gebhart/patrepeval huggingface dataset:
Peptide sequences for sucrose splitting and glucan binding within Streptococcus sobrinus glucosyltransferase (water-insoluble glucan synthetase) (1991)

The gene encoding glucosyltransferase responsible for water-insoluble glucan synthesis (GTF-I) of Streptococcus sobrinus (formerly Streptococcus mutans 6715) was cloned, expressed, and sequenced. A gene bank from S. sobrinus 6715 DNA was constructed in vector pUC18 and screened with anti-GTF-I antibody to detect clones producing GTF-I peptide. Five immunopositive clones were isolated, all of which produced peptides that bound alpha-1,6 glucan. GTF-I activity was found in only two large peptides: one stretching over the full length of the GTF-I peptide and composed of about 1,600 amino acid residues (AB1 clone) and the other lacking about 80 N-terminal residues and about 260 C-terminal residues (AB2 clone). A deletion study of the AB2 clone indicated that specific glucan binding, which is essential for water-insoluble glucan synthesis, was lost prior to sucrase activity with an increase in deletion from the 3' end of the GTF-I gene. These results suggest that the GTF-I peptide consists of three segments: that for sucrose splitting (approximately 1,100 residues), that for glucan binding (approximately 240 residues), and that of unknown function (approximately 260 residues), in order from the N terminus. The primary structure of the GTF-I peptide, deduced by DNA sequencing of the AB1 clone, was found to be very similar to that of the homologous protein from another strain of S. sobrinus.
Working memory‐related changes in functional connectivity persist beyond task disengagement (2012)

We examined whether altered connectivity in functional networks during working memory performance persists following conclusion of that performance, into a subsequent resting state. We conducted functional magnetic resonance imaging (fMRI) in 50 young adults during an initial resting state, followed by an N-back working memory task and a subsequent resting state, in order to examine changes in functional connectivity within and between the default-mode network (DMN) and the task-positive network (TPN) across the three states. We found that alterations in connectivity observed during the N-back task persisted into the subsequent resting state within the TPN and between the DMN and TPN, but not within the DMN. Further, both speed of working memory performance and TPN connectivity strength during the N-back task predicted connectivity strength in the subsequent resting state. Finally, DMN connectivity measured before and during the N-back task predicted individual differences in self-reported inattentiveness, but this association was not found during the post-task resting state. Together, these findings have important implications for models of how the brain recovers following effortful cognition, as well as for experimental designs using resting and task scans.
Semibatch Hydrothermal Hydrolysis of Cellulose in a Filter Paper by Dilute Organic Acids (2015)

Cellulose in a filter paper is hydrolyzed by six dilute organic acids (0.01–1 wt %) under hydrothermal conditions (260 °C and 5 MPa) using a semibatch reactor. The rate of degradation increases with an increase in the concentration of the acid. The cellulose sample is completely degraded by the acids (1 wt %) in 60 min. While the yields of the different products are dependent on the nature of the organic acid used, cellulose is essentially converted to mono- and oligosaccharides, with glucose as the major product. The observed increase in the rate of degradation in the presence of formic or citric acid at 1 wt % allows for the degradation of the cellulose sample in a short time (20 min) and results in the highest yield of glucose (approximately 60%) observed in this study. The rate of conversion of the cellulose sample to glucose correlates directly with [H+].
Eine neue Methode der Knochensterilisation - A New Technique for Bone Sterilization (1989)

Bone transplantation is associated with two major problems: the sterility in particular with respect to HIV, and the osteoinductivity of the transplant. We describe a procedure which sterilizes the graft while keeping the osteoinductive potential of the bone. After harvesting the material the bone is immediately deep frozen (-80 degrees C), and then freeze dried. To sterilize the bone it is treated with gamma-radiation at a dose of 2.5 Mrad in an argon atmosphere. All grafts are subsequently stored in argon at -80 degrees C.
Peptide Nucleic Acids (PNAs) as Diagnostic Devices for Genetic and Cytogenetic Analysis (2008)

