gebhart/patrepeval huggingface dataset:
Brain-to-text: decoding spoken phrases from phone representations in the brain (2015)

It has long been speculated whether communication between humans and machines based on natural speech related cortical activity is possible. Over the past decade, studies have suggested that it is feasible to recognize isolated aspects of speech from neural signals, such as auditory features, phones or one of a few isolated words. However, until now it remained an unsolved challenge to decode continuously spoken speech from the neural substrate associated with speech and language processing. Here, we show for the first time that continuously spoken speech can be decoded into the expressed words from intracranial electrocorticographic (ECoG) recordings.Specifically, we implemented a system, which we call Brain-To-Text that models single phones, employs techniques from automatic speech recognition (ASR), and thereby transforms brain activity while speaking into the corresponding textual representation. Our results demonstrate that our system can achieve word error rates as low as 25% and phone error rates below 50%. Additionally, our approach contributes to the current understanding of the neural basis of continuous speech production by identifying those cortical regions that hold substantial information about individual phones. In conclusion, the Brain-To-Text system described in this paper represents an important step toward human-machine communication based on imagined speech.
Combination probes with intercalating anchors and proximal fluorophores for DNA and RNA detection (2016)

A new class of modified oligonucleotides (combination probes) has been designed and synthesised for use in genetic analysis and RNA detection. Their chemical structure combines an intercalating anchor with a reporter fluorophore on the same thymine nucleobase. The intercalator (thiazole orange or benzothiazole orange) provides an anchor, which upon hybridisation of the probe to its target becomes fluorescent and simultaneously stabilizes the duplex. The anchor is able to communicate via FRET to a proximal reporter dye (e.g. ROX, HEX, ATTO647N, FAM) whose fluorescence signal can be monitored on a range of analytical devices. Direct excitation of the reporter dye provides an alternative signalling mechanism. In both signalling modes, fluorescence in the unhybridised probe is switched off by collisional quenching between adjacent intercalator and reporter dyes. Single nucleotide polymorphisms in DNA and RNA targets are identified by differences in the duplex melting temperature, and the use of short hybridization probes, made possible by the stabilisation provided by the intercalator, enhances mismatch discrimination. Unlike other fluorogenic probe systems, placing the fluorophore and quencher on the same nucleobase facilitates the design of short probes containing multiple modifications. The ability to detect both DNA and RNA sequences suggests applications in cellular imaging and diagnostics.
Collision Sensing by Stereo Vision and Radar Sensor Fusion (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> To take advantage of both stereo cameras and radar, this paper proposes a fusion approach to accurately estimate the location, size, pose, and motion information of a threat vehicle with respect to a host one from observations that are obtained by both sensors. To do that, we first fit the contour of a threat vehicle from stereo depth information and find the closest point on the contour from the vision sensor. Then, the fused closest point is obtained by fusing radar observations and the vision closest point. Next, by translating the fitted contour to the fused closest point, the fused contour is obtained. Finally, the fused contour is tracked by using rigid body constraints to estimate the location, size, pose, and motion of the threat vehicle. Experimental results from both synthetic data and real-world road test data demonstrate the success of the proposed algorithm. </para>
Kinetics and differentiation of marrow stromal cells in diffusion chambers in vivo (1986)

Rabbit marrow cells inoculated into diffusion chambers (10(7) cells/chamber) were implanted intraperitoneally into athymic mouse hosts and cultured in vivo for 20 days. A connective tissue consisting of bone, cartilage and fibrous tissues is formed by the stromal fibroblastic cells of marrow within the chambers. Cell kinetics and tissue differentiation have been studied using histomorphometric and biochemical analyses. Haemopoietic cell numbers decrease to less than 0.05% of the initial inoculum during the 20-day period. At 3 days an average of 15 stromal fibroblastic cells only are identifiable within the chambers. After 3 days there is a high rate of stromal cell proliferation with a doubling time of 14.5 h during the period from 3 to 8 days and an increase in the total stromal cell population by more than six orders of magnitude from 3 to 20 days. Thirteen to fourteen population doublings occur before expression of the first observable differentiation parameter, alkaline phosphatase activity. The data demonstrate that the mixture of connective tissues formed within the chamber is generated by a small number of cells with high capacity for proliferation and differentiation. This is consistent with the current hypothesis that stromal stem cells are present in bone marrow.
The gatekeeper residue controls autoactivation of ERK2 via a pathway of intramolecular connectivity (2006)

