gebhart/patrepeval huggingface dataset:
Comparative investigation into formycin A and pyrazofurin A biosynthesis reveals branch pathways for the construction of C -nucleoside scaffolds (2019)

ABSTRACT Formycin A (FOR-A) and pyrazofurin A (PRF-A) are purine-related C -nucleoside antibiotics, in which ribose and a pyrazole-derived base are linked by a C -glycosidic bond, however, the logic underlying the biosynthesis of these molecules has remained largely unexplored. Here, we report the discovery of the pathways for FOR-A and PRF-A biosynthesis from diverse actinobacteria, and demonstrate that their biosynthesis is initiated by a lysine N 6 -monooxygenase. Moreover, we show that the forT and prfE (individually related to FOR-A and PRF-A biosynthesis) mutants are correspondingly capable of accumulating the unexpected pyrazole-related intermediates, compound 11 and 9a . We also decipher the enzymatic basis of ForT/PrfE for the C -glycosidic bond formation in FOR-A/PRF-A biosynthesis. To our knowledge, ForT/PrfE represents the first example of β-RFA-P (β-ribofuranosyl-aminobenzene 5’-phosphate) synthase-like enzymes governing C -nucleoside scaffold construction in natural product biosynthesis. These data establish a foundation for combinatorial biosynthesis of related purine nucleoside antibiotics, and also open the way for target-directed genome mining of PRF-A/FOR-A related antibiotics. IMPORTANCE Formycin A (FOR-A) and pyrazofurin A (PRF-A) are well known for their unusual chemical structures and remarkable biological activities. Actually, deciphering FOR-A/PRF-A biosynthesis will not only expand biochemical repertoire for novel enzymatic reactions, but also permit the target-oriented genome mining of FOR-A/PRF-A related C -nucleoside antibiotics.
A cochlear prosthesis: Further clinical observations; preliminary results of physiological studies (1973)

Abstract A series of simple psychoacoustic studies were conducted on three deaf patients with indwelling scala tympani electrodes to determine better what they hear as a consequence of electrical stimulation. Physiological experiments on cats implanted with a similar electrode were conducted to determine how the sensation heard by these patients is generated and encoded in the auditory nervous system. Some preliminary results of these animal experiments are described. Additional improvements in the surgical implantation procedure are detailed. Results of these studies suggest the following: 1. long‐term intracochlear implantation is technically feasible without unusual complications; 2. mechanical stability of the implant prosthesis has been improved by fixing the implant to the temporal bone with methyl methacrylate cement; 3. with simple periodic electrical stimuli the implanted patients described tonal sensation for frequencies ranging from about 100 Hz to more than 10 kHz; 4. apparent pitch changes rapidly as a function of stimulus frequency at frequencies below about 500 Hz; 5. subjects are able to identify many common environmental sounds and a few words, but conventional speech discrimination is poor; 6 . the sound sensation generated by electrical stimulation arises as a consequence of simultaneous excitation of a broad segment of the acoustic nerve; therefore, no “place” coding of the electrical stimuli occurs in the cochlea; 7. if no cochlear place coding occurs then tonal quality ascribed to sounds heard with electrical stimulation at low stimulus frequencies must be encoded by the temporal ordering of discharges in stimulated neurons.
Glycoproteins in the Sera of Oncological Patients (2019)

Vchodiska: Glykosylace je posttranslan modifikace, kter je zapojena do mnoha bio logickch proces a vznamn zasahuje i do dj spojench s ndorovou progres. Zmny glykanovch struktur na povrchu ndorovch bunk zpsoben alterujcmi hladinami exprese glykosyltransferz a glykosidz ovlivuj proliferaci, adhezi, migraci i bunnou signalizaci
Weighted optimization for multiobjective full-information control problems (2002)

We consider a nonlinear multiobjective full-information optimal control problem, where a controller is to be designed such that a number of constraints are to be satisfied for all possible disturbances. We show that, under certain continuity assumptions, such a controller exists if and only if, for every weighted combination of the constraints, there exists a controller satisfying the weighted constraint. Our analysis is based extensively on nonlinear H/sub /spl infin// dynamic programming methods.
Heterogeneous coarse-grained processing elements: a template architecture for embedded processing acceleration (2009)

