inverse of the proportion of PSA complexed to ACT in serum.
Expression Cloning of Oncogenes by Retroviral Transfer of cDNA Libraries (1995)

a cDNA library transfer system based on retroviral vectors has been developed for expression cloning in mammalian cells. The use of retroviral vectors results in stable cDNA transfer efficiencies which are at least 100-fold higher than those achieved by transfection and therefore enables the transfer and functional screening of very large libraries. In our initial application of retroviral transfer of cDNA libraries, we have selected for cDNAs which induce oncogenic transformation of NIH 3T3 fibroblasts, as measured by loss of contact inhibition of proliferation. Nineteen different transforming cDNAs were isolated from a total of 300,000 transferred cDNA clones. Three of these cDNAs were derived from known oncogenes (raf-1, lck, and ect2), while nine others were derived from genes which had been cloned previously but were not known to have the ability to transform fibroblasts (beta-catenin, thrombin receptor, phospholipase C-gamma 2 and Spi-2 protease inhibitor genes). The Spi-2 cDNA was expressed in antisense orientation and therefore is likely to act as an inhibitor of an endogenous transformation suppressor. Seven novel cDNAs with transforming activities, including those for three new members of the CDC24 family of guanine nucleotide exchange factors, were also cloned from the retroviral cDNA libraries. Retroviral transfer of libraries should be generally useful for cloning cDNAs which confer selectable phenotypes on many different types of mammalian cells.
Optical elements with ultrahigh spatial-frequency surface corrugations (1983)

In this paper we discuss the properties of optical elements fabricated by holographically recording an ultrahigh spatial-frequency pattern in a photoresist mask followed by reactive ion etching to transfer this pattern into the surface of a quartz substrate. Such optical elements are environmentally durable, potentially easy to replicate, and exhibit diffraction efficiencies in excess of 85%. In addition, two other properties are reported for the first time. Such elements at normal (0°) incidence are antireflective, with broadband reflection coefficients as low as 0.035%. Also, the elements exhibit artificially produced birefringence making them useful as wave plates. These results may be particularly significant in the UV and IR, where damage-resistant antireflection coatings and transparent birefringent materials may not exist.
Human CTL epitopes encoded by human papillomavirus type 16 E6 and E7 identified through in vivo and in vitro immunogenicity studies of HLA-A*0201-binding peptides. (1995)

Human papillomavirus type 16 (HPV16) is strongly associated with cervical carcinogenesis. The HPV16 E6 and E7 oncoproteins are constitutively expressed in the majority of cervical tumor cells and are, therefore, attractive targets for CTL-mediated immunotherapy. In mice, the outgrowth of a lethal dose of HPV16-induced tumor cells has been prevented by vaccination with a CTL epitope encoded by HPV16 E7, indicating the feasibility of peptide immunization to obtain antitumor CTL responses. In the present study, the immunogenicity of 9 HLA-A*0201-binding peptides encoded by HPV16 E6 and E7 was analyzed in vivo in HLA-A*0201Kb transgenic mice and in vitro in CTL cultures induced from PBMC of HLA-A*0201+ healthy donors. Four peptides with a good binding affinity were immunogenic in HLA-A*0201Kb transgenic mice, and three of them were also highly immunogenic in CTL induction experiments with PBMC of HLA-A*0201+ healthy donors. Human CTL clones specific for these three peptides were capable of lysing the HPV16 E7-containing HLA-A*0201+ cervical carcinoma cell line CaSki. These E7-derived peptides (11-20, YMLDLQPETT; 82-90, LLMGTLGIV; 86-93, TLGIVCPI), therefore, are likely to represent naturally processed human CTL epitopes of HPV16. Additionally, these three HPV16-encoded peptides have the highest affinity of binding to the HLA-A*0201 molecule. In this study, peptides with a lower binding affinity were less immunogenic. Therefore, our data illustrate that the HLA-binding affinity of a peptide has a major impact on its immunogenicity. In conclusion, we have identified immunogenic peptides encoded by HPV16 E6 and E7 that could be used in vaccines for the prevention and treatment of cervical carcinoma.
Expression of E- and P-cadherin in gastric carcinomas. (1991)

