gebhart/patrepeval huggingface dataset:
Molecular Analysis of Expression of the Lantibiotic Pep5 Immunity Phenotype (1999)

The lantibiotic Pep5 is produced by Staphylococcus epidermidis 5. Within its biosynthetic gene cluster, the immunity gene pepI, providing producer self-protection, is localized upstream of the structural gene pepA. Pep5 production and the immunity phenotype have been found to be tightly coupled (M. Reis, M. Eschbach-Bludau, M. I. Iglesias-Wind, T. Kupke, and H.-G. Sahl, Appl. Environ. Microbiol. 60:2876-2883, 1994). To study this phenomenon, we analyzed pepA and pepI transcription and translation and constructed a number of strains containing various fragments of the gene cluster and expressing different levels of immunity. Complementation of a pepA-expressing strain with pepI in trans did not result in phenotypic immunity or production of PepI. On the other hand, neither pepA nor its product was found to be involved in immunity, since suppression of the translation of the pepA mRNA by mutation of the ATG start codon did not reduce the level of immunity. Moreover, homologous and heterologous expression of pepI from a xylose-inducible promoter resulted in significant Pep5 insensitivity. Most important for expression of the immunity phenotype was the stability of pepI transcripts, which in the wild-type strain, is achieved by an inverted repeat with a free energy of -56.9 kJ/mol, localized downstream of pepA. We performed site-directed mutagenesis to study the functional role of PepI and constructed F13D PepI, I17R PepI, and PepI 1-65; all mutants showed reduced levels of immunity. Western blot analysis indicated that F13D PepI and PepI 1-65 were not produced correctly or were partially degraded, while I17R PepI apparently was less efficient in providing self-protection than the wild-type PepI.
Purification and Characterization of a Soluble Cyclic Nucleotide‐Independent Ca2+‐Calmodulin‐Sensitive Protein Kinase from Rat Brain (1986)

Following partial purification, the characteristics of a cytosol protein kinase were investigated. The protein kinase was purified by ammonium sulfate precipitation and diethylaminoethyl-cellulose, ATP-agarose, and hydroxyapatite chromatography. Analysis of the purified protein kinase preparation by polyacrylamide gel electrophoresis revealed three major protein bands. The cytosol protein kinase was purified approximately 442-fold, as calculated from the cyclic nucleotide independent protein kinase activity in the 40,000 g supernatant. The activity of the kinase was found to be independent of either cyclic AMP or cyclic GMP. Moreover, the kinase activity was unaffected by the addition of the endogenous protein kinase inhibitor, or the regulatory subunit from the type II cyclic AMP-dependent protein kinase from bovine heart. The molecular weight of the enzyme was determined to be 95,000 by Sephadex G-200 gel filtration. The activity of the kinase was increased approximately twofold in the presence of 10 microM Ca+2 and calmodulin. This increase was reversed by the addition of EGTA. The subcellular distribution of the protein kinase was also examined. The soluble fraction from nerve terminal was found to have the highest concentration of the kinase activity.
Application of complementary DNA microarray technology to carcinogen identification, toxicology, and drug safety evaluation. (1999)

One major challenge facing today's cancer researchers and toxicologists is the development of new approaches for the identification of carcinogens and other environmental hazards. Here, we describe the potential impact of emerging technologies for measuring gene expression profiles on carcinogen identification and on the general field of toxicology. An example of one of these technologies is the use of cDNA microarray chips. We provide an overview to the key questions that are confronting investigators charged with determining the relative safety of natural or synthetic chemicals to which humans are exposed, followed by a discussion of how cDNA microarray technology may be applied to these questions. Gene chip technology is still a relatively new technology, and only a handful of studies have demonstrated its utility. However, as the technical hurdles to development are passed, the use of this methodology in addressing the questions raised here will be critical to increase the sensitivity of detection of the potential toxic effects of environmental chemicals and to understand their risks to humans.
A critical examination of 3D stackable NAND Flash memory architectures by simulation study of the scaling capability (2010)

