gebhart/patrepeval huggingface dataset:
Cloning of a Transcriptionally Active Human TATA Binding Factor (1990)

Transcription factor IID (TFIID) binds to the TATA box promoter element and regulates the expression of most eukaryotic genes transcribed by RNA polymerase II. Complementary DNA (cDNA) encoding a human TFIID protein has been cloned. The human TFIID polypeptide has 339 amino acids and a molecular size of 37,745 daltons. The carboxyl-terminal 181 amino acids of the human TFIID protein shares 80% identity with the TFIID protein from Saccharomyces cerevisiae. The amino terminus contains an unusual repeat of 38 consecutive glutamine residues and an X-Thr-Pro repeat. Expression of DNA in reticulocyte lysates or in Escherichia coli yielded a protein that was competent for both DNA binding and transcription activation.
Dynamic Networks for Motion Planning in Multi-Robot Space Systems (2003)

A new motion planning framework is presented that enables multiple mobile robots with limited ranges of sensing and communication to maneuver and achieve goals safely in dynamic environments. The framework is applicable to both planetary rover and free-floating space robot applications. To combine the respective advantages of centralized and decentralized planning, this framework is based on the concept of centralized planning within dynamic robot networks. As the robots move in their environment, localized robot groups form networks, within which world models and robot goals can be shared. Whenever a new network gets formed, a fast centralized planner computes new coordinated trajectories on the fly, for all robots in the network. But planning over several robot networks is decentralized and distributed. The trajectory of each robot is re-computed whenever this robot contributes to forming a new network, as new information then becomes available to all robots in this network. Both simulated and real-robot experiments have validated the approach. The applicability of the framework to planetary rovers was demonstrated in both simulations and real robot experiments. Also, the framework&amp;apos;s applicability to free-floating robots in a 3D space environment was demonstrated in simulation.
A Highly Convergent Synthesis of the Lewisy Blood Group Determinant in Conjugatable Form (1994)

The versatility of glycals both as glycosyl donors and as glycosyl acceptors is used in the synthesis of the Lewis y determinant. This and the oligosaccharide described in the following communication consist of a determinant, a carbohydrate spacer, and a group suitable for the conjugation to a carrier protein. The spacer present in these new glycoproteins minimizes the likelihood that the protein carrier will distort the recognition property of the determinant.
Construction of a defective retrovirus containing the human hypoxanthine phosphoribosyltransferase cDNA and its expression in cultured cells and mouse bone marrow. (1987)

Defective ecotropic and amphotropic retroviral vectors containing the cDNA for human hypoxanthine phosphoribosyltransferase (HPRT) were developed for efficient gene transfer and high-level cellular expression of HPRT. Helper cell clones which produced a high viral titer were generated by a simplified method which minimizes cell culture. We used the pZIP-NeoSV(X) vector containing a human hprt cDNA. Viral titers (1 X 10(3) to 5 X 10(4)/ml) of defective SVX HPRT B, a vector containing both the hprt and neo genes, were increased 3- to 10-fold by cocultivation of the ecotropic psi 2 and amphotropic PA-12 helper cells. Higher viral titers (8 X 10(5) to 7.5 X 10(6] were obtained when nonproducer NIH 3T3 cells or psi 2 cells carrying a single copy of SVX HPRT B were either transfected or infected by Moloney leukemia virus. The SVX HPRT B defective virus partially corrected the HPRT deficiency (4 to 56% of normal) of cultured rodent and human Lesch-Nyhan cells. However, instability of HPRT expression was detected in several infected clones. In these unstable variants, both retention and loss of the SVX HPRT B sequences were observed. In the former category, cells which became HPRT- (6-thioguanine resistant [6TGr]) also became G418s, indicative of a cis-acting down regulation of expression. Both hypoxanthine-aminopterin-thymidine resistance (HATr) and G418r could be regained by counterselection in hypoxanthine-aminopterin-thymidine. In vitro mouse bone marrow experiments indicated low-level expression of the neo gene in in vitro CFU assays. Individual CFU were isolated and pooled, and the human hprt gene was shown to be expressed. These studies demonstrated the applicability of vectors like SVX HPRT B for high-titer production of defective retroviruses required for hematopoietic gene transfer and expression.
All-fiber zero-insertion-loss add–drop filter for wavelength-division multiplexing (1998)