The expression pattern of two Ca2(+)-dependent intercellular adhesion molecules, E- and P-cadherin, in 54 surgically resected gastric adenocarcinomas was examined immunohistochemically. E-cadherin was expressed uniformly at the cell-cell borders of most of the differentiated and adherent-type undifferentiated gastric adenocarcinomas, showing that E-cadherin serves as the main cadherin molecule responsible for intercellular binding in these carcinomas. Scattered-type undifferentiated gastric adenocarcinomas which apparently lacked this tight intercellular adhesion were divisible into two groups on the basis of E-cadherin expression. In a minor group composed of 4 carcinomas, E-cadherin could not be detected, suggesting that the absence of E-cadherin made the cancer cells separate. In contrast, cancer cells of 19 carcinomas which belonged to the major group showed similar scattering but had definite expression of E-cadherin on their cell surfaces, suggesting that there was some mechanism(s) disturbing the function of E-cadherin in these carcinomas. However, immunoblotting showed no evidence of gross alterations of the E-cadherin molecule, such as partial deletion, in these carcinomas. P-cadherin was expressed in 29 (54%) of the examined gastric carcinomas, and the expression was unstable in most of them, a characteristic feature compared with the stable expression of E-cadherin. Since P-cadherin is known to be expressed temporarily in the foregut during embryogenesis and was proved to be occasionally expressed, although weakly, in the proliferative zone of noncancerous gastric epithelia in this study, expression of P-cadherin in gastric carcinomas may be an oncofetal phenomenon and/or may reflect their marked proliferative potential.
Variable-frequency synthesis: An improved harmonic coding scheme (2005)

The Harmonic Coding concept has already shown its potential for efficiently coding speech. Previous implementations have usec a frame rate of one every 16 ms. This was mainly due to the fact that, with longer frames, even a nonstationary spectral model (of low order) cannot reproduce the zones of fast-varying pitch with the desirable quality. However, the high framing rate is a limitation, since it implies that fewer bits will be available for encoding each frame. A solution for this problem has been devised: the signal is synthesized in the time domain, as a superimposition of "harmonics" whose instantaneous frequency varies continuously along an interpolation curve, within each frame. In this way, fast pitch variations can be tracked with no difficulty. Experimental results are presented, confirming these facts. The integration of this synthesis scheme in a speech coder is discussed.
Reverse Draw Solute Permeation in Forward Osmosis: Modeling and Experiments (2010)

Osmotically driven membrane processes are an emerging set of technologies that show promise in water and wastewater treatment, desalination, and power generation. The effective operation of these systems requires that the reverse flux of draw solute from the draw solution into the feed solution be minimized. A model was developed that describes the reverse permeation of draw solution across an asymmetric membrane in forward osmosis operation. Experiments were carried out to validate the model predictions with a highly soluble salt (NaCl) as a draw solution and a cellulose acetate membrane designed for forward osmosis. Using independently determined membrane transport coefficients, strong agreement between the model predictions and experimental results was observed. Further analysis shows that the reverse flux selectivity, the ratio of the forward water flux to the reverse solute flux, is a key parameter in the design of osmotically driven membrane processes. The model predictions and experiments demonstrate that this parameter is independent of the draw solution concentration and the structure of the membrane support layer. The value of the reverse flux selectivity is determined solely by the selectivity of the membrane active layer.
The complete cDNA and amino acid sequence of bovine fetuin. Its homology with alpha 2HS glycoprotein and relation to other members of the cystatin superfamily. (1990)

The cDNA sequence encoding the bovine fetal protein fetuin is reported. The deduced amino acid sequence is identical with that obtained from amino acid sequencing. The protein is a single chain preceded by a signal sequence. The three N-linked glycosylation sites have been determined. The sequence of fetuin shows over 70% similarity to human alpha 2HS glycoprotein. All of the cysteine residues are conserved in both proteins, suggesting that fetuin has the same arrangement of disulfide loops as alpha 2HS glycoprotein and may also be a member of the cystatin family. Southern blot analysis indicates that a single gene codes for fetuin. No evidence for a separate gene for a bovine alpha 2HS glycoprotein was obtained; thus, fetuin in cattle and alpha 2HS glycoprotein in the human are equivalent proteins.
Tissue Oxygenation and Perfusion in Inferior Pedicle Reduction Mammaplasty by Near-Infrared Reflection Spectroscopy and Color-Coded Duplex Sonography (2003)