Studies of protein kinases have identified a "gatekeeper" residue, which confers selectivity for binding nucleotides and small-molecule inhibitors. We report that, in the MAP kinase ERK2, mutations at the gatekeeper residue unexpectedly lead to autoactivation due to enhanced autophosphorylation of regulatory Tyr and Thr sites within the activation lip that control kinase activity. This occurs through an intramolecular mechanism, indicating that the gatekeeper residue indirectly constrains flexibility at the activation lip, precluding access of the phosphoacceptor residues to the catalytic base. Other residues that interact with the gatekeeper site to form a hydrophobic cluster in the N-terminal domain also cause autoactivation when mutated. Hydrogen-exchange studies of a mutant within this cluster reveal perturbations in the conserved DFG motif, predicting a route for side chain connectivity from the hydrophobic cluster to the activation lip. Mutations of residues along this route support this model, explaining how information about the gatekeeper residue identity can be transmitted to the activation lip. Thus, an N-terminal hydrophobic cluster that includes the gatekeeper forms a novel structural unit, which functions to maintain the "off" state of ERK2 before cell signal activation.
Making cardiomyocytes: How mechanical stimulation can influence differentiation of pluripotent stem cells (2013)

Pluripotent stem cells (PSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) have promise in regenerative medicine for a variety of applications. Their potential in the treatment of cardiovascular disease is of particular interest due to its severity and prevalence. In order to be successful for cell therapy, PSCs must be pre-differentiated into cardiomyocytes to prevent teratoma formation in vivo. Current methods focus on the supplementation of soluble factors to culture medium to drive differentiation into mesodermal lineages; however, these methods are costly with varying cardiomyocyte yields. Since cardiomyocytes are exposed to dynamic environments in vivo, there is potential in using mechanical stimulation to further drive differentiation in vitro. In this review, we will describe the most recent developments in how mechanical stimulation, including fluid shear, cyclic strain, and magnetically mediated strain, can guide cardiomyogenesis in PSCs.
Molecular characterization of hasA from an operon required for hyaluronic acid synthesis in group A streptococci. (1994)

The mechanism by which group A streptococci produce the antiphagocytic hyaluronate (hyaluronic acid) capsule is incompletely understood. Enzymes known to be essential for synthesis of this polysaccharide include the membrane-associated hyaluronate synthase as well as those required for production of the substrate sugars UDP-N-acetylglucosamine and UDP-glucuronic acid. In this study, a Tn916 insertion that inactivates hyaluronate synthetic activity was localized to a gene designated hasA in the hyaluronic acid synthesis operon. This gene has recently been preliminarily identified as the group A streptococcal hyaluronate synthase. The DNA sequence and transcription start site of hasA were determined, and the predicted HasA protein was shown to have characteristics of a membrane protein. Amino acid sequence homology suggests that HasA is related to a family of proteins involved in polysaccharide production and cell differentiation. Finally, in addition to the loss of hyaluronate synthase activity, the hasA::Tn916 insertion was demonstrated to correlate with a loss of UDP-glucuronic acid dehydrogenase activity. These results suggest that the genes required for hyaluronate synthase activity and production of the UDP-glucuronic acid substrate are transcribed as a unit in group A streptococci.
Encapsulation of ATP into liposomes by different methods: optimization of the procedure (2004)