Reconfigurable Architectures are good candidates for application accelerators that cannot be set in stone at production time. FPGAs however, often suffer from the area and performance penalty intrinsic in gate-level reconfigurability. To reduce this overhead, coarse-grained reconfigurable arrays (CGRAs) are reconfigurable at the ALU level, but a successful design needs more than computational power---the main bottleneck usually being memory transfers. Just like the integration of hardwired multiplier and memory blocks enabled FPGAs to efficiently implement digital signal processing applications, in this paper we study a customizable architecture template based on heterogeneous processing elements (multipliers, ALU clusters and memories) that provides enough flexibility to realize fast pipelined implementations of various loop kernels on a CGRA.
Control of microbial contamination in dental unit water systems using tetra-sodium EDTA (2009)

Inexpensive, effective and safe products for reducing the microbial load of water from DUWS are needed to meet ADA and other national guidelines. Tetra-sodium EDTA can significantly reduce microbial biofilms and bacterial counts in outflowing water, and is compatible for use in DUWS.
Derivation of Mesenchymal Stem Cells from Human Induced Pluripotent Stem Cells Cultured on Synthetic Substrates (2012)

Human-induced pluripotent stem cells (hiPSCs) may represent an ideal cell source for research and applications in regenerative medicine. However, standard culture conditions that depend on the use of undefined substrates and xenogeneic medium components represent a significant obstacle to clinical translation. Recently, we reported a defined culture system for human embryonic stem cells using a synthetic polymer coating, poly[2-(methacryloyloxy)ethyl dimethyl-(3-sulfopropyl)ammonium hydroxide] (PMEDSAH), in conjunction with xenogeneic-free culture medium. Here, we tested the hypothesis that iPSCs could be maintained in an undifferentiated state in this xeno-free culture system and subsequently be differentiated into mesenchymal stem cells (iPS-MSCs). hiPSCs were cultured on PMEDSAH and differentiated into functional MSCs, as confirmed by expression of characteristic MSC markers (CD166+, CD105+, CD90+,CD73+, CD31-, CD34-, and CD45-) and their ability to differentiate in vitro into adipogenic, chondrogenic, and osteoblastic lineages. To demonstrate the potential of iPS-MSCs to regenerate bone in vivo, the newly derived cells were induced to osteoblast differentiation for 4 days and transplanted into calvaria defects in immunocompromised mice for 8 weeks. MicroCT and histologic analyses demonstrated de novo bone formation in the calvaria defects for animals treated with iPS-MSCs but not for the control group. Moreover, positive staining for human nuclear antigen and human mitochondria monoclonal antibodies confirmed the participation of the transplanted hiPS-MSCs in the regenerated bone. These results demonstrate that hiPSCs cultured in a xeno-free system have the capability to differentiate into functional MSCs with the ability to form bone in vivo.
Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of nsp5 Main Protease (2021)

Summary The coronavirus 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), spread around the world with unprecedented health and socio-economic effects for the global population. While different vaccines are now being made available, very few antiviral drugs have been approved. The main viral protease (nsp5) of SARS-CoV-2 provides an excellent target for antivirals, due to its essential and conserved function in the viral replication cycle. We have expressed, purified and developed assays for nsp5 protease activity. We screened the nsp5 protease against a custom chemical library of over 5,000 characterised pharmaceuticals. We identified calpain inhibitor I and three different peptidyl fluoromethylketones (FMK) as inhibitors of nsp5 activity in vitro , with IC 50 values in the low micromolar range. By altering the sequence of our peptidomimetic FMK inhibitors to better mimic the substrate sequence of nsp5, we generated an inhibitor with a subnanomolar IC 50 . Calpain inhibitor I inhibited viral infection in monkey-derived Vero E6 cells, with an EC50 in the low micromolar range. The most potent and commercially available peptidyl-FMK compound inhibited viral growth in Vero E6 cells to some extent, while our custom peptidyl FMK inhibitor offered a marked antiviral improvement.
Noise-induced transitions in spatially distributed and coupled pendulums (1997)

We observe two classes of nonequilibrium noise-induced transitions in two-dimensional nearest-neighbor coupled pendulums. One is characterized by the drastic change of the shape of the stationary probability density and the other by the symmetry-breaking order parameter. The corresponding mechanisms are proposed. The nature of each transition is discussed. The cooperative effect of the two phenomena is presented. The mean-field results are consistent with the ones from the numerical calculations.
Crucial Role of Antibodies to Pertactin inBordetella pertussisImmunity (2003)

