gebhart/patrepeval huggingface dataset:
Hedgehog activity, independent of Decapentaplegic, participates in wing disc patterning (1997)

In the Drosophila wing imaginal disc, the Hedgehog (Hh) signal molecule induces the expression of decapentaplegic (dpp) in a band of cells abutting the anteroposterior (A/P) compartment border. It has been proposed that Dpp organizes the patterning of the entire wing disc. We have tested this proposal by studying the response to distinct levels of ectopic expression of Hh and Dpp, using the sensory organ precursors (SOPs) of the wing and notum and the presumptive wing veins as positional markers. Here, we show that Dpp specifies the position of most SOPs in the notum and of some of them in the wing. Close to the A/P compartment border, however, SOPs are specified by Hh rather than by Dpp alone. We also show that late signaling by Hh, after setting up dpp expression, is responsible for the formation of vein 3 and the scutellar region, and also for the determination of the distance between veins 3 and 4. One of the genes that mediates the Hh signal is the zinc-finger protein Cubitus interruptus (Ci). These results indicate that Hh has a Dpp-independent morphogenetic effect in the region of the wing disc near the A/P border.
Disruption of Plasmodium falciparum Erythrocyte Rosettes by Standard Heparin and Heparin Devoid of Anticoagulant Activity (1992)

We have studied the ability of heparin to disrupt spontaneous rosettes formed between Plasmodium falciparum-infected and uninfected red blood cells, which has been proposed to have importance in the pathogenesis of cerebral malaria. Substantial variation in this activity was found among six laboratory stains of P. falciparum. Rosettes formed by three of these strains were highly sensitive to heparin (50% disruption at 0.5-25 micrograms/ml; 1 microgram/ml corresponds to 0.15 IU/ml). The rosettes formed by two other strains showed a much lower sensitivity (50% disruption at 700-2,500 micrograms/ml), while the rosettes formed by another strain were almost completely resistant to heparin (20% disruption at 6,500 micrograms/ml). The ability of heparin (65 or 650 micrograms/ml) to disrupt rosettes formed by 54 fresh Gambian isolates of P. falciparum also varied. Rosettes of 27 (50%) of the 54 isolates were disrupted to a significant degree (greater than or equal to 15%), while rosettes of the other 27 isolates remained unaffected at the concentrations tested. Heparin was fractionated by molecular weight and/or affinity for antithrombin III. We found that its property of rosette disruption was associated, to some extent, with size (high molecular weight) but not with its anticoagulant potential (affinity for antithrombin III). A heparin fraction with low affinity for antithrombin III and one with combined high molecular weight and low affinity for antithrombin III were as effective at disrupting rosettes as standard heparin, while a chemically modified (N-acetylated) high molecular weight-heparin fraction, similarly devoid of anticoagulant activity, lacked strong anti-rosette potential.(ABSTRACT TRUNCATED AT 250 WORDS)
Towards a Formal Language for the Common Description of Aircraft Intent (2006)

This paper summarizes the key characteristics of several different methods applied to encode aircraft intent in TP implementations. The differences appear to be significant. We conclude that a standardized formal method to express aircraft intent information (understood as input to the trajectory computation process) is a key enabler to achieve the required consistency. This paper identifies the need for a formal language for the common description of aircraft intent in the context of trajectory computation. Such a language, denoted as aircraft intent description language (AIDL), would allow expressing the aircraft intent with different levels of detail within a single standard unifying framework. By using the AIDL as a common standard for intent sharing, different TP clients could interoperate on the basis of a consistent input to the TP, regardless of their individual requirements. The proposed approach is considered as a possible solution to ensure interoperability among future ATM automation components.
Increased Frequency of N-Region Insertion in a Murine Pre-B-Cell Line Infected with a Terminal Deoxynucleotidyl Transferase Retroviral Expression Vector (1987)