The peptide nucleic acids (PNAs) constitute a remarkable new class of synthetic nucleic acids analogs, based on peptide-like backbone. This structure gives to PNAs the capacity to hybridize with high affinity and specificity to complementary RNA and DNA sequences, and a great resistance to nucleases and proteinases. Originally conceived as ligands for the study of double stranded DNA, the unique physico-chemical properties of PNAs have led to the development of a large variety of research and diagnostic assays in the field of genetics, including genome mapping and mutation detection. Over the last few years, the use of PNAs has also proven its powerful usefulness in cytogenetics for the rapid in situ identification of human chromosomes and the detection of aneuploidies. Recent studies have reported the successful use of chromosome-specific PNA probes on human lymphocytes, amniocytes, spermatozoa as well as on isolated oocytes and blastomeres. Multicolor peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) protocols have been described for the identification of several human chromosomes, indicating that PNAs could become a powerful tool for in situ chromosomal investigation.
FKHR Binds the Insulin Response Element in the Insulin-Like Growth Factor Binding Protein-1 Promoter (1999)

The insulin response element (IRE) in the IGFBP-1 promoter, and in other gene promoters, contains a T(A/G)TTT motif essential for insulin inhibition of transcription.Studies presented here test whether FKHR may be the transcription factor that confers insulin inhibition through this IRE motif.Immunoblots using antiserum to the synthetic peptide FKHR 413-430 , RNase protection, and Northerns blots show that FKHR is expressed in HEP G2 human hepatoma cells.Southwestern blots, electromobility shift assays, and DNase I protection assays show that Escherichia coli-expressed GST-FKHR binds specifically to IREs from the IGFBP-1, PEPCK and TAT genes; how-ever, unlike HNF3, another protein proposed to be the insulin regulated factor, GST-FKHR does not bind the insulin unresponsive G/C-A/C mutation of the IGFBP-1 IRE.When HEP G2 cells were cotransfected with FKHR expression vectors and with IGFBP-1 promoter plasmids containing either native or mutant IREs, FKHR expression induced a 5-fold increase in activity of the native IGFBP-1 promoter but no increase in activity of promoter constructs containing insulin unresponsive IRE mutants.These data suggest that FKHR, and/or a related family member, is the important T(G/A)TTT binding protein that confers the inhibitory effect of insulin on gene transcription.
Development and application of in vivo molecular traps reveals that dynein light chain occupancy differentially affects dynein-mediated processes (2010)

The ability to rapidly and specifically regulate protein activity combined with in vivo functional assays and/or imaging can provide unique insight into underlying molecular processes. Here we describe the application of chemically induced dimerization of FKBP to create nearly instantaneous high-affinity bivalent ligands capable of sequestering cellular targets from their endogenous partners. We demonstrate the specificity and efficacy of these inducible, dimeric "traps" for the dynein light chains LC8 (Dynll1) and TcTex1 (Dynlt1). Both light chains can simultaneously bind at adjacent sites of dynein intermediate chain at the base of the dynein motor complex, yet their specific function with respect to the dynein motor or other interacting proteins has been difficult to dissect. Using these traps in cultured mammalian cells, we observed that induction of dimerization of either the LC8 or TcTex1 trap rapidly disrupted early endosomal and lysosomal organization. Dimerization of either trap also disrupted Golgi organization, but at a substantially slower rate. Using either trap, the time course for disruption of each organelle was similar, suggesting a common regulatory mechanism. However, despite the essential role of dynein in cell division, neither trap had a discernable effect on mitotic progression. Taken together, these studies suggest that LC occupancy of the dynein motor complex directly affects some, but not all, dynein-mediated processes. Although the described traps offer a method for rapid inhibition of dynein function, the design principle can be extended to other molecular complexes for in vivo studies.
Individuality and variation in gene expression patterns in human blood (2003)