Pertussis, a serious infectious disease of the respiratory tract caused by Bordetella pertussis, is reemerging in vaccinated populations. Efforts to curtail this disease are hampered by limited insight into the basis of protective immunity. Opsonophagocytosis was recently found to play a central role in cellular bactericidal activity against B. pertussis. In the present study, we studied the specificity of opsonic antibodies. Anti-pertactin antibodies, but not anti-pertussis toxin, anti-fimbriae, or anti-filamentous hemagglutinin antibodies, were found to be crucial for B. pertussis phagocytosis. These data are consistent with field studies showing that levels of antibodies to pertactin correlate with protection.
Dissecting ribosomal particles throughout the kingdoms of life using advanced hybrid mass spectrometry methods (2018)

Biomolecular mass spectrometry has matured strongly over the past decades and has now reached a stage where it can provide deep insights into the structure and composition of large cellular assemblies. Here, we describe a three-tiered hybrid mass spectrometry approach that enables the dissection of macromolecular complexes in order to complement structural studies. To demonstrate the capabilities of the approach, we investigate ribosomes, large ribonucleoprotein particles consisting of a multitude of protein and RNA subunits. We identify sites of sequence processing, protein post-translational modifications, and the assembly and stoichiometry of individual ribosomal proteins in four distinct ribosomal particles of bacterial, plant and human origin. Amongst others, we report extensive cysteine methylation in the zinc finger domain of the human S27 protein, the heptameric stoichiometry of the chloroplastic stalk complex, the heterogeneous composition of human 40S ribosomal subunits and their association to the CrPV, and HCV internal ribosome entry site RNAs.
Epigenetic Regulation of Tumor Necrosis Factor Alpha (2007)

Tumor necrosis factor alpha (TNF-alpha) is a potent cytokine which regulates inflammation via the induction of adhesion molecules and chemokine expression. Its expression is known to be regulated in a complex manner with transcription, message turnover, message splicing, translation, and protein cleavage from the cell surface all being independently regulated. This study examined both cell lines and primary cells to understand the developmental regulation of epigenetic changes at the TNF-alpha locus. We demonstrate that epigenetic modifications of the TNF-alpha locus occur both developmentally and in response to acute stimulation and, importantly, that they actively regulate expression. DNA demethylates early in development, beginning with the hematopoietic stem cell. The TNF-alpha locus migrates from heterochromatin to euchromatin in a progressive fashion, reaching euchromatin slightly later in differentiation. Finally, histone modifications characteristic of a transcriptionally competent gene occur with myeloid differentiation and progress with differentiation. Additional histone modifications characteristic of active gene expression are acquired with stimulation. In each case, manipulation of these epigenetic variables altered the ability of the cell to express TNF-alpha. These studies demonstrate the importance of epigenetic regulation in the control of TNF-alpha expression. These findings may have relevance for inflammatory disorders in which TNF-alpha is overproduced.
Rational Design and Functions of Electron Donor–Acceptor Dyads with Much Longer Charge-Separated Lifetimes than Natural Photosynthetic Reaction Centers (2009)

Abstract The natural photosynthetic reaction center utilizes sequential multi-step electron transfer from the excited chromophore to the terminal electron acceptor via electron mediators to attain a long lifetime of the final charge-separated (CS) state. Contrary to natural systems, simple electron donor–acceptor dyads have been developed to attain a long-lived CS state, where the donor and acceptor molecules are linked with a short spacer. In the case of a directly linked zinc chlorin–fullerene dyad, the lifetime of the CS state at −150 °C is as long as 120 s. This value is the longest CS lifetime ever reported for porphyrin-based donor–acceptor linked systems. The use of 9-mesityl-10-methylacridinium ion, which has an extremely long-lived CS state, enables the construction of highly efficient photocatalytic systems such as oxygenation of aromatic compounds and hydrogen evolution.
PEG Thiazolidine-2-thione, a Novel Reagent for Facile Protein Modification:  Conjugation of Bovine Hemoglobin (1996)

