gebhart/patrepeval huggingface dataset:
Purification and structure of mutacin B‐Ny266: a new lantibiotic produced by <i>Streptococcus mutans</i> (1997)

Mutacins are bactericidal substances of proteinaceous nature produced by Streptococcus mutans. Lantibiotics are antibacterial substances containing post-translationally modified amino acids such as lanthionine. Mutacin B-Ny266 was purified from the cell pellet of S. mutans strain Ny266 by ethanol extraction at pH 2.0 followed by reversed-phase chromatography (Sep-Pak cartridge) and by HPLC on a C18 column. The mean purification factor was 3240 +/- 81 and the mean yield was 1.0 +/- 0.1%. Molecular mass of mutacin B-Ny266 as determined by mass spectroscopy is 2270.29 +/- 0.21 Da. The amino acid sequence of the purified active fraction was obtained by Edman degradation after treatment with alkaline ethanethiol. Twenty-one amino acids were detected in this analysis. Mutacin B-Ny266 belongs to the type A lantibiotics. The proposed sequence is: F-K-A-W-U-F-A-Abu-P-G-A-A-K-O-G-A-F-N-U-Y-A. The molecule differs from that of epidermin/staphylococcin 1580 and gallidermin at positions 1, 2, 4, 5 and 6.
Fibroblast growth factor 2‐antagonist activity of a long‐pentraxin 3‐derived anti‐angiogenic pentapeptide (2009)

Fibroblast growth factor-2 (FGF2) plays a major role in angiogenesis. The pattern recognition receptor long-pentraxin 3 (PTX3) inhibits the angiogenic activity of FGF2. To identify novel FGF2-antagonistic peptide(s), four acetylated (Ac) synthetic peptides overlapping the FGF2-binding region PTX3-(97-110) were assessed for their FGF2-binding capacity. Among them, the shortest pentapeptide Ac-ARPCA-NH(2) (PTX3-[100-104]) inhibits the interaction of FGF2 with PTX3 immobilized to a BIAcore sensorchip and suppresses FGF2-dependent proliferation in endothelial cells, without affecting the activity of unrelated mitogens. Also, Ac-ARPCA-NH(2) inhibits angiogenesis triggered by FGF2 or by tumorigenic FGF2-overexpressing murine endothelial cells in chick and zebrafish embryos, respectively. Accordingly, the peptide hampers the binding of FGF2 to Chinese Hamster ovary cells overexpressing the tyrosine-kinase FGF receptor-1 (FGFR1) and to recombinant FGFR1 immobilized to a BIAcore sensorchip without affecting heparin interaction. In all the assays the mutated Ac-ARPSA-NH(2) peptide was ineffective. In keeping with the observation that hydrophobic interactions dominate the interface between FGF2 and the FGF-binding domain of the Ig-like loop D2 of FGFR1, amino acid substitutions in Ac-ARPCA-NH(2) and saturation transfer difference-nuclear magnetic resonance analysis of its mode of interaction with FGF2 implicate the hydrophobic methyl groups of the pentapeptide in FGF2 binding. These results will provide the basis for the design of novel PTX3-derived anti-angiogenic FGF2 antagonists.
Development of a prototype lignin concentration sensor (1993)

The US Department of Energy, Office of Industrial Technologies, is sponsoring a research and development program for the development of a real-time, in-situ sensor to measure the concentration of lignin in wood pulp. The program is composed of phase I showing feasibility which is now complete, phase II for development and testing of a Field Prototype, in progress, Phase III commercialization. Phase I work (funded entirely by B W) demonstrated a correlation between the fluorescence intensity and lignin concentration (as measured by TAPPI procedure, T 236 hm-85 Kappa Number of Pulp) for undiluted wood pulp samples. In Phase II, a laboratory test program directed at characterizing the fluorescence of wood pulp has been conducted as a prelude to the design of a prototype sensor. The current report summarizes the testing completed in Phase I and documents the Phase II laboratory testing completed through December 1991. Future Phase II efforts include additional laboratory testing, design and fabrication of a prototype sensor, and field testing of the prototype sensor. Phase III of the program will concentrate on the incorporation of the sensor into a control system and commercialization of the sensor.
Drift compensation for reduced spatial resolution transcoding (2002)

