gebhart/patrepeval huggingface dataset:
Untersuchung eines Eye Tracker Prototypen zur automatischen Operationsmikroskopsteuerung (2008)

Die Durchfuhrung mikrochirurgischer Operationen wird erst durch die Verwendung von Operationsmikroskopen moglich. Die Mikroskopoptik wird mittels einer Fussteuerung zentriert. Der hier untersuchte Prototyp eines Eye Tracking Systems (ETS) verwendete zwei separate Bildverarbeitungsalgorithmen, um in Situationsbildern am vorderen Augenabschnitt den Irismittelpunkt bzw. in Situationsbildern am hinteren Augenabschnitt das Helligkeitszentrum zu berechnen. Die Zentrierung der Mikroskopoptik wurde mittels dieser Berechnungen automatisiert. Die Funktionstuchtigkeit des Prototyps sollte unter realistischen Bedingungen untersucht werden. Des Weiteren waren die Auswirkungen des Prototyps auf die Arbeitsbedingungen des Operateurs Gegenstand dieser Untersuchung. 30 pars-plana-Vitrektomien, teilweise in Kombination mit Phakoemulsifikation und Hinterkammerlinsenimplantation, wurden in diese Untersuchung eingeschlossen. Die durch den Prototyp berechneten Koordinaten der Irismittelpunkte bzw. der Helligkeitszentren wurden mit den tatsachlichen Koordinaten verglichen. Des Weiteren wurde die interne Qualitatskontrolle des Prototyps untersucht. Die Haufigkeit von Operationsmikroskopzentrierungen durch den Operateur und die Zentrierung des Blickfeldes unter konventionellen Bedingungen wurden mit den Ergebnissen der Operationen unter Verwendung der automatischen Operationsmikroskopsteuerung verglichen. 64,2% der Irismittelpunkte sowie 91,0% der Helligkeitszentren konnten durch den Prototyp richtig bestimmt werden. Die interne Qualitatskontrolle des Prototyps war mit den verwendeten Systemparametern nicht in der Lage, den Anteil falsch bestimmter Irismittelpunkte bzw. Helligkeitszentren ausreichend zu unterdrucken. Die Haufigkeit von Operationsmikroskopzentrierungen durch den Operateur wurde bei Prozeduren am vorderen Augenabschnitt durch das ETS nicht vermindert sondern sogar noch um 50% gesteigert. Bei Prozeduren am hinteren Augenabschnitt konnte demgegenuber eine Verminderung um bis zu 100% festgestellt werden. Die mittlere Zentrierung des Blickfeldes wurde bei Prozeduren am vorderen Augenabschnitt leicht verbessert. Bei Prozeduren am hinteren Augenabschnitt war das Ergebnis inkonsistent: in zwei der nach Toleranz gegliederten Gruppen war eine bessere Zentrierung feststellbar, in der dritten zeigte sich jedoch eine leichte Verschlechterung. Die Ergebnisse deuten auf den moglichen Nutzen sowie die Realisierbarkeit eines Eye Tracking Systems hin. Um das untersuchte Gerat im klinischen Alltag erfolgreich einsetzen zu konnen, sind die Beseitigung der herausgearbeiteten Fehlerquellen sowie die Verbesserung der Funktionstuchtigkeit erforderlich.
Detection of staphylococcal membrane receptors on virus-infected cells by direct adhesin overlay (1986)

We partially characterized the interaction between 125I-labeled surface proteins of Staphylococcus aureus, obtained by thermal extraction, and purified plasma membranes from uninfected and influenza virus A/FM/1/47-infected Madin-Darby canine kidney cells. The radioactivity profile of surface-labeled proteins, derived from anion-exchange high-pressure liquid chromatography, showed a mixture of acidic polypeptides in a peak which contained approximately 5% of the total protein injected; adsorption with purified plasma membranes reduced radioactivity by 5 to 7% and altered elution profiles. Using a direct adhesin overlay procedure, we found that these surface-labeled proteins reacted with polypeptides located on the external surface of plasma membranes which were shared by both virus-infected and uninfected cells or were unique to virus-infected cells. Our data may help explain the enhanced adherence of S. aureus to influenza virus A-infected cells in vitro.
High Yields of 2,3-Butanediol and Mannitol in Lactococcus lactis through Engineering of NAD + Cofactor Recycling (2011)