A novel PEG linker that employs a thiazolidine-2-thione group has been synthesized. Kinetic studies done on this compound demonstrate a relatively long half-life compared to those of traditional succinimidyl linkers. This new PEG derivative reacts with proteins under mild conditions and was utilized to conjugate bovine hemoglobin (bHb) to provide a PEG amide-linked protein. The physical characteristics of this conjugate were compared with those of the known PEG carbamate-linked bHb.
A Flexible Method for the Stable, Covalent Immobilization of Enzymes at Electrode Surfaces (2017)

Abstract Stable, site‐specific immobilization of redox proteins and enzymes is of interest for the development of biosensors and biofuel cells, where the long‐term stability of enzymatic electrodes as well as the possibility of controlling the orientation of the biomolecules at the electrode surface have a great importance. Ideally, it would be desirable to immobilize redox proteins and enzymes in a specific orientation, but still with some flexibility to optimize reaction kinetics. In this work, we establish such an approach by using site‐directed mutagenesis to introduce cysteine residues at specific locations on the protein surface and the reaction between the free thiol group and maleimide groups attached to the electrode surface to immobilize the mutated enzymes. Using cellobiose dehydrogenase (CDH) as a model system, carbon nanotube electrodes were first covalently modified with maleimide groups following a modular approach based on electrografting of primary amines at the carbon surface and solid‐phase synthesis methodology to elaborate the surface‐modified electrode. The CDH‐modified electrodes were tested for direct electron transfer (DET), showing high catalytic currents as well as excellent long‐term storage stability. The key advantage of this method is its great flexibility, as the main components of the modification can be independently varied to change the local environment at the electrode surface and a wide range of redox proteins or enzymes can be specifically engineered to present cysteine residues at their surface for oriented immobilization.
Molecular and mechanistic validation of delayed healing rat wounds as a model for human chronic wounds (1999)

The purpose of this study was to provide molecular and mechanistic evaluation of an ischemic wound model in rats to determine if it is a valid model for human chronic wounds. Compared to acute wounds, human chronic wounds contain markedly elevated levels of proinflammatory cytokines and matrix metalloproteinases, while matrix metalloproteinase inhibitors and growth factor activity are diminished. Accordingly, tissue from ischemic and normal rat wounds were analyzed for cytokine, proteases and growth factor levels. Dorsal full thickness punch wounds were created in rats using a reproducible template. The ischemic wound group (n = 10) had six uniformly placed wounds within a bipedicled dorsal flap. The control group (n = 10) had the same wounds created without elevation of a flap. On postwound days 3, 6 and 13 wounds were excised and analyzed. Protein levels for tumor necrosis factor-alpha were determined with a rat-specific enzyme-linked immunosorbent assay, while mRNA was determined by RNase protection assay. Matrix metalloproteinases and serine protease detection was done using gelatin and casein zymography, respectively. Significant delay in healing was achieved in the ischemic group: 50% healing for control wounds was at 7 days and 11 days for ischemic wounds (p < 0.001). No significant differences between wound groups were found for interleukin-1beta, and mRNA for tumor necrosis factor-alpha and interleukin-1beta. However, at day 13 ischemic wounds contained significantly more tumor necrosis factor-alpha than controls and normal skin (586 +/- 106 pg/biopsy vs. 79 +/- 7 pg/biopsy vs. 52 +/- 2 pg/biopsy; p < 0. 001). Zymography showed substantially greater quantities of matrix metalloproteinase-2, matrix metalloproteinase-9, and serine proteases in ischemic wounds. This model of delayed healing in rats shares many of the key biochemical, molecular and mechanistic characteristics found in human chronic wounds, namely elevated tumor necrosis factor-alpha and protease levels. As such, this model will likely prove to be useful in chronic wound research, particularly in developing novel therapeutics.
Supplemental data from CD20-TCB with Obinutuzumab Pretreatment as Next-Generation Treatment of Hematologic Malignancies (2023)

&lt;p&gt;Supplemental data details&lt;/p&gt;
Effect of Small-Molecule Modification on Single-Cell Pharmacokinetics of PARP Inhibitors (2014)

