gebhart/patrepeval huggingface dataset:
Designing optimal pulse-shapers for ultra-wideband radios (2003)

Ultra-wideband (UWB) technology is gaining increasing interest for its potential application to short-range indoor wireless communications. Utilizing ultra-short pulses, UWB baseband transmissions enable rich multipath diversity, and can be demodulated with low complexity receivers. Compliance with the FCC spectral mask, and interference avoidance to, and from, co-existing narrow-band services, calls for judicious design of UWB pulse shapers. This paper introduces pulse shaper designs for UWB radios, which optimally utilize the bandwidth and power allowed by the FCC spectral mask. The resulting baseband UWB systems can be either single-band, or, multi-band. More important, the novel pulse shapers can support dynamic avoidance of narrow-band interference, as well as efficient implementation of fast frequency hopping, without invoking analog carriers.
Wnt/β-catenin signaling is sufficient and necessary for synovial joint formation (2004)

A critical step in skeletal morphogenesis is the formation of synovial joints, which define the relative size of discrete skeletal elements and are required for the mobility of vertebrates. We have found that several Wnt genes, including Wnt4, Wnt14, and Wnt16, were expressed in overlapping and complementary patterns in the developing synovial joints, where beta-catenin protein levels and transcription activity were up-regulated. Removal of beta-catenin early in mesenchymal progenitor cells promoted chondrocyte differentiation and blocked the activity of Wnt14 in joint formation. Ectopic expression of an activated form of beta-catenin or Wnt14 in early differentiating chondrocytes induced ectopic joint formation both morphologically and molecularly. In contrast, genetic removal of beta-catenin in chondrocytes led to joint fusion. These results demonstrate that the Wnt/beta-catenin signaling pathway is necessary and sufficient to induce early steps of synovial joint formation. Wnt4, Wnt14, and Wnt16 may play redundant roles in synovial joint induction by signaling through the beta-catenin-mediated canonical Wnt pathway.
An Architecture for Generating Semantics-Aware Signatures (2006)

Identifying new intrusions and developing effective signatures that detect them is essential for protecting computer networks.We present Nemean, a system for automatic generation of intrusion signatures from honeynet packet traces.Our architecture is distinguished by its emphasis on a modular design framework that encourages independent development and modification of system components and protocol semantics awareness which allows for construction of signatures that greatly reduce false alarms.The building blocks of our architecture include transport and service normalization, intrusion profile clustering and automata learning that generates connection and session aware signatures.We demonstrate the potential of Nemean's semantics-aware, resilient signatures through a prototype implementation.We use two datasets to evaluate the system: (i) a production dataset for false-alarm evaluation and (ii) a honeynet dataset for measuring detection rates.Signatures generated by Nemean for NetBIOS exploits had a 0% false-positive rate and a 0.04% false-negative rate.
Mobilization of seed storage lipid by Arabidopsis seedlings is retarded in the presence of exogenous sugars (2002)

Growth in the presence of exogenous glucose significantly retards mobilization of seed storage lipid in germinating seeds from wild-type Arabidopsis. This effect is not solely due to the osmotic potential of the media, as substantially higher concentrations of sorbitol than of glucose are required to exert significant effects on lipid breakdown. The inhibitory effect of glucose on lipid breakdown is limited to a narrow developmental window, suggesting that completion of some critical metabolic transition results in loss of sensitivity to the inhibitory effect of glucose on lipid breakdown.
Flexible and Stretchable Electronics for Biointegrated Devices (2012)

Advances in materials, mechanics, and manufacturing now allow construction of high-quality electronics and optoelectronics in forms that can readily integrate with the soft, curvilinear, and time-dynamic surfaces of the human body. The resulting capabilities create new opportunities for studying disease states, improving surgical procedures, monitoring health/wellness, establishing human-machine interfaces, and performing other functions. This review summarizes these technologies and illustrates their use in forms integrated with the brain, the heart, and the skin.
Intracellular Metabolism of the Nucleotide Prodrug GS-9131, a Potent Anti-Human Immunodeficiency Virus Agent (2007)