Near-infrared reflection spectroscopy has been used in various experimental and clinical settings to investigate tissue perfusion and oxygenation noninvasively. Its application in plastic surgery has only recently been reported. The current study used near-infrared reflection spectroscopy to monitor cutaneous microcirculation in breast skin flaps after inferior pedicle reduction mammaplasty. Thirty patients underwent bilateral reduction mammaplasty by a modified Robbins technique. Near-infrared reflection spectroscopy measurements were performed preoperatively and postoperatively at several defined positions of the breast. The reflection spectroscopy system was capable of detecting absolute values of total hemoglobin in milligrams per milliliter of tissue and tissue hemoglobin oxygen saturation in percent. Color-coded duplex sonography was used to visualize nutrient vessels of the inferior dermoglandular pedicle and to measure systolic peak flow in the arteries supplying the nipple-areola complex. Reflection spectroscopy values were examined for changes during the postoperative course. Reflection spectroscopy and duplex sonography values were analyzed for differences between patients with normal and compromised skin flap perfusion and wound healing, which was assessed clinically and by ultrasound. Preoperative reflection spectroscopy values demonstrated local, regional, and interindividual variations. Postoperatively, characteristic changes of tissue hemoglobin oxygen saturation and total hemoglobin were observed in all patients during the 2-week follow-up. Reflection spectroscopy values differed significantly between breast and nipple-areola skin. Tissue hemoglobin oxygen saturation was significantly lower, and total hemoglobin significantly higher, in patients with impaired wound healing compared with patients having normal wound healing. However, systolic peak flow in arteries of the inferior dermoglandular pedicle did not reveal differences between patients with impaired or normal wound healing of the nipple-areola complex. Near-infrared reflection spectroscopy allows the detection of hemoglobin content and oxygenation in skin flaps. Changes in tissue hemoglobin oxygen saturation and total hemoglobin reflect hemodynamic changes in skin flaps during normal and pathological wound healing. Because of considerable intraindividual and interindividual variations, trend values seem to be superior to single measurements. Although in this study, near-infrared reflection spectroscopy was capable of distinguishing between normal and impaired perfusion in skin flaps in a clinical model, its future implication may be the early detection of vascular compromise in free flaps.
Synthesis of Novel 2-Benzothiopyran and 3-Benzothiepin Derivatives and Their Stimulatory Effect on Bone Formation (1999)

In a search for therapeutic agents for the treatment of osteoporosis and bone fracture, we found that 2-benzothiopyran-1-carboxamide derivatives 1, derived from ipriflavone as a lead compound, increase cellular alkaline phosphatase activity in cultures of rat bone marrow stromal cells. Further modification of 1 has led to the discovery of more potent 3-benzothiepin-2-carboxamide derivatives 2. Of these, 3-benzothiepin derivatives bearing a 4-(dialkoxyphosphorylmethyl)phenyl group on the 2-carboxamide moiety such as 2h and 2q exhibited significant improvement of activity compared to ipriflavone. Asymmetric synthesis of 2h and 2q revealed that the (-)-isomers possessed activities superior to those of the (+)-isomers. Further evaluation of these compounds using the mouse osteoblastic cell line MC3T3-E1 revealed that (-)-2q enhanced the effect of bone morphogenetic protein. In addition, application of a sustained-release agent containing 2q increased the area of newly formed bone in a rat skull defect model. Based on these findings, (-)-2q was selected for further investigation as a new drug stimulating bone formation. Synthesis and structure-activity relationships for this novel series of 2-benzothiopyran and 3-benzothiepin derivatives are detailed.
Pharmacological Evaluation of a Novel Cannabinoid 2 (CB2) Ligand, PF-03550096, In Vitro and In Vivo by Using a Rat Model of Visceral Hypersensitivity (2008)

