gebhart/patrepeval huggingface dataset:
Delivering CRISPR: a review of the challenges and approaches (2018)

Gene therapy has long held promise to correct a variety of human diseases and defects. Discovery of the Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR), the mechanism of the CRISPR-based prokaryotic adaptive immune system (CRISPR-associated system, Cas), and its repurposing into a potent gene editing tool has revolutionized the field of molecular biology and generated excitement for new and improved gene therapies. Additionally, the simplicity and flexibility of the CRISPR/Cas9 site-specific nuclease system has led to its widespread use in many biological research areas including development of model cell lines, discovering mechanisms of disease, identifying disease targets, development of transgene animals and plants, and transcriptional modulation. In this review, we present the brief history and basic mechanisms of the CRISPR/Cas9 system and its predecessors (ZFNs and TALENs), lessons learned from past human gene therapy efforts, and recent modifications of CRISPR/Cas9 to provide functions beyond gene editing. We introduce several factors that influence CRISPR/Cas9 efficacy which must be addressed before effective in vivo human gene therapy can be realized. The focus then turns to the most difficult barrier to potential in vivo use of CRISPR/Cas9, delivery. We detail the various cargos and delivery vehicles reported for CRISPR/Cas9, including physical delivery methods (e.g. microinjection; electroporation), viral delivery methods (e.g. adeno-associated virus (AAV); full-sized adenovirus and lentivirus), and non-viral delivery methods (e.g. liposomes; polyplexes; gold particles), and discuss their relative merits. We also examine several technologies that, while not currently reported for CRISPR/Cas9 delivery, appear to have promise in this field. The therapeutic potential of CRISPR/Cas9 is vast and will only increase as the technology and its delivery improves.
Advancing the Oxygen Generation Assembly Design to Increase Reliability and Reduce Costs for a Future Long Duration Mission (2015)

Bellevue, Washington
Design and Synthesis of C-Ring Lactone- and Lactam-Based Podophyllotoxin Analogues as Anticancer Agents (2010)

A series of novel podophyllotoxin (PDT) analogues was synthesized in which the lactone moiety was shifted to C ring. Some of the derivatives were also synthesized with modified A ring. Analogues 23 and 25 exhibited potent in vitro cytotoxicity against colon cancer (CaCO(2)) cell line. p-Demethylated E-ring analogues exhibited better potency than the corresponding methylated analogues. These analogues showed toxicity comparable to PDT against human erythrocytes albeit at much higher concentrations (100 microg/ml) than their cytotoxicity values.
Influence of electrical axis of stimulation on excitation of cardiac muscle cells. (1991)

Orthogonal sequential shock can defibrillate the heart with greater efficacy compared with single shock defibrillation. In this study we tested the hypothesis that cardiac cells have a preferred orientation in their response to excitatory extracellular electric fields, so that orthogonal shocks may stimulate distinct populations of cells. A micropaddle electrode system was used to deliver rectangular pulses for extracellular field stimulation of individual heart cells. We found that single frog and guinea pig ventricular myocytes are excitable with rectangular pulse field stimulation over a wide range of pulse durations, ranging from 10 msec to as little as 20 microseconds. The excitation field strength varies inversely with pulse duration as described by the Weiss-Lapicque equation, although the frog myocytes show a significant "notch" at pulse durations of approximately 1-2 msec, and the guinea pig myocytes are more excitable than predicted for pulse durations of less than 0.2 msec. Every myocyte tested was more excitable when the long axis of the cell was oriented parallel to the stimulating field than when perpendicular to the field. For 2-msec pulses, the difference in field strength was a factor of 5.8 +/- 2.0 (n = 30) for frog and 2.6 +/- 0.5 (n = 23) for guinea pig myocytes. Complete excitation strength-duration curves were obtained in seven frog and 14 guinea pig cells for both parallel and perpendicular cell orientations.(ABSTRACT TRUNCATED AT 250 WORDS)
Chemistry and technology of 2‐alkenyl azlactones (2001)