Different methods and conditions for ATP incorporation into PEGylated liposomes were compared in order to obtain a preparation with a maximized ATP content. Such a preparation may find the application for the in vivo treatment of ischemic tissues suffering from an insufficient ATP supply. Several different methods of liposome preparation and purification were used and HPLC was employed to determine the concentration of ATP in the liposomes. Thin lipid film hydration produced vesicles with the lowest ATP encapsulation (ca. 5 mol%). A pH gradient method yielded liposomes with ca. 10 mol% of ATP. Reverse phase evaporation and freezing-thawing methods resulted in a maximum entrapment of ATP on the level of 36-38 mol%. The freezing-thawing method was chosen for further investigation because of its simplicity and absence of a need to use organic solvents. The separation of the non-entrapped ATP by gel-filtration, centrifugation or dialysis yielded virtually identical liposomal preparations. The incorporation of PEG (as PEG-distearoyl phosphatidylethanolamine, PEG-DSPE) into the liposomal membrane decreases the quantity of the entrapped ATP (from 38 mol% for liposomes with 0.5 mol% of PEG-DSPE to only 17 mol% for liposomes with 5 mol% of PEG-DSPE).
Eighty-Kilodalton N-Terminal Moiety of Bordetella pertussis Filamentous Hemagglutinin: Adherence, Immunogenicity, and Protective Role (2002)

Bordetella pertussis, the etiological agent of whooping cough, produces a number of factors, such as toxins and adhesins, that are required for full expression of virulence. Filamentous hemagglutinin (FHA) is the major adhesin of B. pertussis. It is a protein of approximately 220 kDa, found both associated at the bacterial cell surface and secreted into the extracellular milieu. Despite its importance in B. pertussis pathogenesis and its inclusion in most acellular pertussis vaccines, little is known about the functional importance of individual domains in infection and in the induction of protective immunity. In this study, we analyzed the role of the approximately 80-kDa N-terminal domain of FHA, designated Fha44, in B. pertussis adherence, colonization, and immunogenicity. Although Fha44 contains the complete heparan sulfate-binding domain, it is not sufficient for adherence to epithelial cells or macrophages. It also cannot replace FHA during colonization of the mouse respiratory tract. Infection with a B. pertussis strain producing Fha44 instead of FHA does not induce anti-FHA antibodies, whereas such antibodies can readily be induced by intranasal administration of purified Fha44. In addition, mice immunized with purified Fha44 were protected against challenge with wild-type B. pertussis, indicating that Fha44 contains protective epitopes. Compared to FHA, Fha44 is much smaller and much more soluble and is therefore easier to purify and to store. These advantages may perhaps warrant considering Fha44 for inclusion in acellular pertussis vaccines.
Abstract 647: Xenograft Models of Breast Cancer: the Link between Characteristics of Biomarker Expression and the Anti-tumor Effect of the Representative Therapies (2010)

Abstract Gene expression analysis has led to the identification of 5 subtypes of breast cancer (basal-like, HER2-like, luminal A and B, and normal-like) that have distinct biological features, clinical outcomes, and responses to conventional chemotherapy and targeted therapy. Animal models possessing genetic and other biomarker abnormalities similar to each subtype of the human counterpart are thus of crucial importance in the development of new therapeutic strategies. Human breast cancer xenograft model is one of the more difficult models with transplantation of either established cell lines or primary tumors. We have successfully established 6 xenograft models derived from established cell lines and 2 xenograft models by transplanting primary human tumor fragments. The immunohistochemical results classified the 9 models into 4 major groups: ER negative and HER2 negative (MX-1, MDA-MB-231, MCF-7-CB1, and SKBR3-CB1), ER negative and HER2 positive (BT-474-CB1), ER positive and HER2 negative (MCF-7), and ER positive and HER2 positive (BT-474), which well resembled basal-like/normal-like, HER2-like, luminal A, and luminal B breast cancer types in human. The mutation status of TP53, BRCA1, BRCA2 and EGFR was investigated, and compared with the in vivo efficacy results by using various test drugs including cytotoxic agents, paclitaxel and doxorubicin; ER antagonist, tamoxifen; anti-HER2 monoclonal antibody, trastuzumab; HER2 inhibitor, HKI-272 and EGFR inhibitor, erlotinib. These data closely mimicked the heterogeneity in clinical outcomes of the human disease. Therefore, these models provide valuable platform for the development of personalized therapy for breast cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 647.
Application of the FICTION technique for the simultaneous detection of immunophenotype and chromosomal abnormalities in routinely fixed, paraffin wax embedded bone marrow trephines: Figure 1 (2005)