Manipulation of NADH-dependent steps, and particularly disruption of the las-located lactate dehydrogenase (ldh) gene in Lactococcus lactis, is common to engineering strategies envisaging the accumulation of reduced end products other than lactate. Reverse transcription-PCR experiments revealed that three out of the four genes assigned to lactate dehydrogenase in the genome of L. lactis, i.e., the ldh, ldhB, and ldhX genes, were expressed in the parental strain MG1363. Given that genetic redundancy is often a major cause of metabolic instability in engineered strains, we set out to develop a genetically stable lactococcal host tuned for the production of reduced compounds. Therefore, the ldhB and ldhX genes were sequentially deleted in L. lactis FI10089, a strain with a deletion of the ldh gene. The single, double, and triple mutants, FI10089, FI10089ΔldhB, and FI10089ΔldhBΔldhX, showed similar growth profiles and displayed mixed-acid fermentation, ethanol being the main reduced end product. Hence, the alcohol dehydrogenase-encoding gene, the adhE gene, was inactivated in FI10089, but the resulting strain reverted to homolactic fermentation due to induction of the ldhB gene. The three lactate dehydrogenase-deficient mutants were selected as a background for the production of mannitol and 2,3-butanediol. Pathways for the biosynthesis of these compounds were overexpressed under the control of a nisin promoter, and the constructs were analyzed with respect to growth parameters and product yields under anaerobiosis. Glucose was efficiently channeled to mannitol (maximal yield, 42%) or to 2,3-butanediol (maximal yield, 67%). The theoretical yield for 2,3-butanediol was achieved. We show that FI10089ΔldhB is a valuable basis for engineering strategies aiming at the production of reduced compounds.
Real-life voice activity detection with LSTM Recurrent Neural Networks and an application to Hollywood movies (2013)

A novel, data-driven approach to voice activity detection is presented. The approach is based on Long Short-Term Memory Recurrent Neural Networks trained on standard RASTA-PLP frontend features. To approximate real-life scenarios, large amounts of noisy speech instances are mixed by using both read and spontaneous speech from the TIMIT and Buckeye corpora, and adding real long term recordings of diverse noise types. The approach is evaluated on unseen synthetically mixed test data as well as a real-life test set consisting of four full-length Hollywood movies. A frame-wise Equal Error Rate (EER) of 33.2% is obtained for the four movies and an EER of 9.6% is obtained for the synthetic test data at a peak SNR of 0 dB, clearly outperforming three state-of-the-art reference algorithms under the same conditions.
A Functional Dermatan Sulfate Epitope Containing Iduronate(2-O-sulfate)α1–3GalNAc(6-O-sulfate) Disaccharide in the Mouse Brain (2005)