We developed and fabricated an all-fiber add-drop filter by recording a Bragg grating in the waist of an asymmetric mode converter-coupler formed by adiabatic tapering and fusing of two locally dissimilar, single-mode optical fibers. The insertion loss of the device was ~0.1 dB .A narrow spectral bandwidth (<1 nm) and a large add-drop efficiency (>90%) were also demonstrated. In addition, the filter was polarization independent.
Helix Stability Confers Salt Resistance upon Helical Antimicrobial Peptides (2004)

Salt sensitivity of antimicrobial peptides poses a major obstacle in their development as novel antibiotics. Here we report the use of helix-capping motifs to confer salt resistance upon helical antimicrobial peptides. The helical content of the template peptide [RLLR](5) was almost completely destroyed at salt concentrations over 200 mm NaCl, leading to a 8-32-fold decrease in antimicrobial activity. However, the introduction of helix-capping motifs at the helix termini resulted in a structurally stable peptide, which retained membrane-permeabilizing and antimicrobial activities upon exposure to salt. Furthermore, the peptide with helix-capping motifs directly inhibited the in vivo growth of Streptococcus pyogenes, which causes localized fasciitis in mice, and prevented the necrosis of the epidermis, dermis, and subcutaneous muscle layers. Results indicate that the adoption of helix-capping motifs into salt-sensitive antimicrobial peptides provides the necessary structural stability for the peptides to permeabilize cell membranes and cause cell death at physiological salt concentrations.
OVARIAN SUPPORT OF PREGNANCY IN AGEING INBRED MICE (1975)

The principal cause of reduced fertility in 10- to 12-month-old female CBA/H-T6 and CBA mice was found to be loss of embryos at the time of, or soon after, implantation. Treatment with exogenous progesterone, but not with oestradiol benzoate, increased the number of old females having implantation sites but did not increase either the average number of implantations/female or postimplantation survival to Day 10. When bovine prolactin or HCG was administered to pregnant old mice, the implantation rate was not increased. It was concluded that the function of the CL of pregnancy in old mice may have been impaired because the lutein cells were failing to respond adequately to the luteotrophic stimulus.
In Vivo Osteogenic Differentiation of Human Adipose-Derived Stem Cells in an Injectable In Situ –Forming Gel Scaffold (2009)

The sol-to-gel transition occurring at around body temperature makes the MPEG-PCL diblock copolymer an ideal candidate material for use as an injectable in situ-forming gel containing human adipose tissue-derived stem cells (hADSCs). The sol can be prepared at room temperature, and the gel forms at body temperature. Solutions of the copolymer containing hADSCs and osteogenic factors injected into rats formed gel scaffolds at the injection sites. The gels thus formed showed the interconnective pore structure required to support growth, proliferation, and differentiation of hADSCs. Bromodeoxyuridine-labeled hADSCs were confirmed to be present in gels formed in vivo. Bone formation was observed only in gel implants containing both hADSCs and osteogenic factors. Subcutaneous implantation of the in situ-forming gel scaffold demonstrated that hADSCs embedded in the gel stimulated much lower host tissue responses than did the gel alone, probably because of the unique immunomodulatory properties of hADSCs. In conclusion, our data on hADSCs embedded in an in situ gel scaffold suggest that this formulation may provide numerous benefits as a noninvasive alternative for tissue-engineered bone formation.
Histopathology of ruby and argon laser lesions in monkey and human retina. A comparative study. (1975)

Suprathreshold fundus lesions produced by ruby and argon laser photocoagulation were studied within 24 hours by light and electron microscopy. It was shown that damage was maximal in the outer retina in all ruby laser lesions and extramacular argon laser lesions. In both monkey and human, inner retinal damage occurred independently of outer retinal damage in macular lesions produced by the argon laser. In lesions produced by equal energy, inner retinal damage was more severe in humans than in monkeys. In both species outer retinal damage was less severe in the foveal than the parafoveal region and this disparity was greater in humans than in monkeys. These findings are important to the therapeutic use of argon laser energy for mascular disease. In particular, absortion of energy in the inner retina reduces the energy available in the treatment of subretinal lesions in the foveal area, and causes unwanted neuroretinal damage. The higher sensitivity to argon laser irradiation of the human fovea compared with the monkey fovea, has not been appreciated when defining laser safety limits.
Attomolar Ultrasensitive MicroRNA Detection by DNA-Scaffolded Silver-Nanocluster Probe Based on Isothermal Amplification (2012)