Previous studies have shown that cannabinoid 2 (CB(2))-receptor agonists might have analgesic effects on visceral hypersensitivity. To extend these results, we have determined the pharmacological characteristics of a newly designed CB(2) ligand, N-[(1S)-1-(aminocarbonyl)-2,2-dimethylpropyl]-3-(3-hydroxy-3-methylbutyl)-2-oxo-2,3-dihydro-1H-benzimidazole-1-carboxamide (PF-03550096), in vitro and in vivo. PF-03550096 showed high affinity to human (K(i) = 7.9 +/- 1.7 nM) and rat CB(2) receptors (K(i) = 47 +/- 5.6 nM). In a cell-based functional assay, PF-03550096 behaved as a full agonist and showed high selectivity for human CB(2) receptors. Orally administered PF-03550096 (3, 10 mg/kg) inhibited the 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced decrease in colonic pain threshold with statistical significance. The inhibitory effect of PF-03550096 (10 mg/kg) was significantly reversed by a selective CB(2) antagonist, N-(1S)-endo-1,3,3-trimethylbicyclo[2.2.1]heptan-2-yl-5-(4-chloro-3-methylphenyl)-1(4-methylbenzyl)-pyrazole-3-carboxamide (SR144528), while SR144528 itself did not modify colonic pain threshold. These results indicate that PF-03550096 is a potent CB(2) agonist and possesses efficacy in a rat model of visceral hypersensitivity.
Optimizing Touchscreen Keyboards for Gesture Typing (2015)

Despite its growing popularity, gesture typing suffers from a major problem not present in touch typing: gesture ambiguity on the Qwerty keyboard. By applying rigorous mathematical optimization methods, this paper systematically investigates the optimization space related to the accuracy, speed, and Qwerty similarity of a gesture typing keyboard. Our investigation shows that optimizing the layout for gesture clarity (a metric measuring how unique word gestures are on a keyboard) drastically improves the accuracy of gesture typing. Moreover, if we also accommodate gesture speed, or both gesture speed and Qwerty similarity, we can still reduce error rates by 52% and 37% over Qwerty, respectively. In addition to investigating the optimization space, this work contributes a set of optimized layouts such as GK-D and GK-T that can immediately benefit mobile device users.
Random oracles are practical (1993)

We argue that the random oracle model—where all parties have access to a public random oracle—provides a bridge between cryptographic theory and cryptographic practice. In the paradigm we suggest, a practical protocol P is produced by first devising and proving correct a protocol PR for the random oracle model, and then replacing oracle accesses by the computation of an “appropriately chosen” function h. This paradigm yields protocols much more efficient than standard ones while retaining many of the advantages of provable security. We illustrate these gains for problems including encryption, signatures, and zero-knowledge proofs.
AGR2, an Endoplasmic Reticulum Protein, Is Secreted into the Gastrointestinal Mucus (2014)

The MUC2 mucin is the major constituent of the two mucus layers in colon. Mice lacking the disulfide isomerase-like protein Agr2 have been shown to be more susceptible to colon inflammation. The Agr2(-/-) mice have less filled goblet cells and were now shown to have a poorly developed inner colon mucus layer. We could not show AGR2 covalently bound to recombinant MUC2 N- and C-termini as have previously been suggested. We found relatively high concentrations of Agr2 in secreted mucus throughout the murine gastrointestinal tract, suggesting that Agr2 may play extracellular roles. In tissue culture (CHO-K1) cells, AGR2 is normally not secreted. Replacement of the single Cys in AGR2 with Ser (C81S) allowed secretion, suggesting that modification of this Cys might provide a mechanism for circumventing the KTEL endoplasmic reticulum retention signal. In conclusion, these results suggest that AGR2 has both intracellular and extracellular effects in the intestine.
Microbiology of Helicobacter pylori. (1993)

The new genus name Helicobacter was first published in October 1989. H. pylori is a unipolar, multiflagellate, gently spiral organism found on the human gastric mucosa, but in culture and under unfavorable conditions, coccoidal forms emerge, which may be indicative of a dormant state. The biology and metabolism of H. pylori, together with growth requirements and methods of detection in clinical specimens, are described in this article. Enzymes, hemagglutinins, and antibiotic susceptibilities of H. pylori are delineated.