Oversulfated chondroitin sulfate (CS), dermatan sulfate (DS), and CS/DS hybrid structures bind growth factors, promote the neurite outgrowth of hippocampal neurons in vitro, and have been implicated in the development of the brain. To investigate the expression of functional oversulfated DS structures in the brain, a novel monoclonal antibody (mAb), 2A12, was generated against DS (An-DS) from ascidian Ascidia nigra, which contains a unique iD disaccharide unit, iduronic acid (2-O-sulfate)alpha1-->3GalNAc(6-O-sulfate), as a predominant disaccharide. mAb 2A12 specifically reacted with the immunogen, and recognized iD-enriched decasaccharides as minimal structures. The 2A12 epitope was specifically observed in the hippocampus and cerebellum of the mouse brain on postnatal day 7, and the expression in the cerebellum disappeared in the adult brain, suggesting a spatiotemporally regulated expression of this epitope. Embryonic hippocampal neurons were immunopositive for 2A12, and the addition of the antibody to the culture medium significantly reduced the neurite growth of hippocampal neurons. In addition, two minimum 2A12-reactive decasaccharide sequences with multiple consecutive iD units were isolated from the An-DS chains, which exhibited stronger inhibitory activity against the binding of various growth factors and neurotrophic factors to immobilized embryonic pig brain CS/DS chains (E-CS/DS) than the intact E-CS/DS, suggesting that the 2A12 epitope at the neuronal surface acts as a receptor or co-receptor for these molecules. Thus, we have selected a unique antibody that recognizes iD-enriched oversulfated DS structures, which are implicated in the development of the hippocampus and cerebellum in the central nervous system. The antibody will also be applicable for investigating structural alterations in CS/DS in aging and pathological conditions.
Patterns of Colorectal Cancer Screening Uptake among Men and Women in the United States (2006)

Colorectal cancer testing is increasing for both men and women, although the prevalence of testing remains higher in men. Our data support previous findings documenting socioeconomic disparities in colorectal cancer test use. Access barriers to screening could be particularly difficult to overcome if colonoscopy becomes the preferred colorectal cancer screening modality.
Structural alterations of the epidermal growth factor receptor gene in human gliomas. (1992)

The epidermal growth factor receptor (EGFR) gene is amplified in 40% of malignant gliomas, and the amplified genes are frequently rearranged. We have characterized the genetic alterations associated with these rearrangements in five malignant gliomas. In one tumor the rearrangement resulted in the deletion of most of the extracytoplasmic domain of the receptor, resulting in a hybrid mRNA between new sequences and the truncated EGFR sequence. The predicted amino acid sequence of the protein from this tumor was remarkably similar to that described for several viral erbB oncogenes. Four other tumors were noted to have internal deletions of the EGFR gene. These rearrangements brought about in-frame deletions affecting either of two cysteine-rich domains in the extracytoplasmic portion of the molecule. The clonal nature of these alterations, and the fact that identical alterations were seen in more than one tumor, suggests a role for these mutant receptor proteins in tumorigenesis. Further, these studies document the existence of tumor-specific cell surface molecules resulting from somatic mutation.
Colloidal Alphabet Soup:  Monodisperse Dispersions of Shape-Designed LithoParticles (2007)

By lithographically mass-producing exotic colloids, or “LithoParticles”, we generate unique model systems that have not been previously obtained either through self-assembly or bottom-up growth processes. Customizable control over the features of LithoParticles is achieved at the micron and submicron scales using automated stepper lithography, providing high-throughput production in combination with exquisite fidelity of the shapes. Billions of copies of colloidal fluorescent polymeric particles comprising all 26 letters of the Latin alphabet are stably dispersed in a liquid, yielding multicolored “colloidal alphabet soup”. Multilayer hybrid polymer particles with complex three-dimensional shapes and different internal compositions demonstrate the full potential of the approach. Colloidal LithoParticles in solution exhibit significant Brownian motion driven by thermal energy, making them excellent model systems for exploring new phenomena, such as phase transitions, jamming, and self-assembly, in which the shapes of the particles play a key role.
SmgGDS-558 regulates the cell cycle in pancreatic, non-small cell lung, and breast cancers (2014)