MicroRNAs (miRNAs) play vital roles in a plethora of biological and cellular processes. The levels of miRNAs can be useful biomarkers for cellular events or disease diagnosis, thus the method for sensitive and selective detection of miRNAs is imperative to miRNA discovery, study, and clinical diagnosis. Here we develop a novel method to quantify miRNA expression levels as low as attomolar sensitivity by target-assisted isothermal exponential amplification coupled with fluorescent DNA-scaffolded AgNCs and demonstrated its feasibility in the application of detecting miRNA in real samples. The method reveals superior sensitivity with a detection limit of miRNA of 2 aM synthetic spike-in target miRNA under pure conditions (approximately 15 copies of a miRNA molecule in a volume of 10 μL) and can detect at least a 10 aM spike-in target miRNA in cell lysates. The method also shows the high selectivity for discriminating differences between miRNA family members, thus providing a promising alternative to standard approaches for quantitative detection of miRNA. This simple and cost-effective strategy has a potential of becoming the major tool for simultaneous quantitative analysis of multiple miRNAs (biomarkers) in tissues or cells and supplies valuable information for biomedical research and clinical early diagnosis.
A new gene involved in DNA double-strand break repair and V(D)J recombination is located on human chromosome 10p (2000)

V(D)J recombination, accountable for the diversity of T cell receptor- and immunoglobulin-encoding genes, is initiated by a lymphoid-specific DNA double-strand break. The general DNA repair machinery is responsible for the resolution of this break. Any defect in one of the known components of the DNA repair/V(D)J recombination machinery (Ku70, Ku80, DNA-PKcs, XRCC4 and DNA ligase IV) leads to abortion of the V(D)J rearrangement process, early block in both T and B cell maturation, and ultimately to severe combined immune deficiency (SCID) in several animal models. A human SCID condition is also characterized by an absence of mature T and B lymphocytes, and is associated with an increase in sensitivity to DNA-damaging agents (RS-SCID). None of the above-mentioned genes are defective in these patients, arguing for the likelihood of the existence of yet another unknown component of the V(D)J recombination/DNA repair apparatus. Athabascan-speaking (SCIDA) Navajo and Apache Native Americans have a very high incidence of T(-)B(-)SCID. The SCIDA locus is highly linked with markers on chromosome 10p, although the exact molecular defect has not been recognized in these patients. We show here that cells with the SCIDA defect are impaired in the DNA repair phase of V(D)J recombination similarly to RS-SCID, precisely an absence of V(D)J coding joint formation. Moreover, genotyping analysis in several RS-SCID families corroborates a linkage of the RS-SCID locus to the SCIDA region on chromosome 10p. These results demonstrate the presence of a new essential DNA repair/V(D)J recombination gene in this region, the mutation of which causes RS-SCID in humans.
Comparative Evaluation of the Effects of Different Photoablative Laser Irradiation Protocols on the Gingiva of Periodontopathic Patients (2012)

This study indicates that periodontopathogens can persist within cells outside the pocket epithelium, despite conventional periodontal treatment. Nd:YAG and diode lasers are able to eradicate intra- and extracellular bacteria from these sites, suggesting that they can be considered suitable devices to improve the clinical outcome of periodontal disease.
A toolkit for detecting and analyzing malicious software (2003)

We present PEAT: the Portable Executable Analysis Toolkit. It is a software prototype designed to provide a selection of tools that an analyst may use in order to examine structural aspects of a Windows Portable Executable (PE) file, with the goal of determining whether malicious code has been inserted into an application after compilation. These tools rely on structural features of executables that are likely to indicate the presence of inserted malicious code. The underlying premise is that typical application programs are compiled into one binary, homogeneous from beginning to end with respect to certain structural features; any disruption of this homogeneity is a strong indicator that the binary has been tampered with. For example, it could now harbor a virus or a Trojan horse program. We present our investigation into structural feature analysis, the development of these ideas into the PEAT prototype, and results that illustrate PEAT's practical effectiveness.
Expression of vascular permeability factor/vascular endothelial growth factor by melanoma cells increases tumor growth, angiogenesis, and experimental metastasis. (1996)