Various 3D NAND Flash array architectures including P-BiCS, TCAT, VSAT, and VG are critically examined in this work by extensive 3D TCAD simulations. All structures have X,Y lateral scaling limitation since the minimal ONO thickness (~20 nm) and poly channel thickness (~10nm) can not be scaled further. Among them VG may have the best X-direction scalability to F~2X nm node, and no penalty of increasing Z layer number since the channel current flows horizontally. We propose a buried-channel junction-free NAND to improve the read current for all 3D NAND arrays and our simulation results well support this structure. For the first time, “Z-interference” in 3D NAND Flash is examined and it indicates a new Z-direction scaling limitation. The present work is of crucial importance in understanding various 3D NAND Flash approaches.
Simplified channel estimation for OFDM systems with multiple transmit antennas (2002)

Multiple transmit-and-receive antennas can be used in orthogonal frequency division multiplexing (OFDM) systems to improve communication quality and capacity. In this paper, we present two techniques to improve the performance and reduce the complexity of channel parameter estimation: optimum training-sequence design and simplified channel estimation. The optimal training sequences not only simplify the initial channel estimation, but also attain the best estimation performance. The simplified channel estimation significantly reduces the complexity of the channel estimation at the expense of a negligible performance degradation. The effectiveness of the new techniques is demonstrated through the simulation of an OFDM system with two-transmit and two-receive antennas. The space-time coding with 240 information bits per codeword is used for transmit diversity. From the simulation, the required signal-to-noise ratio is only about 9 dB for a 10% word error rate for a channel with the typical urban- or hilly-terrain delay profile and a 40-Hz Doppler frequency.
Control of the Proinflammatory State in Cystic Fibrosis Lung Epithelial Cells by Genes from the TNF-αR/NFκB Pathway (2001)

Wild-type CFTR and CPX both suppress proinflammatory IL-8 secretion from CF epithelial cells. The mechanism, as defined by pharmacogenomic analysis, involves identified genes from the TNF-alphaR/NFkappaB pathway. The close relationship between IL-8 secretion and genes from the TNF-alphaR/NFkappaB pathway suggests that molecular or pharmaceutical targeting of these novel genes may have strategic use in the development of new therapies for CF. From the perspective of global gene expression, both gene and drug therapy have similar genomic consequences. This is the first example showing equivalence of gene and drug therapy in CF, and suggests that a gene therapy-defined endpoint may prove to be a powerful paradigm for CF drug discovery. Finally, because the GENESAVER algorithm is capable of isolating disease-relevant genes in a hypothesis-driven manner without recourse to any a priori knowledge about the system, this new algorithm may also prove useful in applications to other genetic diseases.
Charcot-Marie-Tooth–Linked Mutant GARS Is Toxic to Peripheral Neurons Independent of Wild-Type GARS Levels (2011)

Charcot-Marie-Tooth disease type 2D (CMT2D) is a dominantly inherited peripheral neuropathy caused by missense mutations in the glycyl-tRNA synthetase gene (GARS). In addition to GARS, mutations in three other tRNA synthetase genes cause similar neuropathies, although the underlying mechanisms are not fully understood. To address this, we generated transgenic mice that ubiquitously over-express wild-type GARS and crossed them to two dominant mouse models of CMT2D to distinguish loss-of-function and gain-of-function mechanisms. Over-expression of wild-type GARS does not improve the neuropathy phenotype in heterozygous Gars mutant mice, as determined by histological, functional, and behavioral tests. Transgenic GARS is able to rescue a pathological point mutation as a homozygote or in complementation tests with a Gars null allele, demonstrating the functionality of the transgene and revealing a recessive loss-of-function component of the point mutation. Missense mutations as transgene-rescued homozygotes or compound heterozygotes have a more severe neuropathy than heterozygotes, indicating that increased dosage of the disease-causing alleles results in a more severe neurological phenotype, even in the presence of a wild-type transgene. We conclude that, although missense mutations of Gars may cause some loss of function, the dominant neuropathy phenotype observed in mice is caused by a dose-dependent gain of function that is not mitigated by over-expression of functional wild-type protein.
Hormonal regulation of fluxes through pyruvate dehydrogenase and the citric acid cycle in mammalian tissues. (1987)