The role of terminal deoxynucleotidyl transferase (TdT) in the insertion of N regions into the junctional sites of immunoglobulin genes was investigated. Pre-B-cell lines capable of continuous rearrangement of immunoglobulin light-chain genes and differing only in the presence or apparent absence of TdT were derived by infecting cells with a TdT retroviral expression vector or a control vector. The cell lines were then superinfected with a retrovirus-based artificial immunoglobulin gene rearrangement substrate. The substrate was allowed to rearrange in the cell lines and the rearranged proviruses were rescued from the cell lines. Nucleotide sequence analysis of the V-J junctions of the proviral rearranged genes showed a fivefold greater frequency of N-region insertion in proviruses rescued from the TdT+ cell lines than in those rescued from the TdT- cell lines, so that at least 50% of the rearrangements that occurred in the presence of TdT had N regions. It is thus evident that TdT can stimulate N-region insertion, and the enzyme is presumably directly responsible for adding nucleotides at V-J and other immunoglobulin and T-cell receptor gene junctions.
Dot-ELISA for human leptospirosis employing immunodominant antigen. (1995)

A dot enzyme-linked immunosorbent assay which uses a proteinase-K resistant antigen (PK-Dot-ELISA) to detect antileptospiral IgM antibodies was compared to the microscopic agglutination test (MAT). The assay was evaluated in serum samples from patients with leptospirosis (n = 89), typhoid fever (n = 10), malaria (n = 19), syphilis (n = 20), hepatitis (n = 16) and clinically healthy individuals (n = 92). The PK-Dot-ELISA presented a sensitivity of 92.1% and a specificity of 97.5%. The overall results of the PK-Dot-ELISA were similar to those of the MAT. However, the PK-Dot-ELISA was capable of detecting antibody activity in 43% of acute-phase sera which were negative by the MAT. Our data suggest that PK-Dot-ELISA can be used as an important portable field serodiagnostic assay for acute leptospirosis.
Dynamic Microscopy Study of Ultrafast Charge Transfer in a Hybrid P3HT/Hyperbranched CdSe Nanoparticle Blend for Photovoltaics (2012)

We present a spectroscopic investigation on a new hyperbranched cadmium selenide nanocrystals (CdSe NC)/poly(3-hexylthiophene) (P3HT) blend, a potentially good active component in hybrid photovoltaics. Combined ultrafast transient absorption spectroscopy and morphological investigations by means of an ultrafast confocal microscope reveal a strong influence of the complex local structure on the photogenerated carrier dynamics. In particular, we map the electron-transfer process across the hybrid NC/polymer interface, and we reveal that charge separation occurs through a preferential pathway from the CdSe nanobranches to the P3HT chains. Efficient charge generation at the distributed heterojunction is also confirmed by scanning kelvin probe force microscopy measurements.
The human LT system. VIII. A target cell-dependent enzymatic activation step required for the expression of the cytotoxic activity of human lymphotoxin. (1980)

Abstract We have used various protease inhibitors to examine the role of esterases in a class human lymphotoxin (α-LT) mediated lysis of mitomycin C-treated murine L-929 cells in vitro. Seven protease inhibitors were shown to inhibit lysis by a-LT when present throughout the reaction in vitro. These inhibitors were of two types, the reversible substrate analogues (PME, TME, LME, TAME, and BAEE) and the irreversible protease inactivators (TPCK and TLCK). The concentrations needed for optimum inhibition by the seven inhibitors ranged from 2.5 × 10−5 M to 2.5 × 10−2 M. There was enhanced lysis with EACA, and no measurable effect on lysis when Trasylol and soybean trypsin inhibitor were tested. Since TLCK irreversibly inactivates enzymes, it was used to determine whether the esterase necessary for lysis was associated with the target cell or the a-LT molecule. The a-LT was shown to be fully active after treatment with TLCK and subsequent dialysis. Similar experiments with DFP gave the same results. However, pretreatment of the L-929 cells with TLCK partially inhibited a-LT-mediated lysis. To determine whether intact protease substrates were required for inhibition, the products of hydrolysis of PME, LME, TAME, and BAEE were tested for their ability to inhibit lysis and were shown to be ineffective. The results of these studies indicate that an esterase(s), probably derived from the L-929 cell, is required for α class human LT-mediated cytolysis in vitro. These studies therefore suggest that a-LT is carried by the lymphocyte in an inactive form and requires an esterase or possibly protease-mediated activation step to enable it to lyse the L-929 target cell.
Speech Analysis and Synthesis by Linear Prediction of the Speech Wave (1971)