Abstract The chronology of 2‐alkenyl azlactone research at 3M is discussed in terms of its origination; consideration of economics, overall safety, and opportunities for patent protection; elaboration of the chemistry; and, finally, applying lessons learned toward the development of commercial technologies. The chemistry is dominated by the presence of three electrophilic reaction centers and a readily polymerizable 2‐alkenyl group. Technological development has been focused in four general areas: acrylamide monomers, acrylamide materials, azlactone materials, and polymer modification. Application areas disinclude lithographic printing plates, contact lens materials, adhesives, dispersants for printing inks, and supports for immobilizing enzymes. © 2001 John Wiley &amp; Sons, Inc. J Polym Sci Part A: Polym Chem 39: 3655–3677, 2001
New Scalable Decoder Architectures for Reed–Solomon Codes (2015)

In this paper, we devise new scalable decoder architectures for Reed-Solomon (RS) codes, comprising three parts: error-only decoding, error-erasure decoding, and their decoding for singly extended RS codes. New error-only decoders are devised through algorithmic transformations of the inversionless Berlekamp-Massey algorithm (IBMA). We first generalize the Horiguchi-Koetter formula to evaluate error magnitudes using the error locator polynomial Λ(x) and the auxiliary polynomial B(x) produced by IBMA, which effectively eliminates the computation of error evaluator polynomial. We next devise an enhanced parallel inversionless Berlekamp-Massey algorithm (ePIBMA) that effectively takes advantage of the generalized Horiguchi-Koetter formula. The derivative ePIBMA architecture requires only 2t + 1 (t denotes the error correction capability) systolic cells, in contrast with 3t or more cells of the existing regular architectures based on IBMA or the Euclidean algorithm. Moreover, it may literally function as a linear-feedback-shift-register encoder. New error-erasure decoders are devised through algorithmic transformations of the inversionless Blahut algorithm (IBA). The proposed split parallel inversionless Blahut algorithm (SPIBA) yields merely 2t + 1 systolic cells, which is the same number as the error-only decoder ePIBMA. The task is partitioned into two separate steps, computing the complementary errorerasure evaluator polynomial followed by computing error-erasure locator polynomial, both utilizing SPIBA. Surprisingly, it has exactly the same number of cells and literally the same complexity and throughput as the proposed error-only decoder architecture ePIBMA; it employs 33% less hardware and at the same time achieves more than twice faster throughput, than the serial architecture IBA. we further propose a unified parallel inversionless Blahut algorithm (UPIBA) by incorporating the key virtues of the error-only decoder ePIBMA into SPIBA. The complexity and throughput of the rderivative UPIBA architecture are literally the same as ePIBMA and SPIBA, while performing almost equally efficiently as ePIBMA on error-only decoding and as SPIBA on error-erasure decoding. UPIBA also inherits the dynamic power saving feature of ePIBMA and SPIBA. Indeed, UPIBA renders highly attractive for on-the-fly implementation of error-erasure decoding. We finally demonstrate that the proposed decoders, i.e., ePIBMA, SPIBA, and UPIBA, can be magically migrated to decode singly extended RS codes, with negligible add-ons, except that an extra multiplexer is added to their critical paths. To the author's best knowledge, this is the first time that a high-throughput decoder for singly extended RS codes is explored.
Broadcast Authentication with Practically Unbounded One-way Chains (2008)

A protocol for assuring the authenticity of information broadcasted over long periods of time is proposed. The protocol is based on time synchronization and uses one-way chains constructed with the squaring function which gives the possibility to construct a one-way chain of whose length is unbounded in practice. Although the computational cost is somewhat increased, compared to the use of hash chains, these computational requirements are affordable for the addressed scenario. In brief, the protocol assures information authenticity at the reduced cost of almost one modular multiplication for each broadcasted packet. Time synchronization issues are discussed and the security of the protocol is equivalent to the integer factorization problem since the squaring function is used in the construction of the one-way chain. A failure mode analysis of the protocol is done; this is an aspect of novelty and applies to other protocols based on time synchronization as well. Also, a formal proof on the security of the protocol is sketched.
Rat liver UDP-glucuronosyltransferase. cDNA sequence and expression of a form glucuronidating 3-hydroxyandrogens. (1986)