Three key dehydrogenases in the mitochondria of higher animals have been found to be activated by Ca2+ ions; these are pyruvate dehydrogenase and two enzymes in the citric acid cycle, NAD-isocitrate dehydrogenase and oxoglutarate dehydrogenase. Activation can also be demonstrated within permeabilized and intact mitochondria. Evidence is summarized that when hormones and other extracellular stimuli increase the cytoplasmic concentration of Ca2+, then this results in an increase in the intramitochondrial concentration of Ca2+. In this way, rates of pyruvate oxidation and citric acid cycle flux are increased, and hence there is an increase in NADH supply for the respiratory chain under conditions where there is an enhanced demand for ATP. In contrast, the activation of pyruvate dehydrogenase which is observed in adipose and other tissues exposed to insulin is brought about by a Ca2+-independent mechanism.
Physiology of cold tolerance in insects (1985)

From the available experimental data a relatively clear picture can be established with regard to the physiological importance of some of the mechanisms involved in insect cold hardening. In freeze-avoiding insects, all potent ice-nucleating agents are removed or inactivated, leading to a depression of the supercooling points to about 20 degrees C. Accumulation of polyols causes a further depression with a magnitude of about twice the corresponding melting-point depression. Production of thermal hysteresis factors causes a stabilization of the supercooled state. In freeze-tolerant insects, potent ice-nucleating agents are produced in the extracellular body fluid, ensuring a protective extracellular freezing at a few degrees below zero. Accumulation of polyols causes a steep drop in the lethal temperature, due to a reduction of the amount of ice by a colligative mechanism. However, there is still much to be learned about the mechanisms by which ice-nucleating agents, polyols, and thermal hysteresis agents are acting. Furthermore, the regulatory mechanisms involved in the production and elimination of these components from the body fluid of the insects are not understood. Also, when it comes to the influence of environmental factors, like photoperiod and temperature, there is much to be learned. In addition to giving attention to these topics, future research should be focused on the possible role of other factors in cold hardening such as bound water, dehydration, low-molecular-weight solutes other than polyols, and the biochemical mechanisms forming the basis of the seasonal changes in the cold hardiness of insects.
Activity in fetal bovine serum that stimulates erythroid colony formation in fetal mouse livers is insulinlike growth factor I. (1985)

In the present study, the erythropoietic activity of fetal serum was characterized. Using fetal bovine serum (FBS) as a source of the erythropoietic activity and serum-free cultures of fetal mouse livers (FMLC assay) as a detection system, we found that FBS stimulated colony formation from late erythroid progenitor cells (CFU-E) in a dose-dependent fashion. The slope of the dose-response curve, however, was significantly different from that for erythropoietin (Ep), the best-characterized erythropoietic activity so far. The erythropoietic activity of FBS was found in the 120-160- and 40-70-kD range at neutral pH. In the presence of 1 M acetic acid, however, the erythropoietic activity had an apparent molecular mass between 3 and 13 kD. From ion exchange experiments with DEAE-cellulose, the isoionic point of the activity was estimated to about pH 5. Furthermore, the erythropoietic activity of FBS was found to be co-eluted on Sephadex G-150 with the binding proteins of insulinlike growth factors (IGF). The IGF I concentration determined by radioimmunoassay was 70 ng IGF I/ml. The Ep activity of FBS was less than 5 mU/ml when determined with the posthypoxic polycythemic mouse assay for Ep. These results suggest that the erythropoietic activity of FBS is related to IGF and not to Ep. The erythropoietic activity of FBS was abolished by an antiserum against IGF I. Furthermore, IGF I was a factor of approximately 40 more potent than IGF II in stimulating erythroid colony formation. All of these findings suggest that the erythropoietic activity of FBS is IGF I.
On the performance of one bit time reversal for multi-user wireless communications (2007)