GS-9131 is a phosphonoamidate prodrug of the novel ribose-modified phosphonate nucleotide analog GS-9148 that demonstrates potent anti-human immunodeficiency virus type 1 (HIV-1) activity and an excellent resistance profile in vitro. Prodrug moieties were optimized for the efficient delivery of GS-9148 and its active diphosphate (DP) metabolite to lymphoid cells following oral administration. To understand the intracellular pharmacology of GS-9131, incubations were performed with various types of lymphoid cells in vitro. The intracellular accumulation and antiviral activity levels of GS-9148 were limited by its lack of cellular permeation, and GS-9131 increased the delivery of GS-9148-DP by 76- to 290-fold relative to that of GS-9148. GS-9131 activation was saturable at high extracellular concentrations, potentially due to a high-affinity promoiety cleavage step. Once inside the cells, GS-9148 was efficiently phosphorylated, forming similar amounts of anabolites in primary lymphoid cells. The levels of GS-9148-DP formed in peripheral blood mononuclear cells infected with HIV-1 were similar to that in uninfected PBMCs, and approximately equivalent intracellular concentrations of GS-9148-DP and tenofovir (TVF)-DP were required to inhibit viral replication by 90%. Once it was formed, GS-9148-DP was efficiently retained in activated CD4(+) cells, with a half-life of 19 h. In addition, GS-9131 showed a low potential for drug interactions with other adenine nucleoside/nucleotide reverse transcriptase inhibitors, based on the lack of competition for anabolism between suprapharmacologic concentrations of GS-9148 and TVF and the lack of activity of GS-9131 metabolites against purine nucleoside phosphorylase, an enzyme involved in the clearance of 2',3'-dideoxyinosine. Together, these observations elucidate the cellular pharmacology of GS-9131 and illustrate its efficient loading of lymphoid cells, resulting in a prolonged intracellular exposure to the active metabolite GS-9148-DP.
Multiple Isozymes of Heparan Sulfate/Heparin GlcNAcN-Deacetylase/GlcN N-Sulfotransferase (2001)

We report the cloning and partial characterization of the fourth member of the vertebrate heparan sulfate/heparin: GlcNAc N-deacetylase/GlcN N-sulfotransferase family, which we designate NDST4. Full-length cDNA clones containing the entire coding region of 872 amino acids were obtained from human and mouse cDNA libraries. The deduced amino acid sequence of NDST4 showed high sequence identity to NDST1, NDST2, and NDST3 in both species. NDST4 maps to human chromosome 4q25-26, very close to NDST3, located at 4q26-27. These observations, taken together with phylogenetic data, suggest that the four NDSTs evolved from a common ancestral gene, which diverged to give rise to two subtypes, NDST3/4 and NDST1/2. Reverse transcription-polymerase chain reaction analysis of various mouse tissues revealed a restricted pattern of NDST4 mRNA expression when compared with NDST1 and NDST2, which are abundantly and ubiquitously expressed. Comparison of the enzymatic properties of the four murine NDSTs revealed striking differences in N-deacetylation and N-sulfation activities; NDST4 had weak deacetylase activity but high sulfotransferase, whereas NDST3 had the opposite properties. Molecular modeling of the sulfotransferase domains of the murine and human NDSTs showed varying surface charge distributions within the substrate binding cleft, suggesting that the differences in activity may reflect preferences for different substrates. An iterative model of heparan sulfate biosynthesis is suggested in which some NDST isozymes initiate the N-deacetylation and N-sulfation of the chains, whereas others bind to previously modified segments to fill in or extend the section of modified residues.
Intracellular Induction of Listeria monocytogenes actA Expression (2002)

Following entry into the host cytosol, the bacterial pathogen Listeria monocytogenes dramatically increases the expression of several key virulence factors. The expression of actA, whose protein product is required for L. monocytogenes actin-based intracellular motility, is increased by more than 200-fold in cytosolic bacteria in comparison to broth-grown cultures. Two distinct promoter elements have been reported to regulate actA expression. One promoter is located immediately upstream of actA coding sequences, while the second promoter is contributed by the upstream mpl gene via the generation of an mpl-actA-plcB transcript. A series of L. monocytogenes mutants were constructed to define the contributions of individual promoter elements to actA expression. The intracellular induction of actA expression was found to be dependent upon the actA proximal promoter; the mpl promoter appeared to contribute to the extracellular induction of actA but did not affect intracellular levels of expression. The actA promoter is dependent upon a regulatory factor known as PrfA for transcriptional activation; however, no increase in actA expression was detected following the introduction of a high-affinity PrfA binding site within the actA promoter. The presence of a mutationally activated form of PrfA, known as PrfA*, increased overall actA expression in broth-grown cultures of both wild-type and actA promoter mutant strains, but the levels of induction observed were still approximately 50-fold lower than those observed for intracellularly grown L. monocytogenes. Collectively, these results indicate that the dramatic induction of actA expression that occurs in the host cell cytosol is mediated through a single promoter element. Furthermore, intracellular induction of actA appears to require additional steps or factors beyond those necessary for the activation and binding of PrfA to the actA promoter.
Comparison of upgrade techniques for mobile communication systems (2002)