We describe a procedure for efficient encoding of the speech wave by representing it in terms of time-varying parameters related to the transfer function of the vocal tract and the characteristics of the excitation. The speech wave, sampled at 10 kHz, is analyzed by predicting the present speech sample as a linear combination of the 12 previous samples. The 12 predictor coefficients are determined by minimizing the mean-squared error between the actual and the predicted values of the speech samples. Fifteen parameters—namely, the 12 predictor coefficients, the pitch period, a binary parameter indicating whether the speech is voiced or unvoiced, and the rms value of the speech samples—are derived by analysis of the speech wave, encoded and transmitted to the synthesizer. The speech wave is synthesized as the output of a linear recursive filter excited by either a sequence of quasiperiodic pulses or a white-noise source. Application of this method for efficient transmission and storage of speech signals as well as procedures for determining other speech characteristics, such as formant frequencies and bandwidths, the spectral envelope, and the autocorrelation function, are discussed.
Multi‐carrier platform for wireless communications. Part 1: High‐performance, high‐throughput TDMA and DS‐CDMA via multi‐carrier implementations (2002)

Abstract Multi‐carrier technologies in general, and OFDM and MC‐CDMA in particular, are quickly becoming an integral part of the wireless landscape. In this first of a two‐part survey, the authors present the innovative transmit/receive multi‐carrier implementation of TDMA and DS‐CDMA systems. Specifically, at the transmit side, the pulse shape (in TDMA) and the chip shape (in DS‐CDMA) corresponds to a linear combining of in‐phase harmonics (called a CI signal). At the receiver side, traditional time‐domain processing (equalization in TDMA and RAKE reception in DS‐CDMA) is replaced by innovative frequency based processing. Here, receivers decompose pulse (or chip) shapes into carrier subcomponents and recombine these in a manner achieving both high frequency diversity gain and low MAI. The resulting system outperforms traditional TDMA and DS‐CDMA systems by 10–14 dB at typical BERs, and, by application of pseudo‐orthogonal pulse shapes (chip shapes), is able to double system throughput while maintaining performance gains of up to 8 dB. Copyright © 2002 John Wiley &amp; Sons, Ltd.
Experimental production of subdural hematomas (1974)

✓ Experimental evidence is offered to refute the hypothesis that cerebrospinal fluid alters blood coagulation or clots to favor the formation of chronic subdural hematomas. Rather, the envelopment of preformed blood clots in membranes containing neovascular sinusoidal channels and their subsequent regression from the subdural space are seen as a normal biological process analogous to that occurring elsewhere in the body. The presence of fibrin and its contact with the dura have been found to be essential precursors to membrane formation. Histological evidence of bleeding into both blood and fibrin subdural clots is presented, and theoretical considerations are discussed to explain possible mechanisms of enlargement and chronicity of subdural hematomas as well as repeated failures to obtain an experimental small animal model.
DRUG INTERACTIONS WITH METHADONE* (1976)

The language-based theory of regions, stemming from the area of Petri net synthesis, forms a fundamental basis for Integer Linear Programming (ILP)-based process discovery. Based on example behavior in an event log, a process model is derived that aims to describe the observed behavior. Building on top of the existing ILP-formulation, we present a new ILP-based process discovery formulation that unifies two existing types of language-based regions and, additionally, we present a generalized ILP objective function that captures both region-types and helps us to find suitable process discovery results.
A Contextual Medical Image Viewer (2007)

The conventional visualization of medical images is not enough for a rich and comprehensive electronic healthcare record. We believe that it is necessary to provide a viewer with more advanced capabilities than those of regular medical image viewers. In this paper, we propose an architecture that allows the use of contextual information to assist the healthcare professional in his regular tasks. The proposed architecture for the context is composed of an ontology describing the hospital and an inference engine. The result is a Java-based implementation of the architecture, named Dynamic N-dimensional Image Viewer, (ODIN in Portuguese) that is able to adapt its behavior according to the contextual information.
Surface presentation of Shigella flexneri invasion plasmid antigens requires the products of the spa locus (1992)