Time reversal (TR) technique can be used to achieve temporal focusing (compression of the effective channel impulse response in time) and spatial focusing (concentration of the transmit energy in space). In this paper the performance advantage and its trade off in the traditional time reversal system and its simplified version the one bit time reversal systems are discussed. Analytical solutions for the temporal and spatial focusing metrics are derived and served as the base for the comparison on the performance of the two TR systems. It is showed that although there is some degradation in the temporal focusing performance of the one bit TR system, its spatial focusing performance surprisingly outperforms that of the traditional TR system. The analytical investigations are verified using measurement data from recent UWB measurement campaign.
Pointer Networks (2015)

We introduce a new neural architecture to learn the conditional probability of an output sequence with elements that are discrete tokens corresponding to positions in an input sequence. Such problems cannot be trivially addressed by existent approaches such as sequence-to-sequence and Neural Turing Machines, because the number of target classes in each step of the output depends on the length of the input, which is variable. Problems such as sorting variable sized sequences, and various combinatorial optimization problems belong to this class. Our model solves the problem of variable size output dictionaries using a recently proposed mechanism of neural attention. It differs from the previous attention attempts in that, instead of using attention to blend hidden units of an encoder to a context vector at each decoder step, it uses attention as a pointer to select a member of the input sequence as the output. We call this architecture a Pointer Net (Ptr-Net). We show Ptr-Nets can be used to learn approximate solutions to three challenging geometric problems -- finding planar convex hulls, computing Delaunay triangulations, and the planar Travelling Salesman Problem -- using training examples alone. Ptr-Nets not only improve over sequence-to-sequence with input attention, but also allow us to generalize to variable size output dictionaries. We show that the learnt models generalize beyond the maximum lengths they were trained on. We hope our results on these tasks will encourage a broader exploration of neural learning for discrete problems.
Pasting Quantum Codes (1996)

I describe a method for pasting together certain quantum error-correcting codes that correct one error to make a single larger one-error quantum code. I show how to construct codes encoding 7 qubits in 13 qubits using the method, as well as 15 qubits in 21 qubits and all the other "perfect" codes.
The nucleotide sequence of the gene for human protein C. (1985)

A human genomic DNA library was screened for the gene for protein C by using a cDNA probe coding for the human protein. Three different overlapping lambda Charon 4A phage were isolated that contain inserts for the gene for protein C. The complete sequence of the gene was determined by the dideoxy method and shown to span about 11 kilobases of DNA. The coding and 3' noncoding portion of the gene consists of eight exons and seven introns. The eight exons code for a preproleader sequence of 42 amino acids, a light chain of 155 amino acids, a connecting dipeptide of Lys-Arg, and a heavy chain of 262 amino acids. The preproleader sequence and the connecting dipeptide are removed during processing, resulting in the mature protein composed of a heavy and a light chain held together by a disulfide bond. The heavy chain also contains the catalytic region for the serine protease. Two Alu sequences and two homologous repeats of about 160 nucleotides were found in intron E. The seven introns in the gene for protein C are located in essentially the same positions in the amino acid sequence as the seven introns in the gene for human factor IX, while the first three introns in protein C are located in the same positions as the first three in the gene for human prothrombin.
Infectious vaccine-derived rubella viruses emerge, persist, and evolve in cutaneous granulomas of children with primary immunodeficiencies (2019)