For current mobile communication systems, two limitations exist which restrict their capacity and range of application. They can be characterised as an equipment limit which is determined by the maximum number of mobile stations that can be supported by a base station with given equipment, and an interference limit, which corresponds to a maximum number of carriers that can be used in a cell if a given signal-to-interference ratio must be guaranteed. Depending on base station (BS) equipment dimensioning and propagation conditions in the cell coverage area, one of the two limits will apply and define a maximum capacity of the base station that cannot be exceeded without modifications of the base station. Several techniques for base station upgrades have been developed which focus on one of the two limits or both. In the paper, traditional techniques such as spectrum upgrade, sectorisation, codec rate reduction and cell splitting are revised and compared to a new technique called A-SDMA (adaptive space division multiple access), which is introduced. Based on the comparison, evolution plans for different areas of application are developed which take these upgrade techniques into account and provide upgrade paths for mobile communication system infrastructures, applicable to current systems such as GSM as well as future systems (UMTS, FPLMTS).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Analysis of Intraocular Straylight, Especially in Relation to Age (1995)

Purpose. To analyze straylight resulting from different sources (cornea, lens, wall translucency, and fundus reflectance) in combination with different properties (age and pigmentation). To give formulas for straylight calculations. Methods. In straylight on the retina multiple scattering can be assumed to be unimportant. Consequently, an additive model can be applied. Results. An efficient parameter to quantify straylight is the “straylight parameter” s(θ), with θ the scatter angle. The model reads s(θ)=scornea(θ) + slens(θ) + swall(θ) + sfundus(θ) and each of these sources is analyzed as sx(θ)=sxbase(θ) + a(age)*sxage(θ) + p(pigm.)*sxpigm (θ). Conclusions. The most important effects, VIZ., Slenage, swall+fundus,plgm. an sComea +lens + fundus, base as well as a(age) and p(pigm.) were estimated. With the straylight parameter different effects of straylight, notably its disabling effect of contrast reduction, follow directly.
Application of CRISPR-Cas12a temperature sensitivity for improved genome editing in rice, maize, and Arabidopsis (2019)

Our study demonstrates the use of high-temperature regimes to achieve high editing efficiencies with Cas12a systems in rice, Arabidopsis, and maize and sheds light on the mechanism of temperature sensitivity for Cas12a in plants.
Ethylene Polymerization Behavior of Tris(pyrazolyl)borate Titanium(IV) Complexes (2002)

A set of Tp‘TiCl3 and Tp‘TiCl2(OR) complexes containing tris(pyrazolyl)borate ligands with diverse steric properties has been evaluated for ethylene polymerization under MAO activation conditions (Tp‘ = HB(3-mesitylpyrazolyl)2(5-mesitylpyrazolyl)- (TpMs*), HB(3-mesitylpyrazolyl)3 - (TpMs), HB(3,5-Me2-pyrazolyl)3 - (Τp*), HB(pyrazolyl)3 - (Tp), BuB(pyrazolyl)3 - (BuTp)). The activity of Tp‘TiX3/MAO varies in the order TpMs*TiCl3 (10c) > TpMsTiCl3 ≫ Τp*TiCl3, TpTiCl3, BuTpTiCl3, Tp*TiCl2(OtBu), Tp*TiCl2(O-2-tBu-C6H4). The activity of 10c/MAO is similar to that of Cp2ZrCl2/MAO. High MAO levels or addition of AlMe3 decrease the activity of 10c/MAO, probably due to coordination of AlMe3 to the active Ti species. The predominant chain transfer mechanism for 10c/MAO is chain transfer to AlMe3, which results in broad molecular weight distributions at low Al/Ti ratios (Al/Ti = 200−1000). At very high Al levels (10c/5000 MAO or 10c/1000 MAO/4000 AlMe3) bimodal molecular weight distributions comprising a major low molecular weight fraction (M w/M n ca. 3) and a minor high molecular weight fraction are observed, which suggests that several active species are present, only one of which undergoes efficient chain transfer to Al.
Antistreptolysin O and Anti-Deoxyribonuclease B Titers: Normal Values for Children Ages 2 to 12 in the United States (1998)