The use of interphase fluorescence in situ hybridisation (FISH) to study cytogenetic abnormalities in routinely fixed paraffin wax embedded tissue has become commonplace over the past decade. However, very few studies have applied FISH to routinely fixed bone marrow trephines (BMTs). This may be because of the acid based decalcification methods that are commonly used during the processing of BMTs, which may adversely affect the suitability of the sample for FISH analysis. For the first time, this report describes the simultaneous application of FISH and immunofluorescent staining (the FICTION technique) to formalin fixed, EDTA decalcified and paraffin wax embedded BMTs. This technique allows the direct correlation of genetic abnormalities to immunophenotype, and therefore will be particularly useful for the identification of genetic abnormalities in specific tumour cells present in BMTs. The application of this to routine clinical practice will assist diagnosis and the detection of minimal residual disease.
Globus: a Metacomputing Infrastructure Toolkit (1997)

The Globus system is intended to achieve a vertically integrated treatment of application, middleware, and net work. A low-level toolkit provides basic mechanisms such as communication, authentication, network information, and data access. These mechanisms are used to con struct various higher level metacomputing services, such as parallel programming tools and schedulers. The long- term goal is to build an adaptive wide area resource environment (AWARE), an integrated set of higher level services that enable applications to adapt to heteroge neous and dynamically changing metacomputing environ ments. Preliminary versions of Globus components were deployed successfully as part of the I-WAY networking experiment.
Characterization of apoptosis‐like endonuclease activity in avian thymocytes (1992)

In the current study the internucleosomal DNA cleavage activity associated with apoptosis was investigated in avian thymocytes. Thymocyte nuclear proteins from glucocorticoid-treated chickens were incubated with chicken red blood cell (cRBC) nuclei, and DNA degradation was analyzed by agarose gel electrophoresis and fluorescence-activated flow cytometry. The thymocyte nuclear extract contained an endonuclease activity that degraded cRBC chromatin at internucleosomal sites as detected by agarose gel electrophoresis. Flow cytometry analysis of cRBC nuclei that were treated with thymocyte nuclear proteins demonstrated a loss of cellular DNA as a function of the amount of added nuclease activity. Furthermore, it was demonstrated that the thymocyte nuclear extract contained a nuclease activity that was capable of degrading radiolabelled naked 32P-DNA into acid soluble DNA fragments. All three assay methods demonstrate that the thymocyte nuclease activity can be inhibited by EDTA, zinc ions and the nuclease inhibitor aurintricarboxylic acid. Based on the analysis of cofactor requirement of this nuclease activity and its susceptibility to inhibitors, the endonuclease activity present in avian apoptotic thymocytes appears to be identical to the mammalian counterpart.
Synthesis and cytotoxic activities of a series of novelN-methyl-bisindolylmaleimide amide derivatives (2014)

A novel series of N-methyl-bisindolylmaleimides were synthesized and evaluated for their inhibitory activities against nine tumor cell lines. Some of the compounds showed an interesting activity against the tested cell lines. The most potent compounds 5e and 5j displayed antiproliferative activity with 50% inhibitory concentration values in the μM range against some tested cell lines.
Two‐dimensional RFLP analyses reveal megabase‐sized clusters of rRNA gene variants in Arabidopsis thaliana, suggesting local spreading of variants as the mode for gene homogenization during concerted evolution (1996)