Vascular permeability factor (VPF)/vascular endothelial growth factor (VEGF) is an angiogenic cytokine expressed by many human and animal tumors. Hypoxia often up-regulates VPF/VEGF expression further. To better define the role of VPF/VEGF in tumor biology, we screened tumorigenic lines for those expressing minimal constitutive and hypoxia-inducible VPF/VEGF. Human melanoma SK-MEL-2 cells best fit these criteria and formed small, poorly vascularized tumors in immunodeficient mice. We transfected SK-MEL-2 cells stably with sense or antisense mouse VPF/VEGF cDNA or with vector alone. Cells transfected with sense VPF/VEGF (V+) expressed and secreted large amounts of mouse VPF/VEGF and formed well-vascularized tumors with hyperpermeable blood vessels and minimal necrosis in nude/SCID mice. Antisense-transfected VPF/VEGF (V-) cells expressed reduced constitutive VPF/VEGF and no detectable mouse VPF/VEGF, and formed small, minimally vascularized tumors exhibiting extensive necrosis. Vector-alone transfectants (N1 cells) behaved like parental cells. V+ cells formed numerous lung tumor colonies in SCID mice, approximately 50-fold more than N1 cells, whereas V- cells formed few or none. These experiments demonstrate that VPF/VEGF promotes melanoma growth by stimulating angiogenesis and that constitutive VPF/VEGF expression dramatically promotes tumor colonization in the lung.
Deep Learning-Based Packet Detection and Carrier Frequency Offset Estimation in IEEE 802.11ah (2021)

Wi-Fi systems based on the IEEE 802.11 standards are the most popular wireless interfaces that use Listen Before Talk (LBT) method for channel access. The distinctive feature of a majority of LBT-based systems is that the transmitters use preambles that precede the data to allow the receivers to perform packet detection and carrier frequency offset (CFO) estimation. Preambles usually contain repetitions of training symbols with good correlation properties, while conventional digital receivers apply correlation-based methods for both packet detection and CFO estimation. However, in recent years, data-based machine learning methods are disrupting physical layer research. Promising results have been presented, in particular, in the domain of deep learning (DL)-based channel estimation. In this paper, we present a performance and complexity analysis of packet detection and CFO estimation using both the conventional and the DL-based approaches. The goal of the study is to investigate under which conditions the performance of the DL-based methods approach or even surpass the conventional methods, but also, under which conditions their performance is inferior. Focusing on the emerging IEEE 802.11ah standard, our investigation uses both the standard-based simulated environment, and a real-world testbed based on Software Defined Radios.
Lideratge i xarxes educatives (2011)

En temps de canvi i incertesa, ser capacos com a centres educatius de transformar-nos i innovar es condicio necessaria per a l'exit educatiu. No es estrany, doncs, que la capacitat d'activar tots els recursos humans en un proces transformador, es a dir, la capacitat d'influencia interpersonal o lideratge, hagi estat considerada maxima responsable d'exits o fracassos. I es que el lideratge es com una caixa negra que es capac d'explicar exits i fracassos en l'accio publica.
Exceptional Fluorescence and Hybridization Properties of a Phenylpyrrolocytosine in Peptide Nucleic Acid (2008)

A phenylpyrrolocytosine derivative possessing bis-(ortho-aminoethoxy) substitution has been designed, synthesized and incorporated into PNA resulting in oligomers that demonstrate increased binding affinity for DNA targets. The phenylpyrrolocytosine is an exceptionally fluorescent modified nucleobase possessing a high quantum yield while the fluorescence intensity displays useful environmental sensitivity.
Identification, Cloning, Expression, and Purification of Three Novel Human Calcium-independent Phospholipase A2 Family Members Possessing Triacylglycerol Lipase and Acylglycerol Transacylase Activities (2004)