This paper discusses the problem of reduced-resolution transcoding of compressed video bitstreams. An analysis of drift errors is provided to identify the sources of quality degradation when transcoding to a lower spatial resolution. Two types of drift error are considered: a reference picture error, which has been identified in previous works, and error due to the noncommutative property of motion compensation and down-sampling, which is unique to this work. To overcome these sources of error, four novel architectures are presented. One architecture attempts to compensate for the reference picture error in the reduced resolution, while another architecture attempts to do the same in the original resolution. We present a third architecture that attempts to eliminate the second type of drift error and a final architecture that relies on an intrablock refresh method to compensate for all types of errors. In all of these architectures, a variety of macroblock level conversions are required, such as motion vector mapping and texture down-sampling. These conversions are discussed in detail. Another important issue for the transcoder is rate control. This is especially important for the intra-refresh architecture since it must find a balance between number of intrablocks used to compensate for errors and the associated rate-distortion characteristics of the low-resolution signal. The complexity and quality of the architectures are compared. Based on the results, we find that the intra-refresh architecture offers the best tradeoff between quality and complexity and is also the most flexible.
Cloning of ornithine delta-aminotransferase cDNA from Vigna aconitifolia by trans-complementation in Escherichia coli and regulation of proline biosynthesis. (1993)

Proline prototrophy was restored to an Escherichia coli proBA proline auxotroph by ornithine and a mothbean (Vigna aconitifolia) cDNA expression library. This novel strategy, "trans-complementation," allowed isolation of a cDNA encoding ornithine delta-aminotransferase (delta-OAT). This enzyme transaminates ornithine to glutamic-gamma-semialdehyde (GSA), thereby bypassing the block in GSA synthesis from glutamate in the proBA mutant. The identity of the mothbean enzyme was confirmed by its high sequence homology to mammalian and yeast delta-OATs as well as to a family of bacterial and fungal omega-aminotransferases and an absence of significant homology to various alpha-aminotransferases. The V. aconitifolia OAT cDNA encodes a polypeptide of 48.1 kDa. The native enzyme expressed in E. coli appears to be a monomer with Km of 2 mM for ornithine and 0.75 mM for alpha-ketoglutarate. Levels of mRNA in V. aconitifolia for delta 1-pyrroline-5-carboxylate synthetase (P5CS) and delta-OAT, the two key enzymes for proline synthesis, were monitored under different physiological conditions. Salt stress and nitrogen starvation induced P5CS mRNA levels and depressed OAT mRNA levels. Conversely, OAT mRNA level was elevated in plants supplied with excess nitrogen while the P5CS mRNA level was reduced. These data suggest that the glutamate pathway is the primary route for proline synthesis in plants during conditions of osmotic stress and nitrogen limitation whereas the ornithine pathway assumes prominence under high nitrogen input.
JNK pathway inhibition selectively primes pancreatic cancer stem cells to TRAIL-induced apoptosis without affecting the physiology of normal tissue resident stem cells (2016)

The combination of JNKi and TRAIL significantly impacts on CSCs, but leaves regular tissue-resident stem cells unaffected - even under hypoxic stress conditions. This concept of selective treatment of pancreatic CSCs warrants further evaluation.
Aerated Underbalanced Drilling System Development (2012)

Abstract Texas A&M University recently has established a new method to develop a drilling expert system to provide consultations related to best practices and trouble shooting in aerated underbalanced drilling. The drilling expert system is based on Bayesian network. A Bayesian network is defined as "probabilistic graphical model that represents a set of random variables and their conditional independencies via a directed acyclic graph (DAG)." To the best of the authors' knowledge, this paper is the first study that shows the use of such method in aerated underbalanced drilling engineering. The paper demonstrates the use of Bayesian network to develop the advisory system for aerated underbalanced drilling. To develop this system, we reviewed the literature and interviewed experts to find best practices in aerated underbalanced drilling. The advisory system can be used as a training tool for engineers to show them basic designing steps for aerated UBD.
Robotic ocular ultramicrosurgery (1998)

A clinically usable system using the same principles appears feasible.
Zinc-Adeninate Metal−Organic Framework for Aqueous Encapsulation and Sensitization of Near-infrared and Visible Emitting Lanthanide Cations (2011)