The age-specific values for GMT and ULN for this group of children from 23 states were slightly higher than previously reported. These values are likely representative of the pediatric population in the United States and should be of clinical value to physicians, epidemiologists, and clinical laboratory personnel.
Insight into the biosensing of graphene oxide: Present and future prospects (2015)

Graphene oxide, a century old material has attracted the interest of researchers owing to its specific 2D structure and unique electronic, optical, thermal, mechanical and electrochemical properties. The recent advancements in the field of biotechnology and biomedical engineering are targeted at exploring the biosensing applications of graphene oxide due to its biocompatibility. It is considered to be one of the most versatile materials, with wide range of applications which can be tailored by functionalization of the different oxygen containing groups present in the structure. In this review the focus is on the biosensing applications of graphene oxide, detection of analytes with high sensitivity and selectivity. This would give insight into the designing of feasible protocols for the analysis of therapeutic diseases and environmental safety, thereby improving the quality of human life.
The 5 minute rule for trading memory for disc accesses and the 10 byte rule for trading memory for CPU time (1987)

If an item is accessed frequently enough, it should be main memory resident. For current technology, “frequently enough” means about every five minutes.Along a similar vein, one can frequently trade memory space for CPU time. For example, bits can be packed in a byte at the expense of extra instructions to extract the bits. It makes economic sense to spend ten bytes of main memory to save one instruction per second.These results depend on current price ratios of processors, memory and disc accesses. These ratios are changing and hence the constants in the rules are changing.
Defensins and other endogenous peptide antibiotics of vertebrates (1995)

Gene-encoded peptide antibiotics are ubiquitous components of host defenses in mammals, birds, amphibia, insects, and plants. Their de novo synthesis or release from storage sites can be induced rapidly, which makes them particularly important in the initial phases of resistance to microbial invasion. The endogenous antimicrobial peptides of animals are products of single genes and are synthesized as preproproteins. Multistep processing yields the mature peptide, which generally acts by inducing microbial membrane permeabilization. Several families of antimicrobial peptides have been identified that differ with respect to the presence of disulfide linkages, amino acid composition, structural conformation, and spectrum of activity. The arginine-rich three disulfide-containing beta-sheet defensins are remarkably abundant and widely distributed in animals and plants. The antibiotic peptides of higher eukaryotes merit further study for their role in natural immunity and their potential as novel therapeutic compounds.
Liposome Drug Delivery Systems (2024)

Guide to current liposome drug delivery technology. Applications, preparation, pharmacokinetics, stability, passive and active targeting, and industrial production. Special emphasis on "stealth" liposomes (liposomes with extended circulation times).
Stem Cell Therapy for Diabetes: A Call for Efficient Differentiation of Pancreatic Progenitors (2012)

Stem Cell Therapy for Diabetes: A Call for Efficient Differentiation of Pancreatic Progenitors Given the capacity of differentiating into functional beta cells in vivo, transplantation of pancreatic progenitors derived from human embryonic stem cells (hESCs) has been considered as a promising avenue in beta cell replacement therapy . Besides the concerns of preventing teratoma formation, reducing host immune system rejection and other related safety issues , generating sufficient number of pancreatic progenitors is one of the priorities before any consideration of clinical application.
Ion-Exchange Chromatography (2004)

Ion-exchange chromatography is one of the most widely used forms of column chromatography. It is used in research, analysis, and process-scale purification of proteins. Ion exchange is ideal for initial capture of proteins because of its high capacity, relatively low cost, and its ability to survive rigorous cleaning regimes. Ion exchange is also ideal for “polishing” of partially purified material on account of the high-resolution attainable and the high capacity giving the ability to achieve a high concentration of product. Ion-exchange chromatography is widely applicable because the buffer conditions can be adapted to suit a broad range of proteins rather than being applicable to a single functional group of proteins.
Low-fidelity Pyrococcus furiosus DNA polymerase mutants useful in error-prone PCR (2004)