The heterogeneous delivery of drugs in tumors is an established process contributing to variability in treatment outcome. Despite the general acceptance of variable delivery, the study of the underlying causes is challenging, given the complex tumor microenvironment including intra- and intertumor heterogeneity. The difficulty in studying this distribution is even more significant for small-molecule drugs where radiolabeled compounds or mass spectrometry detection lack the spatial and temporal resolution required to quantify the kinetics of drug distribution in vivo. In this work, we take advantage of the synthesis of fluorescent drug conjugates that retain their target binding but are designed with different physiochemical and thus pharmacokinetic properties. Using these probes, we followed the drug distribution in cell culture and tumor xenografts with temporal resolution of seconds and subcellular spatial resolution. These measurements, including in vivo permeability of small-molecule drugs, can be used directly in predictive pharmacokinetic models for the design of therapeutics and companion imaging agents as demonstrated by a finite element model.
Generation and synchronous tree‐adjoining grammars (1991)

Tree‐adjoining grammars (TAG) have been proposed as a formalism for generation based on the intuition that the extended domain of syntactic locality that TAGs provide should aid in localizing semantic dependencies as well, in turn serving as an aid to generation from semantic representations. We demonstrate that this intuition can be made concrete by using the formalism of synchronous tree‐adjoining grammars. The use of synchronous TAGs for generation provides solutions to several problems with previous approaches to TAG generation. Furthermore, the semantic monotonicity requirement previously advocated for generation grammars as a computational aid is seen to be an inherent property of synchronous TAGs.
FUNCTIONAL CHARACTERIZATION OF NFKBIZ 3′ UTR MUTATIONS IN DIFFUSE LARGE B‐CELL LYMPHOMA (2019)

Introduction: The activated B-cell-like (ABC) subtype of diffuse large B-cell lymphoma (DLBCL) is characterized by activation of NF-kB signaling and an increased risk of mortality. Recurrent somatic mutations affecting genes such as MYD88, CD79A/B and TNFAIP3 have been shown to constitutively activate the NF-kB pathway through B-cell receptor signaling in ABC DLBCL; however, there still remain cases with no known genetic basis for this pathway activation (Arthur et al. Nat Com 2018). We recently published a meta-analysis of DLBCL genome and targeted sequencing data identifying non-coding mutations. We described novel mutations affection the 3′ untranslated region (UTR) of NFKBIZ in 18% of ABC DLBCLs. Overall, NFKBIZ is mutated (amplifications and UTR mutations) in 34% of ABC DLBCLs. These NFKBIZ mutations are mutually exclusive with MYD88 mutations, implicating them in activation of the NF-kB signaling pathway. NFKBIZ encodes the IkB-ζ protein, which interacts with NF-kB transcription factors and is thought to regulate canonical NF-kB signaling. We hypothesized that these mutations affect the ability of regulatory mechanisms to target this transcript for degradation through disruption of UTR secondary structures. This leads to enhanced mRNA stability and elevated protein levels and represents a novel mechanism of promoting NF-kB signaling in ABC DLBCL. Methods: NFKBIZ 3′ UTR mutations were introduced in a DLBCL cell line using CRISPR-Cas9. NFKBIZ mRNA and protein levels were evaluated using custom designed droplet digital PCR assays and western blot. RNA-sequencing was performed on mutant and wild-type (WT) cell lines to identify genes up-regulated by IkB-ζ. A competitive growth assay with WT and CRISPR mutant lines was set up to assess whether UTR mutations provide a growth advantage in culture. The pool composition was determined by DNA sequencing and comparison of WT and mutant DNA sequences. Results: Introduction of NFKBIZ mutations into DLBCL cell lines confirmed that UTR deletions lead to increased levels of mRNA and protein. Stimulation with LPS revealed that mRNA levels stay elevated for longer in mutant lines. NFKBIZ UTR deletions also give DLBCL cells a selective growth advantage over WT when grown together in culture. RNA-sequencing of mutant and WT lines revealed possible transcriptional targets of IkB-ζ, including TNFRSF14B, HCK, GNAZ, BATF and CD274. These targets are either involved in activation of NF-kB signaling, associated with decreased survival in other lymphomas or potential new drug targets in NFKBIZ mutant DLBCL. Conclusions: This work highlights the role of NFKBIZ and 3′ UTR mutations in driving ABC DLBCL. We demonstrate that these UTR mutations can lead to over-expression of NFKBIZ and activate potentially novel drug targets in ABC DLBCL. These findings contribute to a better understanding of the genetic basis of DLBCL, which is necessary to guide personalized therapeutic strategies. Keywords: activated B-cell-like (ABC); molecular genetics; NF-kB.