Oncogenic mutation or misregulation of small GTPases in the Ras and Rho families can promote unregulated cell cycle progression in cancer. Post-translational modification by prenylation of these GTPases allows them to signal at the cell membrane. Splice variants of SmgGDS, named SmgGDS-607 and SmgGDS-558, promote the prenylation and membrane trafficking of multiple Ras and Rho family members, which makes SmgGDS a potentially important regulator of the cell cycle. Surprisingly little is known about how SmgGDS-607 and SmgGDS-558 affect cell cycle-regulatory proteins in cancer, even though SmgGDS is overexpressed in multiple types of cancer. To examine the roles of SmgGDS splice variants in the cell cycle, we compared the effects of the RNAi-mediated depletion of SmgGDS-558 vs. SmgGDS-607 on cell cycle progression and the expression of cyclin D1, p27, and p21 in pancreatic, lung, and breast cancer cell lines. We show for the first time that SmgGDS promotes proliferation of pancreatic cancer cells, and we demonstrate that SmgGDS-558 plays a greater role than SmgGDS-607 in cell cycle progression as well as promoting cyclin D1 and suppressing p27 expression in multiple types of cancer. Silencing both splice variants of SmgGDS in the cancer cell lines produces an alternative signaling profile compared with silencing SmgGDS-558 alone. We also show that loss of both SmgGDS-607 and SmgGDS-558 simultaneously decreases tumorigenesis of NCI-H1703 non-small cell lung carcinoma (NSCLC) xenografts in mice. These findings indicate that SmgGDS promotes cell cycle progression in multiple types of cancer, making SmgGDS a valuable target for cancer therapeutics.
“Spot-On” SNP Genotyping: Figure 1. (2000)

As we enter the post-genomic era, where complete reference genome sequences are a given, analyzing the variation among individual genomes is an area of intense investigation. One of the most common forms of genomic variation is single nucleotide polymorphisms, or SNPs. The “science of SNPs” has become a heavy industry, as evidenced by the proliferation of methods for genotyping and deployment of entire commercial enterprises devoted to research centered on SNPs. Why are we seeing such keen interest in these technologies? Applications that utilize SNPs are cropping up in diverse areas of research. Undoubtedly, the area where SNPs are receiving the most attention is their use as genetic markers for the study of complex human traits and pharmacogenomics. Genome-wide complements of SNPs are now being developed as genetic tools in model organisms such as Arabidopsis, Drosophila, and C. elegans. SNPs are finding favor as markers for genetic crosses and selective breeding strategies in livestock and plants of agricultural importance. All of these applications demand a technology that provides simple, robust, highly accurate and cost-effective genotyping of large numbers of SNPs on hundreds or thousands of individuals. Unlike DNA sequencing, where separation-based dideoxy sequencing predominates, no single technology for scoring SNPs has become a widely accepted standard. In this issue, Pastinen and colleagues present a novel arraybased method for SNP genotyping (Pastinen et al. 2000).
Pyridinoline, a Non-Reducible Crosslink of Collagen (1978)

Pyridinoline is a crosslink compound isolated from bovine Achilles tendon collagen. It is a 3-hydroxypyridinium derivative with three amino and three carboxyl groups (Fujimoto, D., Akiba, K., & Nakamura, N. (1977) Biochem. Biophys. Res. Commun. 76, 1124–1129). The contents of pyridinoline in collagens from various sources were determined. The pyridinoline content of bovine Achilles tendon was 0.16 residue per 1,000 residues and that of rat Achilles tendon collagen was 0.017 residue per 1,000 residues. Besides Achilles tendon collagens, pyridinoline was found in collagens from coastal cartilage, rib and femoral bone of rat. It was not found in collagens from the tail tendon and skin of rat. A crosslinked, triple-chained peptide containing pyridinoline was isolated from bovine Achilles tendon collagen after digestion with pronase. Its amino acid composition suggests that the peptide may be involved in an intermolecular crosslink among a carboxyterminal sequence, a sequence near the aminoterminus and a sequence in the helical region.
Real-time binary phase holograms on a reflective ferroelectric liquid-crystal spatial light modulator (1994)

A ferroelectric liquid-crystal spatial light modulator with an active silicon backplane is used to implement reconfigurable reflective phase holograms. Optical results are presented for an optimized computergenerated Fourier hologram.
Copper electron-nuclear double resonance of cytochrome c oxidase. (1980)