An avirulent, invasion plasmid insertion mutant of Shigella flexneri 5 (pHS1059) was restored to the virulence phenotype by transformation with a partial HindIII library of the wild-type invasion plasmid constructed in pBR322. Western immunoblot analysis of pHS1059 whole-cell lysates revealed that the synthesis of the invasion plasmid antigens VirG, IpaA, IpaB, IpaC, and IpaD was similar to that seen in the corresponding isogenic S. flexneri 5 virulent strain, M90T. IpaB and IpaC, however, were not present on the surface of pHS1059 as was found in M90T, suggesting that the transport or presentation of the IpaB and IpaC proteins onto the bacterial surface was defective in the mutant. pHS1059 was complemented by pWR266, which carried contiguous 1.2- and 4.1-kb HindIII fragments of the invasion plasmid. pHS1059(pWR266) cells were positive in the HeLa cell invasion assay as well as colony immunoblot and enzyme-linked immunosorbent assays, using monoclonal antibodies to IpaB and IpaC. These studies established that the antigens were expressed on the surface of the transformed bacteria. In addition, water extraction of pHS1059 and pHS1059(pWR266) whole cells, which can be used to remove IpaB and IpaC antigens from the surface of wild-type M90T bacteria, yielded significant amounts of these antigens from pHS1059(pWR266) but not from pHS1059. Minicell and DNA sequence analysis indicated that several proteins were encoded by pWR266, comprising the spa loci, which were mapped to a region approximately 18 kb upstream of the ipaBCDAR gene cluster. Subcloning and deletion analysis revealed that more than one protein was involved in complementing the Spa- phenotype in pHS1059. One of these proteins, Spa47, showed striking homology to ORF4 of the Bacillus subtilis flaA locus and the fliI gene sequence of Salmonella typhimurium, both of which bear strong resemblance to the alpha and beta subunits of bacterial, mitochondrial, and chloroplast proton-translocating F0F1 ATPases.
Type 1 Diabetes Genes in Rats: Few or Many? (2009)

That type 1 diabetes in humans and in animal models represents a complex genetic disease is universally accepted. Genetic dissection of type 1 diabetes in humans has typically entailed the collection of large numbers of individuals scored on the basis of the presence or absence of clinical disease (case/control subjects). Statistically significant differences in allele frequencies distinguishing the affected subjects from control subjects are used to demonstrate associations. Human major histocompatibility complex (MHC) alleles, primarily but not exclusively within the class II sets of genes, are estimated to contribute up to 50% of genetic risk. Because of the strength of the MHC contribution and the genetic heterogeneity extant in humans, identification of non-MHC susceptibility loci by genome-wide association has required the accumulation of large numbers of case/control populations. Recent studies have identified up to 10 of such non-MHC susceptibility regions under conditions where multiple HLA haplotypes are segregating (1).

In the NOD mouse, the paramount role of the MHC was confirmed by the finding that almost all diabetic mice generated by outcross with diabetes-resistant strains were homozygous for the NOD's susceptibility-conferring H2g7 MHC haplotype. Because inbred strains were used, linkage was ascertained by treating type 1 diabetes as a dichotomous trait, with diabetes susceptibility ( Idd ) genes identified by significant deviations from expected Mendelian ratios in the diabetic segregants. Initial segregation analyses in crosses in which H2g7 was also segregating only suggested effects of several non-MHC Idd genes. However, the true polygenic nature of type 1 diabetes in this model followed the generation of outcross partner strains congenic for NOD's susceptibility-conferring H2g7 , …
Programmable large DNA deletion, replacement, integration, and inversion with twin prime editing and site-specific recombinases (2021)