A cDNA clone, pUDPGTr-4, encoding a form of rat UDP-glucuronosyltransferase has been isolated from a SV40 expression library. Sequence analysis revealed that the cDNA is 1970 base pairs in length and encodes a protein of 530 amino acids, which has amino- and carboxyl-terminal sequences characteristic of signal peptide and transmembrane segments, respectively. There is one potential asparagine-linked glycosylation site. Transfection of UDPGTr-4 cDNA into COS cells resulted in the glucuronidation of etiocholanolone, androsterone, and lithocholic acid in a transient expression assay. Several other common substrates of UDP-glucuronosyltransferase were not conjugated by the UDPGTr-4 enzyme. UDPGTr-4 cDNA is identical in sequence over a common 1.7 kilobase-region of overlap to UDPGTr-1, a cDNA previously isolated in this laboratory (Mackenzie, P. I., Gonzalez, F. J., and Owens, I. S. (1984) J. Biol. Chem. 259, 12153-12160). UDPGTr-4 cDNA, however, contains a shorter 3'-untranslated region. Northern analysis showed that the poly(A) RNA counterparts of UDPGTr-4 and UDPGTr-1 cDNAs are approximately 2.3 and 3.0 kilobases in length, respectively. The steady-state level of UDPGTr-4 poly(A) RNA in the liver is 20-fold higher than that of UDPGTr-1 poly(A) RNA. These data indicate that the UDPGTr-4 enzyme is a 3-hydroxyandrogen UDP-glucuronosyltransferase which is encoded by two distinct species of mRNA transcribed from the same gene.
Single-frame measurement of the complete spatiotemporal intensity and phase of ultrashort laser pulses using wavelength-multiplexed digital holography (2008)

We show that a simple (few-element) arrangement for wavelength-multiplexed digital holography allows the measurement of the electric field E(x,y,t) of a femtosecond laser pulse on a single shot. A slightly rotated two-dimensional diffractive optical element and a variable-wavelength filter together generate multiple spectrally resolved digital holograms that are simultaneously captured in a single frame by a digital camera. An additional simultaneous measurement of the spectral phase for a spatially filtered replica of the pulse with frequency-resolved optical gating completes this three-dimensional measurement. An experimental implementation of the technique is presented and its current limitations are discussed.
Multiple Proline Substitutions Cumulatively Thermostabilize Bacillus Cereus ATCC7064 Oligo‐1,6‐Glucosidase (1994)

Nine residues of Bacillus cereus ATCC7064 oligo-1,6-glucosidase were replaced stepwise with proline residues. Of the nine residues, Lys121, Glu208 and Glu290 were at second sites of beta turns; Asn109, Glu175 and Thr261 were at N-caps of alpha helices; Glu216, Glu270 and Glu378 were in coils within loops. The replacements were carried out in the order, Lys121-->Pro, Glu175-->Pro, Glu290-->Pro, Glu208-->Pro, Glu270-->Pro, Glu378-->Pro, Thr261-->Pro, Glu216-->Pro and Asn109-->Pro. The resultant nine active mutant enzymes contained 1-9 more proline residues than B. cereus oligo-1,6-glucosidase. The thermostability of these mutants was additively enhanced with the increase in the number of proline residues introduced. The increase in the thermostability was most remarkable when proline residues were introduced at second sites of beta turns or at N-caps of alpha helices. The above results afforded irrefragable proof for the proline rule as an effective principle for increasing protein thermostability [Suzuki, Y., Oishi, K., Nakano, H. & Nagayama, T. (1987) Appl. Microbiol. Biotechnol. 26, 546-551].
The Role of Growth Hormone, Insulin-Like Growth Factor and Somatostatin in Diabetic Retinopathy (2006)

Growth hormone (GH) and insulin-like growth factor-I (IGF-I) are implicated in the aberrant cell growth and pathological neovascularization that characterises proliferative diabetic retinopathy. While serum levels of IGF-I are reported to be either high or low in diabetic patients, there is evidence that local tissue levels of IGF-I may be more relevant to diabetic retinal pathology. IGF-I and IGF binding proteins (IGFBP) are expressed throughout the retina in vascular, neuronal and glial cells, and are altered in response to hyperglycaemia and hypoxia. Further support for a pathological role for local IGF-I comes from studies showing IGF-I to be increased in the vitreal fluids of patients with proliferative diabetic retinopathy. IGF-I may exert its cell growth promoting properties by stimulating a number of pathways including protein-kinase B (Akt), nuclear factor kB (NF-kappaB)/AP-1 and hypoxic-inducible factor-1alpha (HIF-1alpha). In addition, other growth factors may participate in IGF-I induced cell growth including vascular endothelial growth factor (VEGF), platelet derived growth factor (PDGF) and fibroblast growth factor (FGF). The importance of the GH/IGF system in diabetic retinopathy and retinal neovascularization has been highlighted by the use of agents that inhibit the system. GH receptor antagonists, GH receptor antisense oligonucleotides, somatostatin analogues and receptor neutralising antibodies to IGF-I reduce hypoxic-induced retinal neovascularization. These approaches may also prove to have benefits for improving vascular patency and vision in patients with diabetic retinopathy.
Characterization of the adherence of normal and leukemic CD34+ cells to endothelial monolayers. (1994)