The nature and extent of interindividual and temporal variation in gene expression patterns in specific cells and tissues is an important and relatively unexplored issue in human biology. We surveyed variation in gene expression patterns in peripheral blood from 75 healthy volunteers by using cDNA microarrays. Characterization of the variation in gene expression in healthy tissue is an essential foundation for the recognition and interpretation of the changes in these patterns associated with infections and other diseases, and peripheral blood was selected because it is a uniquely accessible tissue in which to examine this variation in patients or healthy volunteers in a clinical setting. Specific features of interindividual variation in gene expression patterns in peripheral blood could be traced to variation in the relative proportions of specific blood cell subsets; other features were correlated with gender, age, and the time of day at which the sample was taken. An analysis of multiple sequential samples from the same individuals allowed us to discern donor-specific patterns of gene expression. These data help to define human individuality and provide a database with which disease-associated gene expression patterns can be compared.
Surface impact of seeded jets at relatively large background densities (1985)

The large inertia of heavy molecules suspended in a light carrier gas is exploited in the impingement of seeded free jets against surfaces at near-continuum conditions. It emerges that the kinetic energy at impact can be close to the free stream convective kinetic energy, even at near-continuum densities, i.e., at Knudsen numbers of 10−2 or less. Thus, one can simulate collision energies previously obtained only under molecular beam conditions but with the much higher flux densities characteristic of free jets upstream of the transition to free-molecule flow. The principal design parameter in such ‘‘high density seeded free jet’’ experiments is the heavy molecule Knudsen number, analogous to the Stokes number governing the inertial impaction of aerosol particles. When the ratio of masses mp/m for the heavy and the light gases is large, the interspecies transfer of momentum and energy is rather slow, and the Stokes number is of the order of mp/m times larger than the light gas Knudsen number. Thus, there is a region in which the light gas still behaves as a continuum fluid while the heavy component penetrates through it under effectively free-molecular conditions. A hydrodynamic theory capable of predicting the distribution of impact energies for such free jets impinging on solid objects at Stokes numbers of order unity is developed.
Genetic dissection of the budding yeast Arp2/3 complex: A comparison of the in vivo and structural roles of individual subunits (1999)

In previous work, we identified the yeast Arp2/3 complex, which localizes to cortical actin patches and is required for their motility and integrity in vivo. This complex contains proteins homologous to each subunit of the Acanthamoeba and human Arp2/3 complex except for a 40-kDa subunit (p40), which was missing from the purified yeast complex. Here, we demonstrate by using immunoprecipitation and gel-filtration analysis that Arc40p, the homolog of p40 identified from the yeast genome database, associates with the yeast Arp2/3 complex. We have carried out gene disruptions of each subunit of the yeast Arp2/3 complex to study each subunit's role in the function of the complex. Surprisingly, we find that only ARC40 is fully essential for cell viability. Strains lacking each of the other subunits exhibit varying degrees of defects in cell growth and viability and in assembly and polarization of cortical actin patches. We have also examined each subunit's role in maintaining the structural integrity of the Arp2/3 complex. Arp2p, Arp3p, and Arc40p fall into the monomer pool in Deltaarc19 and Deltaarc35 cells, suggesting that Arc19p and Arc35p are the central scaffolding components of the complex. Arp2p and Arp3p do not have major roles in maintaining complex integrity, and Arc15p is required for association of Arp2p and Arc40p, but not other subunits, with the complex. These results provide evidence that each subunit contributes differently to the assembly and function of the Arp2/3 complex.
Compressed sensing with sequential observations (2008)

Compressed sensing allows perfect recovery of sparse signals (or signals sparse in some basis) using only a small number of measurements. The results in the literature have focused on the asymptotics of how many samples are required and the probability of making an error for & fixed batch of samples. We investigate an alternative scenario where observations are available in sequence and can be stopped as soon as there is reasonable certainty of correct reconstruction. This approach does not require knowing how sparse is the signal, and allows reconstruction using the smallest number of samples. Central to our sequential approach is the stopping rule. For the random Gaussian ensemble we show that a simple stopping rule gives the absolute minimum number of observations required for exact recovery, with probability one. However, for other ensembles like Bernoulli or Fourier, this is no longer true, and the rule is modified to trade off delay in stopping and probability of error. We also consider near-sparse signals and describe how to estimate the reconstruction error from the sequence of solutions. This enables stopping once the error falls below a desired tolerance. Our sequential approach to compressed sensing involves a sequence of linear programs, and we outline how such a sequence can be solved efficiently.
CdSe Quantum Dot Sensitized Solar Cells. Shuttling Electrons Through Stacked Carbon Nanocups (2009)