Eukaryotic genes encoding the precursor of 18S, 5.8S and 25S ribosomal RNA (rRNA genes or rDNA) are virtually identical within a species, yet they evolve rapidly between species, a phenomenon known as concerted evolution. The mechanisms by which sequence homogenization and fixation of new rRNA gene variants occurs within a genome are not clear. In diploid Arabidopsis thaliana, approximately 1500 rRNA genes are tandemly arrayed at two nucleolus organizer regions, one on chromosome 2 (NOR2), the other on chromosome 4 (NOR4). This paper shows that NOR2 and NOR4 are similar in size, each spanning approximately 3.5-4.0 Mbp. Using two-dimensional mapping techniques involving a combination of pulsed-field and conventional gel electrophoresis, the distributions of four distinct rRNA gene variants at NOR2 and NOR4 have been determined. rRNA genes at NOR4 are homogeneous with respect to a HindIII site occurring once per gene. In contrast, fewer than 10% of the rRNA genes at NOR2 are HindIII-bearing variants. A single intergenic spacer length is found among rRNA genes at NOR2 but three classes of spacer length variants are present at NOR4. The NOR4 variants are not intermingled with one another; instead, they are highly clustered over distances as large as 1.5 Mbp. These data suggest that in the concerted evolution of rRNA genes, homogenization is a consequence of local spreading of new rRNA gene variants.
[2-(Trimethylsilyl)ethoxy]methyl (SEM) as a novel and effective imidazole and fused aromatic imidazole protecting group (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT[2-(Trimethylsilyl)ethoxy]methyl (SEM) as a novel and effective imidazole and fused aromatic imidazole protecting groupJeffrey P. Whitten, Donald P. Matthews, and James R. McCarthyCite this: J. Org. Chem. 1986, 51, 10, 1891–1894Publication Date (Print):May 1, 1986Publication History Published online1 May 2002Published inissue 1 May 1986https://pubs.acs.org/doi/10.1021/jo00360a044https://doi.org/10.1021/jo00360a044research-articleACS PublicationsRequest reuse permissionsArticle Views3813Altmetric-Citations67LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Stability of La0.6Sr0.4Co0.2Fe0.8O3-δ Perovskite Membranes in Reducing and Nonreducing Environments (1998)

The chemical stability of perovskite La0.6Sr0.4Co0.2Fe0.8O3-δ (LSCF-6428) has been investigated in connection with its potential use as a catalytic membrane for the oxidative coupling of methane (OCM). Once a steady-state oxygen-defect gradient is established (15−20 h), these membranes are found to be very stable under air/nitrogen gradients at temperatures up to 960 °C and they respond instantaneously to temperature changes with an apparent activation energy of 159 kJ/mol. However, serious near-surface etching occurs when one side of the membrane is exposed to 100% CH4 at 850 °C and atmospheric pressure, which resulted in dramatic increases in oxygen flux (a factor of 5). While this also caused an increase in the OCM reaction rate, the selectivity of C2+ hydrocarbons fell from 40 to 10%. It is also shown that stable operation under OCM conditions is possible if CH4 pressures are reduced to 0.1 atm but at a cost of C2+ production rate.
A Review of Phenotypes in Saccharomyces cerevisiae (1997)

A summary of previously defined phenotypes in the yeast Saccharomyces cerevisiae is presented. The purpose of this review is to provide a compendium of phenotypes that can be readily screened to identify pleiotropic phenotypes associated with primary or suppressor mutations. Many of these phenotypes provide a convenient alternative to the primary phenotype for following a gene, or as a marker for cloning a gene by genetic complementation. In many cases a particular phenotype or set of phenotypes can suggest a function for the product of the mutated gene.
Water-soluble fluorescent conjugated polymers and their interactions with biomacromolecules for sensitive biosensors (2010)

Over the past decades, water-soluble conjugated polymers (CPs) have gained increasing attention as optical platforms for sensitive detection of biomacromolecules (DNA, protein and cell) due to the amplification of fluorescent signals. To meet the requirement for high throughput assays, chip and microarray techniques based on CPs have also been developed. Very recently, fluorescence imaging in vivo and at the cellular level have also been successfully accomplished using these water-soluble CPs. In this tutorial review, we provide a brief review of the synthesis and optical properties of CPs, focusing especially on their applications in biosensors and cell imaging.