Electron-nuclear double resonance of copper was observed while monitoring the "intrinsic copper" electron paramagnetic resonance signal of cytochrome c oxidase (ferrocytochrome c:oxygen oxidoreductase, EC 1.9.3.1) near g = 2. This unambiguously establishes the presence of the metal (Cua) in the redox center responsible for this signal. The hyperfine couplings to copper are largely istropic and the maximum value is about half that seen in type I blue copper proteins. The magnetic properties of this oxidized copper center are not consistent with those of a thiyl radical (R-S) coordinated to Cu(I), and thus favor the identification of this redox center as a Cu(II) ion in a unique environment.
Extended lapped transforms for digital multicarrier modulation (2002)

In today's multicarrier modulation systems, such as orthogonal frequency division multiplexing (OFDM) or discrete multitone (DMT), modulation is accomplished digitally by the use of the inverse discrete Fourier transform (IDFT). Instead of the IDFT, any other orthogonal transform can be used. A multicarrier scheme based on extended lapped transforms (ELT) is investigated. With the ELT, a better spectral containment of the subchannels is achieved, which also leads to a superior power spectral density of the multicarrier signal. Further, the ELT multicarrier modulation is shown to be more robust against frequency selective interferers present on the transmission channel.
Rf8 and Rf* Mediate Unique T-urf13-Transcript Accumulation, Revealing a Conserved Motif Associated With RNA Processing and Restoration of Pollen Fertility in T-Cytoplasm Maize (1997)

Rf8 is a newly described nuclear gene that can substitute for Rf1 to partially restore pollen fertility to male-sterile, T-cytoplasm maize. Families segregating for Rf8 were used to investigate the mechanism of this fertility restoration and to compare it to the restoration conditioned by Rf1. Although Rf8 is unlinked to the rf1 locus, it also alters T-urf13 mitochondrial transcript accumulation and reduces the accumulation of the URF13 protein. Like the 1.6- and 0.6-kilobase (kb) T-urf13 transcripts that accumulate in T-cytoplasm plants carrying Rf1, 1.42- and 0.42-kb transcripts accumulate in plants that are partially restored by Rf8. A survey of T-cytoplasm maize lines, inbreds, and F1 hybrids by mitochondrial RNA gel blot analyses revealed that Rf8 is rare in maize germplasm. These surveys revealed the presence of another rare, weak restorer factor, Rf*, which is uniquely associated with the accumulation of 1.4- and 0.4-kb T-urf13 transcripts. Primer extension analyses position the 5' termini of the 1.42/0.42-kb and 1.4/0.4-kb transcripts at +137 and +159 nucleotides, respectively, 3' of the AUG initiation codon of the T-urf13 reading frame. The conserved motif, 5'-CNACNNU-3', overlaps the 5' termini of the Rf1-, Rf8-, and Rf*-associated transcripts and the 380 nucleotide, Rf3-associated orf107 transcript from cytoplasmic male sterility sorghum. These results demonstrate that multiple unlinked, nuclear genes can have similar but distinct effects on the expression of the unique T-urf13 mitochondrial coding sequence to restore pollen fertility to T-cytoplasm maize.
Safety and Immunogenicity of Env 2-3, a Human Immunodeficiency Virus Type 1 Candidate Vaccine, in Combination with a Novel Adjuvant, MTP-PE/MF59 (1996)