Rubella viruses (RV) have been found in an association with granulomas in children with primary immune deficiencies (PID). Here, we report the recovery and characterization of infectious immunodeficiency-related vaccine-derived rubella viruses (iVDRV) from diagnostic skin biopsies of four patients. Sequence evolution within PID hosts was studied by comparison of the complete genomic sequences of the iVDRVs with the genome of the vaccine virus RA27/3. The degree of divergence of each iVDRV correlated with the duration of persistence indicating continuous intrahost evolution. The evolution rates for synonymous and nonsynonymous substitutions were estimated to be 5.7 x 10-3 subs/site/year and 8.9 x 10-4 subs/site/year, respectively. Mutational spectra and signatures indicated a major role for APOBEC cytidine deaminases and a secondary role for ADAR adenosine deaminases in generating diversity of iVDRVs. The distributions of mutations across the genes and 3D hotspots for amino acid substitutions in the E1 glycoprotein identified regions that may be under positive selective pressure. Quasispecies diversity was higher in granulomas than in recovered infectious iVDRVs. Growth properties of iVDRVs were assessed in WI-38 fibroblast cultures. None of the iVDRV isolates showed complete reversion to wild type phenotype but the replicative and persistence characteristics of iVDRVs were different from those of the RA27/3 vaccine strain, making predictions of iVDRV transmissibility and teratogenicity difficult. However, detection of iVDRV RNA in nasopharyngeal specimen and poor neutralization of some iVDRV strains by sera from vaccinated persons suggests possible public health risks associated with iVDRV carriers. Detection of IgM antibody to RV in sera of two out of three patients may be a marker of virus persistence, potentially useful for identifying patients with iVDRV before development of lesions. Studies of the evolutionary dynamics of iVDRV during persistence will contribute to development of infection control strategies and antiviral therapies.
THE METABOLISM OF TESTOSTERONE BY HUMAN MALE SCALP SKIN (1973)

SUMMARY [4- 14 C]Testosterone was incubated with human male scalp skin and the metabolites identified as 5α-androstane-3α, 17β-diol, androsterone, epiandrosterone, dihydrotestosterone, androstenedione and androstanedione. A metabolite not previously reported from incubations of human skin with androgens was isolated and is probably a steroid ester. One bald and one hairy scalp biopsy specimen from each of five subjects were incubated with [4- 14 C]testosterone for 1 h and the radioactivity of each metabolite was measured after separation by thin-layer chromatography. Both the uptake and metabolism of testosterone were greater in bald skin than in hairy skin. Little difference in the percentage of each metabolite in the total metabolite pool was found between bald and hairy skin from the same subject and skin from different subjects. This demonstrated that male pattern baldness was not accompanied by gross changes in testosterone metabolism. The main finding was that bald skin contained increased amounts of 5α-reduced metabolites.
Use of dual-grating sensors formed by different types of fiber Bragg gratings for simultaneous temperature and strain measurements (2004)

We report on a systematic investigation of the dependence of both temperature and strain sensitivities on the fiber Bragg grating type, including the well-known Type I, Type IIA, and a new type that we have designated Type IA, using both hydrogen-free and hydrogenated B/Ge codoped fibres. We have identified distinct sensitivity characteristics for each grating type, and we have used them to implement a novel dual-grating, dual-parameter sensor device. Three dual-grating sensing schemes with different combinations of grating type have been constructed and compared, and that of a Type IA-Type IIA combination exhibits the best performance, which is also superior to that of previously reported grating-based structures. The characteristics of the measurement errors in such dual-grating sensor systems is also presented in detail.
Evaluation of Storage Tubes for Combined Analysis of Circulating Nucleic Acids in Liquid Biopsies (2019)

In the last decade, circulating nucleic acids such as microRNAs (miRNAs) and cell-free DNA (cfDNA) have become increasingly important in serving as potential novel biomarkers for a variety of human diseases. If cell-free nucleic acids are to become routinely used in diagnostics, the difference in plasma miRNA and cfDNA levels between healthy and diseased subjects must exceed pre-analytical and analytical variability. Until now, few studies have addressed the time limitations of pre-processing or explored the potential use of long-term blood storage tubes, which might need to be implemented in real-life diagnostics. In this study, we analyzed the stability of four breast cancer-associated miRNAs and two cancer-associated genes under various storage conditions, to test their limitations for potential application in clinical diagnostics. In two consecutive experiments, we tested the limits of conventional EDTA tubes, as well as long-term storage blood collection tubes (BCTs) from four different manufacturers. We found that circulating miRNAs are relatively stable when stored in EDTA monovettes for up to 12 h before processing. When stored in BCTs, circulating miRNAs and cfDNA are stable for up to 7 days, depending on the manufacturer. Norgen tubes were superior for cfDNA yield, while Streck tubes performed the worst in our study with hemolysis induction. In conclusion, plasma prepared from whole blood is suitable for the quantification of both cf-miRNAs and cfDNA simultaneously.