Genetic knockout of hormone-sensitive lipase in mice has implicated the presence of other intracellular triacylglycerol (TAG) lipases mediating TAG hydrolysis in adipocytes. Despite intense interest in these TAG lipases, their molecular identities thus far are largely unknown. Sequence data base searches for proteins containing calcium-independent phospholipase A2 (iPLA2) dual signature nucleotide ((G/A)XGXXG) and lipase (GXSXG) consensus sequence motifs identified a novel subfamily of three putative iPLA2/lipase family members designated iPLA2epsilon, iPLA2zeta, and iPLA2eta (previously named adiponutrin, TTS-2.2, and GS2, respectively) of previously unknown catalytic function. Herein we describe the cloning, heterologous expression, and affinity purification of the three human isoforms of this iPLA2 subfamily in Sf9 cells, and we demonstrate that each possesses abundant TAG lipase activity. Moreover, iPLA2epsilon, iPLA2zeta, and iPLA2eta also possess acylglycerol transacylase activity utilizing mono-olein as an acyl donor which, in the presence of mono-olein or diolein acceptors, results in the synthesis of diolein and triolein, respectively. (E)-6-(Bromomethylene)-3-(1-naphthalenyl)-2H-tetrahydropyran-2-one, a mechanism-based suicide substrate inhibitor of all known iPLA2s, inhibits the triglyceride lipase activity of each of the three isoforms similarly (IC50=0.1-0.5 microm). Quantitative PCR revealed dramatically increased expression of iPLA2epsilon and iPLA2zeta transcripts during the hormone-induced differentiation of 3T3-L1 cells into adipocytes and identified the presence of all three iPLA2 isoforms in human SW872 liposarcoma cells. Collectively, these results identify three novel TAG lipases/acylglycerol transacylases that likely participate in TAG hydrolysis and the acyl-CoA independent transacylation of acylglycerols, thereby facilitating energy mobilization and storage in adipocytes.
High-performance (Al,Ga)N-based solar-blind ultraviolet p–i–n detectors on laterally epitaxially overgrown GaN (1999)

Solar-blind ultraviolet photodiodes with a band-edge wavelength of 285 nm were fabricated on laterally epitaxially overgrown GaN grown by metalorganic chemical vapor deposition. Current–voltage measurements of the diodes exhibited dark current densities as low as 10 nA/cm2 at −5 V. Spectral response measurements revealed peak responsivities of up to 0.05 A/W. Response times for these diodes were measured to be as low as 4.5 ns for 90%-to-10% fall time. For comparison, diodes were fabricated using the same p–i–n structure deposited on dislocated GaN. These diodes had dark current densities many orders of magnitude higher, as well as a less sharp cutoff, and a significant slow tail under impulse excitation.
Combinatorial optimization with use of guided evolutionary simulated annealing (1995)

Feasible approaches to the task of solving NP-complete problems usually entails the incorporation of heuristic procedures so as to increase the efficiency of the methods used. We propose a new technique, which incorporates the idea of simulated annealing into the practice of simulated evolution, in place of arbitrary heuristics. The proposed technique is called guided evolutionary simulated annealing (GESA). We report on the use of GESA approach primarily for combinatorial optimization. In addition, we report the case of function optimization, treating the task as a search problem. The traveling salesman problem is taken as a benchmark problem in the first case. Simulation results are reported. The results show that the GESA approach can discover a very good near optimum solution after examining an extremely small fraction of possible solutions. A very complicated function with many local minima is used in the second case. The results in both cases indicate that the GESA technique is a practicable method which yields consistent and good near optimal solutions, superior to simulated evolution.
Genomewide Expression Profiling in the Zebrafish Embryo Identifies Target Genes Regulated by Hedgehog Signaling During Vertebrate Development (2006)

Hedgehog proteins play critical roles in organizing the embryonic development of animals, largely through modulation of target gene expression. Little is currently known, however, about the kinds and numbers of genes whose expression is controlled, directly or indirectly, by Hedgehog activity. Using techniques to globally repress or activate Hedgehog signaling in zebrafish embryos followed by microarray-based expression profiling, we have discovered a cohort of genes whose expression responds significantly to loss or gain of Hedgehog function. We have confirmed the Hedgehog responsiveness of a representative set of these genes with whole-mount in situ hybridization as well as real time PCR. In addition, we show that the consensus Gli-binding motif is enriched within the putative regulatory elements of a sizeable proportion of genes that showed positive regulation in our assay, indicating that their expression is directly induced by Hedgehog. Finally, we provide evidence that the Hedgehog-dependent spatially restricted transcription of one such gene, nkx2.9, is indeed mediated by Gli1 through a single Gli recognition site located within an evolutionarily conserved enhancer fragment. Taken together, this study represents the first comprehensive survey of target genes regulated by the Hedgehog pathway during vertebrate development. Our data also demonstrate for the first time the functionality of the Gli-binding motif in the control of Hedgehog signaling-induced gene expression in the zebrafish embryo.