Random mutagenesis constitutes an important approach for identifying critical regions of proteins, studying structure-function relations and developing novel proteins with desired properties. Perhaps, the most popular method is the error-prone PCR, in which mistakes are introduced into a gene, and hence a protein, during DNA polymerase-catalysed amplification cycles. Unfortunately, the relatively high fidelities of the thermostable DNA polymerases commonly used for PCR result in too few mistakes in the amplified DNA for efficient mutagenesis. In this paper, we describe mutants of the family B DNA polymerase from Pyrococcus furiosus (Pfu-Pol), with superb performance in error-prone PCR. The key amino acid changes occur in a short loop linking two long alpha-helices that comprise the 'fingers' sub-domain of the protein. This region is responsible for binding the incoming dNTPs and ensuring that only correct bases are inserted opposite the complementary base in the template strand. Mutations in the short loop, when combined with an additional mutation that abolishes the 3'-5' proof-reading exonuclease activity, convert the extremely accurate wild-type polymerase into a variant with low fidelity. The mutant Pfu-Pols can be applied in error-prone PCR, under exactly the same conditions used for standard, high-fidelity PCR with the wild-type enzyme. Large quantities of amplified product, with a high frequency of nearly indiscriminate mutations, are produced. It is anticipated that the Pfu-Pol variants will be extremely useful for the randomization of gene, and hence protein, sequences.
Increased capillary endothelial cell protease activity in response to angiogenic stimuli in vitro. (1983)

Bovine capillary endothelial (BCE) cells produce increased amounts of the proteases plasminogen activator (PA) and latent collagenase when cultured in the presence of the following preparations which are known to contain angiogenic activities: bovine retinal extract, mouse adipocyte conditioned medium, and human hepatoma cell lysate. These preparations stimulated both BCE cell PA and collagenase activities in a dose-dependent manner. Both activities were increased to about the same level by these preparations as by the tumor promoter 12-O-tetradecanoylphorbol 13-acetate. Mitogens that are not angiogenic, such as insulin, epidermal and fibroblast growth factors, and endothelial cell growth supplement, had no effect on BCE cell PA and collagenase activities. Two of the angiogenic preparations (retinal extract and mouse adipocyte-conditioned medium) had no effect on PA activity in endothelial cells derived from bovine aortae (BAE cells). The angiogenic preparations had little (human hepatoma cell lysate, mouse adipocyte-conditioned medium) or no (bovine retinal extract) effect on BAE cell collagenase activities. In the bovine system, the induction of high levels of both PA and collagenase activities by angiogenic preparations is limited to capillary endothelial cells.
Novel Paromamine Derivatives Exploring Shallow-Groove Recognition of Ribosomal- Decoding-Site RNA (2002)

Natural aminoglycoside antibiotics recognize an internal loop of bacterial ribosomal-decoding-site RNA by binding to the deep groove of the RNA structure. We have designed, synthesized, and tested RNA-targeted paromamine derivatives that exploit additional interactions on the shallow groove face of the decoding-site RNA. An in vitro transcription-translation assay of a series of 6'-derivatives showed the 6'-position to be very sensitive to substitution. This result suggests that the group at the 6'-position plays a pivotal role in RNA target recognition.
A SmartBIST variant with guaranteed encoding (2002)

SmartBIST is a name for a family of streaming scan test pattern decoders that are suitable for on-chip integration. The automatic test pattern generation (ATPG) algorithms are modified to generate scan test stimulus vectors in a highly compacted source format that is compatible with the SmartBIST decoder hardware. The compacted stimulus vectors are streamed from automatic test equipment (ATE) to the decoder, which expands the data stream in real-time into fully expanded scan test vectors. SmartBIST encoding and decoding use simple algebraic techniques similar to those used for LFSR-coding (also known as LFSR-reseeding). The specific SmartBIST implementation shown in this paper guarantees that all test cubes can be successfully encoded by the modified ATPG algorithm irrespective of the number and position of the care bits.