Luminescent metal-organic frameworks (MOFs), Ln(3+)@bio-MOF-1, were synthesized via postsynthetic cation exchange of bio-MOF-1 with Tb(3+), Sm(3+), Eu(3+), or Yb(3+), and their photophysical properties were studied. We demonstrate that bio-MOF-1 encapsulates and sensitizes visible and near-infrared emitting lanthanide cations in aqueous solution.
Modified Veress needle decompression of tension pneumothorax (2013)

Thoracic insufflation produced a reliable and highly reproducible model of tPTX. The mVN is vastly superior to NT for effective and safe tPTX decompression and physiologic recovery. Further research should be invested in the mVN for device refinement and replacement of NT in the field.
ChemInform Abstract: AMINO ACIDS AND PEPTIDES PART 122, SYNTHESIS AND SOME BIOLOGICAL ACTIVITIES OF ANALOGUES OF DEAMINO‐VASOPRESSIN WITH THE DISULPHIDE BRIDGE ALTERED TO A THIOETHER BRIDGE (1974)

Abstract Die Desamino‐vasopressin‐Analogen (I) werden stufenweise nach bekannten Methoden aufgebaut.
Sequence-Specific Electrical Purification of Nucleic Acids with Nanoporous Gold Electrodes (2016)

Nucleic-acid-based biosensors have enabled rapid and sensitive detection of pathogenic targets; however, these devices often require purified nucleic acids for analysis since the constituents of complex biological fluids adversely affect sensor performance. This purification step is typically performed outside the device, thereby increasing sample-to-answer time and introducing contaminants. We report a novel approach using a multifunctional matrix, nanoporous gold (np-Au), which enables both detection of specific target sequences in a complex biological sample and their subsequent purification. The np-Au electrodes modified with 26-mer DNA probes (via thiol-gold chemistry) enabled sensitive detection and capture of complementary DNA targets in the presence of complex media (fetal bovine serum) and other interfering DNA fragments in the range of 50-1500 base pairs. Upon capture, the noncomplementary DNA fragments and serum constituents of varying sizes were washed away. Finally, the surface-bound DNA-DNA hybrids were released by electrochemically cleaving the thiol-gold linkage, and the hybrids were iontophoretically eluted from the nanoporous matrix. The optical and electrophoretic characterization of the analytes before and after the detection-purification process revealed that low target DNA concentrations (80 pg/μL) can be successfully detected in complex biological fluids and subsequently released to yield pure hybrids free of polydisperse digested DNA fragments and serum biomolecules. Taken together, this multifunctional platform is expected to enable seamless integration of detection and purification of nucleic acid biomarkers of pathogens and diseases in miniaturized diagnostic devices.
Slow Wave Applications of Electromagnetically Induced Transparency in Microstrip Resonator (2018)

We report a novel guided-wave resonator that supports multiple bands of electromagnetically induced transparency (EIT). The platform for the spatial and spectral interference is obtained by a microstrip transmission line loaded with proximity-coupled open-circuited stubs. We show experimentally that with two microstrip open stubs, a complete destructive interference takes place leading to a single EIT band with near-unity transmission efficiency. More interestingly, the addition of a third stub results in a supplementary EIT band with a Q-factor of 147 and an effective group refractive index of 530. With the open-stub configuration, the EIT phase response can be dynamically controlled by varying the capacitance between the adjacent stubs without breaking the transmission path of the underlying electromagnetic waves. Therefore, the proposed structure is well suited for buffering and tunable phase modulation applications. Since the proposed structures are compact and fully planar, we anticipate seamless integration with low-profile high frequency electronics.
NS1-Binding Protein (NS1-BP): a Novel Human Protein That Interacts with the Influenza A Virus Nonstructural NS1 Protein Is Relocalized in the Nuclei of Infected Cells (1998)