We investigated the safety and immunogenicity of a candidate HIV-1 vaccine, Env 2-3 (Chiron Biocine Co.), in combination with an adjuvant emulsion, MF59, with or without an additional immune modulator, MTP-PE 78 healthy HIV-1-seronegative adults. Sixteen subjects participated in a dose escalation study of MTP-PE in MF59 without Env 2-3, given at 0 and 1 months; 48 subjects participated in a study of a fixed dose of 30 micrograms of Env 2-3 in MF59 with increasing doses of MTP-PE (0, 5, 10, 25, 50, and 100 micrograms), and 14 subjects participated in a study of 100 micrograms of Env 2-3 in MF59 without MTP-PE. Subjects were assigned to study groups under a randomized, double-blind allocation. Subjects received immunization at 0, 1, and 6 months, and had the option of receiving a fourth dose at 12-18 months. Env 2-3 in MTP-PE/MF59 was associated with significant reactogenicity, in that severe, although self-limited systemic and/or local reactions occurred in 15 of 30 vaccinees. In contrast, Env 2-3 in MF59 without MTP-PE was relatively well tolerated, and severe local and/or systemic reactions occurred in only 2 of 18 subjects. Env 2-3 stimulated serum antibodies to HIV-1 envelope protein (gp120) as detected by Western blot in 39 of 43 subjects and to HIV-1 virus lysate by EIA in 28 of 43 subjects after three injections. The majority of subjects also developed EIA antibodies to recombinant gp120 (SF-2), gp120 (LAI), and V3 peptide (SF-2). Neutralizing antibodies to the homologous SF-2 strain developed in 30 of 43 and 27 of 34 subjects, and fusion inhibition antibodies in 25 of 43 and 15 of 36 subjects after three and four injections, respectively. Lymphoproliferative responses to the immunogen, Env 2-3 were observed in over 80% of the vaccinees examined, and CD4+ cytotoxic T cell activity directed against HIV-1 was noted transiently in 2 of 20 vaccinees. Addition of MTP-PE to Env 2-3 or increasing the dose of Env 2-3 from 30 to 100 micrograms did not augment immunogenicity. Env 2-3 in MF59 was well tolerated and immunogenic in HIV-1-seronegative individuals. The addition of MTP-PE significantly increased reactogenicity, but had little, if any, effect on immunogenicity.
Follicular Lymphoid Hyperplasia of the Skin with High Content of Ki-1 Positive Lymphocytes (1989)

We report the case of a spontaneously regressing lymphocytic lesion on the neck of a 76-year-old man. Routine histopathological examination revealed a heterogeneous infiltrate composed of both lymphoid follicles and preferentially perifollicular and interfollicular sheets of large atypical cells. Immunohistologically, large atypical cells were positive for Ki-1/Ber-H2 (CD30), anti-Il-2 (CD25), Ber T9, anti-HLA-DR, Leu-5b (CD2), T3 (CD3), Leu-3 (CD4), Leu-1 (CD5) and, occasionally, Leu-M1 (CD15); that is, they showed an arrangement and immunophenotype similar to those of perifollicular Ki-1 positive cells in reactive lymphoid tissue. In contrast, antibodies To15 (CD22), anti-immunoglobulins, and anti-CALLA (CD10) stained polyclonal B-cells restricted to lymphoid follicles and small clusters representing remnants of follicles. We suggest that this lesion be termed "follicular lymphoid hyperplasia of the skin with high content of activated T-helper cells."
Carbohydrate Microarrays Methods and Protocols (2012)

Carbohydrate microarrays emerged as a key technology for the deciphering of the glycospace by providing a multiplex technology where tens to hundreds of carbohydrates/protein interactions can be probed in parallel. Carbohydrate Microarrays: Methods and Protocols aims to give the reader the theoretical and experimental clues necessary for the fabrication and implementation of carbohydrate microarrays. This requires three essential steps: 1) to obtain the carbohydrate probes (monosacharides, oligosacchrides, polysacchairdes, glycoconjugates or glycoclusters), 2) to immobilize these probes, and 3) to implement the protocols for biological/biochemical interaction with the desired target. This volume gives an overview of carbohydrate microarray and carbohydrate chemistry and illustrates different detection techniques and their applications. Written in the successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Carbohydrate Microarrays: Methods and Protocols compiles a catalogue of protocols on carbohydrate microarrays to span the needs of researchers around the globe.