The charge separation between excited CdSe semiconductor quantum dots and stacked-cup carbon nanotubes (SCCNTs) has been successfully tapped to generate photocurrent in a quantum dot sensitized solar cell (QDSC). By employing an electrophoretic deposition technique we have cast SCCNT-CdSe composite films on optically transparent electrodes (OTEs). The quenching of CdSe emission, as well as transient absorption measurements, confirms ultrafast electron transfer to SCCNTs. The rate constant for electron transfer increases from 9.51 x 10(9) s(-1) to 7.04 x 10(10) s(-1) as we decrease the size of CdSe nanoparticles from 4.5 to 3 nm. The ability of SCCNTs to collect and transport electrons from excited CdSe has been established from photocurrent measurements. The morphological and excited state properties of SCCNT-CdSe composites demonstrate their usefulness in energy conversion devices.
Biology of Progressive, Castration-Resistant Prostate Cancer: Directed Therapies Targeting the Androgen-Receptor Signaling Axis (2005)

Prostate cancers that are progressing on medical and surgical therapies designed to ablate the action of androgens continue to express androgen receptor (AR) and to depend on signaling through the receptor for growth. A more clinically relevant classification of castration-resistant disease focuses on the mechanisms of receptor activation, which include (1) changes in the level of ligand(s) in tumor tissue; (2) increased levels of the protein due to gene amplification or altered mRNA expression; (3) activating mutations in the receptor that affect structure and function; (4) changes in coregulatory molecules including coactivators and corepressors; and (5) factors that lead to activation of the receptor independent of the level of ligand or receptor allowing kinase cross talk. From an AR perspective, the term "hormone refractory" is inappropriate. On the basis of this schema, we discuss strategies that are focused on the AR either directly or indirectly, as single agents or in combination, that are in clinical development.
MicroRNA regulation of the CUC genes is required for boundary size control inArabidopsismeristems (2004)

We have analysed the role of a microRNA, miR164, in boundary formation during organ initiation from Arabidopsis meristems. The establishment and maintenance of the boundary domain are controlled by three partially redundant genes, CUP-SHAPED COTYLEDON1 (CUC1), CUC2 and CUC3. We show that miR164 overexpression phenocopies the cuc1 cuc2 double mutant by inducing post-transcriptional downregulation of CUC1 and CUC2 but not CUC3 mRNA levels. Disruption of CUC2 regulation by miR164, either by making CUC2 resistant to the miRNA or by reducing miRNA levels leads to similar enlarged boundary domains. We relate this enlargement to the division patterns of the boundary cells. We propose that miR164 constrains the expansion of the boundary domain, by degrading CUC1 and CUC2 mRNAs.
Molecular recognition and binding of thermal hysteresis proteins to ice (2000)

Molecular recognition and binding are two very important processes in virtually all biological and chemical processes. An extremely interesting system involving recognition and binding is that of thermal hysteresis proteins at the ice-water interface. These proteins are of great scientific interest because of their antifreeze activity. Certain fish, insects and plants living in cold weather regions are known to generate these proteins for survival. A detailed molecular understanding of how these proteins work could assist in developing synthetic analogs for use in industry. Although the shapes of these proteins vary from completely alpha-helical to globular, they perform the same function. It is the shapes of these proteins that control their recognition and binding to a specific face of ice. Thermal hysteresis proteins modify the morphology of the ice crystal, thereby depressing the freezing point. Currently there are three hypotheses proposed with respect to the antifreeze activity of thermal hysteresis proteins. From structure-function experiments, ice etching experiments, X-ray structures and computer modeling at the ice-vacuum interface, the first recognition and binding hypothesis was proposed and stated that a lattice match of the ice oxygens with hydrogen-bonding groups on the proteins was important. Additional mutagenesis experiments and computer simulations have lead to the second hypothesis, which asserted that the hydrophobic portion of the amphiphilic helix of the type I thermal hysteresis proteins accumulates at the ice-water interface. A third hypothesis, also based on mutagenesis experiments and computer simulations, suggests that the thermal hysteresis proteins accumulate in the ice-water interface and actually influence the specific ice plane to which the thermal hysteresis protein ultimately binds. The first two hypotheses emphasize the aspect of the protein 'binding or accumulating' to specific faces of ice, while the third suggests that the protein assists in the development of the binding site. Our modeling and analysis supports the third hypothesis, however, the first two cannot be completely ruled out at this time. The objective of this paper is to review the computational and experimental efforts during the past 20 years to elucidate the recognition and binding of thermal hysteresis proteins at the ice-vacuum and ice-water interface.
A Shared Transcription Termination Signal on Negative and Ambisense RNA Genome Segments of Rift Valley Fever, Sandfly Fever Sicilian, and Toscana Viruses (2007)