Summary The targeted deletion, replacement, integration, or inversion of DNA sequences at specified locations in the genome could be used to study or treat many human genetic diseases. Here, we describe twin prime editing (twinPE), a method for the programmable replacement or excision of DNA sequence at endogenous human genomic sites without requiring double-strand DNA breaks. TwinPE uses a prime editor (PE) protein and two prime editing guide RNAs (pegRNAs) that template the synthesis of complementary DNA flaps on opposing strands of genomic DNA, resulting in the replacement of endogenous DNA sequence between the PE-induced nick sites with pegRNA-encoded sequences. We show that twinPE in human cells can perform precise deletions of at least 780 bp and precise replacements of genomic DNA sequence with new sequences of at least 108 bp. By combining single or multiplexed twinPE with site-specific serine recombinases either in separate steps or in a single step, we demonstrate targeted integration of gene-sized DNA plasmids (&gt;5,000 bp) into safe-harbor loci including AAVS1 , CCR5, and ALB in human cells. To our knowledge, these results represent the first RNA-programmable insertion of gene-sized DNA sequences into targeted genomic sites of unmodified human cells without requiring double-strand breaks or homology-directed repair. Twin PE combined with recombinases also mediated a 40,167-bp inversion at IDS that corrects a common Hunter syndrome allele. TwinPE expands the capabilities of precision gene editing without requiring double-strand DNA breaks and synergizes with other tools to enable the correction or complementation of large or complex pathogenic alleles in human cells.
Protein farnesyltransferase in plants: molecular characterization and involvement in cell cycle control. (1996)

Farnesylation is required for membrane targeting, protein-protein interactions, and the biological activity of key regulatory proteins, such as Ras small GTPases and protein kinases in a wide range of eukaryotes. In this report, we describe the molecular identification of a plant protein farnesyltransferase (FTase) and evidence for its role in the control of the cell cycle in plants. A pea gene encoding a homolog of the FTase beta subunit was previously cloned using a polymerase chain reaction-based strategy. A similar approach was used to clone a pea gene encoding a homolog of the FTase alpha subunit. The biochemical function of the pea FTase homologs was demonstrated by the reconstitution of FTase enzyme activity using FTase fusion proteins coexpressed in Escherichia coll. RNA gel blot analyses showed that levels of FTase mRNAs are generally higher in tissues, such as those of nodules, that are active in cell division. The relationship of FTase to cell division was further analyzed during the growth of suspension-cultured tobacco BY-2 cells. A biphasic fluctuation of FTase enzyme activity preceded corresponding changes in mitotic activity at the early log phase of cell growth. Moreover, manumycin, a specific inhibitor of FTase, was effective in inhibiting mitosis and growth in these cells. Using synchronized BY-2 cells, manumycin completely blocked mitosis when added at the early S phase but not when added at the G2 phase. These data suggest that FTase is required for the plant cell cycle, perhaps by modulating the progression through the S phase and the transition from G1 to the S phase.
Electrowetting on Paper for Electronic Paper Display (2010)

The use of paper as a material for various device applications (such as microfluidics and energy storage) is very attractive given its flexibility, versatility, and low cost. Here we demonstrate that electrowetting (EW) devices can be readily fabricated on paper substrates. Several categories of paper have been investigated for this purpose, with the surface coating, roughness, thickness, and water uptake, among the most important properties. The critical parameter for EW devices is the water contact angle (CA) change with applied voltage. EW devices on paper exhibit characteristics very close to those of conventional EW devices on glass substrates. This includes a large CA change in oil ambient (90-95°), negligible hysteresis (∼2°), and fast switching times of ∼20 ms. These results indicate the promise of low-cost paper-based EW devices for video rate flexible e-paper on paper.
Synthesis of 2‐phosphinoxidomethyl‐ and 2‐phosphonomethyl glutaric acid derivatives (2005)

Abstract Michael addition of the corresponding anions derived from diphenylphosphine oxide, dialkylphosphites, and a cyclic phosphite to α‐methylene‐glutaric esters ( 1 ) afforded the title compounds ( 2–6 ). Double debenzylation of 2‐phosphono glutaric esters 4b and 5a by catalytic hydrogenation under the appropriate conditions gave the correspon‐ ding diacides 8 and 9 , respectively. © 2005 Wiley Periodicals, Inc. Heteroatom Chem 16:562–565, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20142