The capacity of normal CD34+ marrow cells and CD34+ leukemic cell lines to adhere to human umbilical vein endothelial cells has been examined. Such interactions have importance since the processes of homing and egress within the marrow microenvironment involve the traverse of sinusoidal endothelium. Umbilical vein endothelial monolayers expressed CD44 and CD54 constitutively, and expression of both E-selectin (ELAM) and vascular cell adhesion molecule-1 (VCAM-1) were inducible with interleukin-1 (IL-1) alpha and beta and tumor necrosis factor (TNF). CD34+ marrow cells bound to unstimulated endothelial layers (33 vs. 16% to plastic), and their adhesion was significantly increased in the presence of IL-1 or TNF. This increased adhesion was not inhibited by functionally blocking antibodies to E-selectin or to CD54 but was partially inhibited by antibodies to VCAM. CD34+ KG1a cells also bound to endothelial monolayers (33 vs. 8% to plastic), and such adhesion was also upregulated by pretreatment of the endothelial cells with IL-1 or TNF. In contrast to normal CD34+ cells, this increased adhesion was inhibited by antibodies to E-selectin but not to VCAM. These findings indicate that adhesion of both normal CD34+ cells and leukemic blasts to endothelial cells can be upregulated by inflammatory mediators such as TNF and IL-1.
Ethanol and anaerobic conditions reversibly inhibit commercial cellulase activity in thermophilic simultaneous saccharification and fermentation (tSSF) (2012)

This work demonstrates a previously unrecognized incompatibility of enzymes secreted by an aerobic fungus with the fermentation conditions of an anaerobic bacterium and suggests that enzymes better suited to industrially relevant fermentation conditions would be valuable. The effects observed may be due to inactivation or starvation of oxygen dependent GH61 activity, and manipulation or replacement of this activity may provide an opportunity to improve biomass to fuel process efficiency.
ChemInform Abstract: BISHETEROCYCLES: PART IV. SYNTHESIS OF 1,1‐BIS(1,2,4‐TRIAZOLINE‐5‐THIONE‐3‐YL)ALKANES AND RELATED COMPOUNDS AS POTENTIAL PESTICIDES (1980)

Abstract Die Malonsäurehydrazide (I) reagieren mit den Isothiocyanaten (II) zu den Bis‐thiosemicarbaziden (III), von denen (IIIa)‐(IIIc) zu den Bis‐(thionotriazolyD‐alkanen (IV) cyclisiert werden.
A diffusible factor from normal retinal cells promotes rod photoreceptor survival in an in vitro model of retinitis pigmentosa (1999)

Transgenic mice expressing a dominant mutation in the gene for the phototransduction molecule rhodopsin undergo retinal degeneration similar to that experienced by patients with the retinal degenerative disease, retinitis pigmentosa (RP). Although the mutation is thought to cause photoreceptor degeneration in a cell-autonomous manner, the fact that rod photoreceptor degeneration is slowed in chimeric wild-type/mutant mice suggests that cellular interactions are also important for maintaining photoreceptor survival. To more fully characterize the nature of the cellular interactions important for rod degeneration in the RP mutant mice, we have used an in vitro approach. We found that when the retinas of the transgenic mice were isolated from the pigmented epithelium and cultured as explants, the rod photoreceptors underwent selective degeneration with a similar time course to that observed in vivo. This selective rod degeneration also occurred when the cells were dissociated and cultured as monolayers. These data indicate that the mutant rod photoreceptors degenerate when removed from their normal cellular relationships and without contact with the pigmented epithelium, thus confirming the relative cell autonomy of the mutant phenotype. We next tested whether normal retinal cells could rescue the mutant photoreceptors in a coculture paradigm. Coculture of transgenic mouse with wild-type mouse or rat retinal cells significantly enhanced transgenic rod photoreceptor survival; this survival-promoting activity was diffusible through a filter, was heat labile, and not present in transgenic retinal cells. Several peptide growth factors known to be present in the retina were tested as the potential survival-promoting molecule responsible for the effects of the conditioned medium; however, none of them promoted survival of the photoreceptors expressing the Pro23His mutant rhodopsin. Nevertheless, we were able to demonstrate that the mutant photoreceptors could be rescued by an antagonist to a retinoic acid receptor, suggesting that the endogeneous survival-promoting activity may function through this pathway. These data thus confirm and extend the findings of previous work that local trophic interactions are important in regulating rod photoreceptor degeneration in retinitis pigmentosa. A diffusible factor found in normal but not transgenic retinal cells has a protective effect on the survival of rod photoreceptors from Pro23His mutant rhodopsin mice. © 1999 John Wiley & Sons, Inc. J Neurobiol 39: 475–490, 1999
Variation in the effective richardson constant of metal—GaAs and Metal—InP contacts due to the effect of processing parameters (1993)