The Phlebovirus genus (family Bunyaviridae) is composed of a diverse group of arboviruses that cause disease syndromes ranging from mild febrile illness to hemorrhagic fever with high fatality. Although antigenically similar, these viruses differ by approximately 25% at the genome level, and their ecologies, including geographic ranges, preferred vector species, and hosts, vary considerably. In contrast to other ambisense viruses, where RNA hairpin structures which serve as transcription termination signals are frequently found separating the opposite-sense open reading frames, no evidence of predicted high-energy hairpin structures was found at the ambisense junctions of phlebovirus S RNA segments. However, a conserved sequence motif was identified on both negative and ambisense genome segments that functions as a transcription termination signal for the N, NSs, and GPC mRNAs in three diverse phleboviruses, namely, Rift Valley fever, sandfly Sicilian, and Toscana viruses. The exact termination of nascent virus mRNA molecules was determined by 3' rapid amplification of cDNA ends. Surprisingly, analysis of the termini of mRNAs from both S and M segments of these three viruses revealed that transcription termination occurred immediately upstream of a conserved sequence motif with the general features 3'-C(1-3)GUCG/A-5'. In contrast, no corresponding sequence motif was found in the L segments, and analysis indicated a "runoff" transcript approach to L mRNA termination. The absolute requirement of the identified transcription termination motif was demonstrated by using a highly efficient Rift Valley fever virus reverse genetics system to generate live recombinant viruses with S segments lacking the termination signal motif for the NP or NSs mRNA and showing that these recombinant viruses generated mRNAs that failed to terminate correctly.
Requirements for Budding of Paramyxovirus Simian Virus 5 Virus-Like Particles (2002)

Enveloped viruses are released from infected cells after coalescence of viral components at cellular membranes and budding of membranes to release particles. For some negative-strand RNA viruses (e.g., vesicular stomatitis virus and Ebola virus), the viral matrix (M) protein contains all of the information needed for budding, since virus-like particles (VLPs) are efficiently released from cells when the M protein is expressed from cDNA. To investigate the requirements for budding of the paramyxovirus simian virus 5 (SV5), its M protein was expressed in mammalian cells, and it was found that SV5 M protein alone could not induce vesicle budding and was not secreted from cells. Coexpression of M protein with the viral hemagglutinin-neuraminidase (HN) or fusion (F) glycoproteins also failed to result in significant VLP release. It was found that M protein in the form of VLPs was only secreted from cells, with an efficiency comparable to authentic virus budding, when M protein was coexpressed with one of the two glycoproteins, HN or F, together with the nucleocapsid (NP) protein. The VLPs appeared similar morphologically to authentic virions by electron microscopy. CsCl density gradient centrifugation indicated that almost all of the NP protein in the cells had assembled into nucleocapsid-like structures. Deletion of the F and HN cytoplasmic tails indicated an important role of these cytoplasmic tails in VLP budding. Furthermore, truncation of the HN cytoplasmic tail was found to be inhibitory toward budding, since it prevented coexpressed wild-type (wt) F protein from directing VLP budding. Conversely, truncation of the F protein cytoplasmic tail was not inhibitory and did not affect the ability of coexpressed wt HN protein to direct the budding of particles. Taken together, these data suggest that multiple viral components, including assembled nucleocapsids, have important roles in the paramyxovirus budding process.