We used the yeast interaction trap system to identify a novel human 70-kDa protein, termed NS1-binding protein (NS1-BP), which interacts with the nonstructural NS1 protein of the influenza A virus. The genetic interaction was confirmed by the specific coprecipitation of the NS1 protein from solution by a glutathione S-transferase-NS1-BP fusion protein and glutathione-Sepharose. NS1-BP contains an N-terminal BTB/POZ domain and five kelch-like tandem repeat elements of approximately 50 amino acids. In noninfected cells, affinity-purified antibodies localized NS1-BP in nuclear regions enriched with the spliceosome assembly factor SC35, suggesting an association of NS1-BP with the cellular splicing apparatus. In influenza A virus-infected cells, NS1-BP relocalized throughout the nucleoplasm and appeared distinct from the SC35 domains, which suggests that NS1-BP function may be disturbed or altered. The addition of a truncated NS1-BP mutant protein to a HeLa cell nuclear extract efficiently inhibited pre-mRNA splicing but not spliceosome assembly. This result could be explained by a possible dominant-negative effect of the NS1-BP mutant protein and suggests a role of the wild-type NS1-BP in promoting pre-mRNA splicing. These data suggest that the inhibition of splicing by the NS1 protein may be mediated by binding to NS1-BP.
Towards Zero-Shot Scale-Aware Monocular Depth Estimation (2023)

Monocular depth estimation is scale-ambiguous, and thus requires scale supervision to produce metric predictions. Even so, the resulting models will be geometry-specific, with learned scales that cannot be directly transferred across domains. Because of that, recent works focus instead on relative depth, eschewing scale in favor of improved up-to-scale zero-shot transfer. In this work we introduce ZeroDepth, a novel monocular depth estimation framework capable of predicting metric scale for arbitrary test images from different domains and camera parameters. This is achieved by (i) the use of input-level geometric embeddings that enable the network to learn a scale prior over objects; and (ii) decoupling the encoder and decoder stages, via a variational latent representation that is conditioned on single frame information. We evaluated ZeroDepth targeting both outdoor (KITTI, DDAD, nuScenes) and indoor (NYUv2) benchmarks, and achieved a new state-of-the-art in both settings using the same pre-trained model, outperforming methods that train on in-domain data and require test-time scaling to produce metric estimates.
A primary side controller for inductive power transfer systems (2010)

Inductive power transfer (IPT) technology is gaining popularity as an efficient wireless power transfer mechanism in numerous applications, ranging from microwatt bio-engineering implants to high power battery charging systems. A typical IPT system employs two separate controllers on both powering and receiving sides of the system to facilitate contactless power transfer in an efficient and controllable way. This paper presents a new primary side control technique for IPT, which requires only a single controller located on the powering side to effectively control the amount of `contactless' power delivery to the receiving side. In order to regulate the load voltage, the track current is controlled in the proposed technique by accurately estimating the mutual coupling and output voltage through the variation of reflected primary voltage. Theoretical analysis and simulated results are presented, with experimental measurements of a prototype IPT system to validate the viability of the proposed technique. In contrast to existing IPT systems, the proposed IPT system with only a single controller is low in cost, more efficient, and is expected to be the popular choice in applications such as biomedical implants.
A phase II, randomized, open-label, 52-week study of seladelpar in patients with primary biliary cholangitis (2022)

2016-002996-91 LAY SUMMARY: Current treatment options for patients living with primary biliary cholangitis (PBC) are not optimal due to inadequate effectiveness or undesirable side effects. Patients with PBC who took seladelpar, a new treatment being developed for PBC, at increasing doses (2, 5, or 10 mg/day) for 1 year had clinically significant, dose-dependent improvements in key liver tests. Treatment appeared safe and was not associated with any worsening in patient self-reported itch scores.
Dedicated Cone-Beam CT System for Extremity Imaging (2013)

A dedicated extremity cone-beam CT scanner capable of imaging upper and lower extremities (including weight-bearing examinations) provides sufficient image quality and favorable dose characteristics to warrant further evaluation for clinical use.
2‘-<i>O</i>-[2-(Methylthio)ethyl]-Modified Oligonucleotide:  An Analogue of 2‘-<i>O</i>-[2-(Methoxy)-ethyl]-Modified Oligonucleotide with Improved Protein Binding Properties and High Binding Affinity to Target RNA (2002)