The value of experimental Richardson constant (A*) is found to be a function of metal film thickness, type of the metal, method of deposition, and condition of semiconductor prior to metal deposition. In the case of Al and W on GaAs, the value of A* is found higher than the theoretical value. However, as the film thickness increases, the value of A* decreases. The larger value of A* is related to electrically active defects at the interface produced during sputtering. Filament evaporation results in smaller values for A*. In the case of WSi0.6 the presence of Si affects the value of A*. For InP, the value of A* is found smaller than the theoretical value. For both GaAs and InP, the value of A* increases when the semiconductor is annealed prior to metal deposition. This increase is significant in the case of InP.
Fowlpox Virus Encodes Nonessential Homologs of Cellular Alpha-SNAP, PC-1, and an Orphan Human Homolog of a Secreted Nematode Protein (1998)

The genome of fowlpox virus (FWPV), type species of the Avipoxviridae, is considerably rearranged compared with that of vaccinia virus (the prototypic poxvirus and type species of the Orthopoxviridae) and is 30% larger. It is likely that the genome of FWPV contains genes in addition to those found in vaccinia virus, probably involved with its replication and survival in the chicken. A 7,470-bp segment of the FWPV genome has five open reading frames (ORFs), two of which encode ankyrin repeat proteins, many examples of which have been found in poxviruses. The remaining ORFs encode homologs of cellular genes not reported in any other virus. ORF-2 encodes a homolog of the yeast Sec17p and mammalian SNAP proteins, crucial to vesicular transport in the exocytic pathway. ORF-3 encodes a homolog of an orphan human protein, R31240_2, encoded on 19p13.2. ORF-3 is also homologous to three proteins (YLS2, YMV6, and C07B5.5) from the free-living nematode Caenorhabditis elegans and to a 43-kDa antigen from the parasitic nematode Trichinella spiralis. ORF-5 encodes a homolog of the mammalian plasma cell antigen PC-1, a type II glycoprotein with exophosphodiesterase activity. The ORFs are present in the virulent precursor, HP1, of the sequenced attenuated virus (FP9) and are conserved in other strains of FWPV. They were shown, by deletion mutagenesis, to be nonessential to virus replication in tissue culture. RNA encoding the viral homolog of PC-1 is expressed strongly early and late in infection, but RNAs encoding the homologs of SNAP and R31240_2 are expressed weakly and late.
Self‐gated cardiac cine MRI (2003)

The need for ECG gating presents many difficulties in cardiac magnetic resonance imaging (CMRI). Real-time imaging techniques eliminate the need for ECG gating in cine CMRI, but they cannot offer the spatial and temporal resolution provided by segmented acquisition techniques. Previous MR signal-based techniques have demonstrated an ability to provide cardiac gating information; however, these techniques result in decreased imaging efficiency. The purpose of this work was to develop a new "self-gated" (SG) acquisition technique that eliminates these efficiency deficits by extracting the motion synchronization signal directly from the same MR signals used for image reconstruction. Three separate strategies are proposed for deriving the SG signal from data acquired using radial k-space sampling: echo peak magnitude, kymogram, and 2D correlation. The SG techniques were performed on seven normal volunteers. A comparison of the results showed that they provided cine image series with no significant differences in image quality compared to that obtained with conventional ECG gating techniques. SG techniques represent an important practical advance in clinical MRI because they enable the acquisition of high temporal and spatial resolution cardiac cine images without the need for ECG gating and with no loss in imaging efficiency.