A novel 2'-modification, 2'-O-[2-(methylthio)ethyl] or 2'-O-MTE, has been incorporated into oligonucleotides and evaluated for properties relevant to antisense activity. The results were compared with the previously characterized 2'-O-[2-(methoxy)ethyl] 2'-O-MOE modification. As expected, the 2'-O-MTE modified oligonucleotides exhibited improved binding to human serum albumin compared to the 2'-O-MOE modified oligonucleotides. The 2'-O-MTE oligonucleotides maintained high binding affinity to target RNA. Nuclease digestion of 2'-O-MTE oligonucleotides showed that they have limited resistance to exonuclease degradation. We analyzed the crystal structure of a decamer DNA duplex containing the 2'-O-MTE modifcation. Analysis of the crystal structure provides insight into the improved RNA binding affinity, protein binding affinity and limited resistance of 2'-O-MTE modified oligonucleotides to exonuclease degradation.
A Countermeasure for Protecting NTRUSign against the Transcript Attack (2007)

NTRUSign is a lattice-based digital signature scheme proposed by Hoffstein et al. NTRUSign is quite different from many other signature schemes in a sense that its security depends on neither the integer factorization problem nor the discrete logarithm problem but on a geometric problem called the close vector searching problem. However, it is known that there is some vulnerability in NTRUSign, namely there is an attack called the transcript attack. In this paper, we propose a countermeasure for protecting NTRUSign against the transcript attack, and give an improved NTRUSign algorithm.
Facile whole mitochondrial genome resequencing from nipple aspirate fluid using MitoChip v2.0 (2008)

We have demonstrated that NAF is a suitable material for mtDNA sequence analysis using the rapid and reliable MCv2. Somatic mtDNA mutations present in NAF of women with benign breast diseases could potentially be used as risk factors for progression to breast cancer, but this will require a much larger study with clinical follow up.
Design and operation of extremely high vacuum field emission electron gun. (1986)

We report a design for extremely high vacuum (EHV) field emission electron gun. The vacuum of 2.5×10-10 Pa has been attained in this system. Field emission stability of the surface-processed TiC<110> tip has been studied using EHV field emission electron gun.
ChemInform Abstract: Novel Cytotoxic 7‐Iminomethyl and 7‐Aminomethyl Derivatives of Camptothecin. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Cephalosporin‐Derived Inhibitors of β‐Lactamase. Part 4. The C3 Substituent. (2002)

Abstract For Abstract see ChemInform Abstract in Full Text.
Coordinated Multi-Point (CoMP) adaptive estimation and prediction schemes using superimposed and decomposed channel tracking (2013)

Performance of future wireless technologies will depend heavily on cooperation between different transmission/reception nodes in the access network. CoMP (Coordinated Multi-Point) transmission increases the cell edge user performance by reducing the inter-cell interference. UEs (User Equipments) simultaneously receive data from multiple base stations (eNBs) grouped into a joint transmission cluster. Clustering choices need to be optimized by joint use of CoMP adaptive channel estimation and prediction schemes for energy efficiency and capacity improvements. In this paper, various multi-point (multi-eNB) channel estimation/prediction schemes are proposed and analyzed to improve the joint transmission set clustering accuracy. Multi-point CIRs (Channel Impulse Responses) can be tracked either by superimposed or decomposed methods. The latter scheme tracks each multipath component of every CoMP measurement set member and yields more accurate estimates, however leads to significantly higher computation complexity as opposed to the superimposed tracking which tracks the overall CIR. Therefore, UEs need to dynamically switch between the two schemes depending on the serving cluster size and recently observed CoMP characteristics. It is shown that increasing the channel estimation/prediction filter size yields significantly more capacity and energy efficiency improvements for UEs served by larger clusters. It is also demonstrated that the serving eNB can maximize the performance gains by setting the channel prediction range equal to observed system delay between the multi-point CSI reports and data transmission.
Efficient implementation of lifting-based discrete wavelet transform (2002)

A recursive architecture for implementing the lifting-based discrete wavelet transform is proposed. Processing of the transform stages is interleaved, improving the hardware utilisation and efficiency.
Data Driven Game Theoretic Cyber Threat Mitigation (2016)

Penetration testing is regarded as the gold-standard for understanding how well an organization can withstand sophisticated cyber-attacks. However, the recent prevalence of markets specializing in zero-day exploits on the darknet make exploits widely available to potential attackers. The cost associated with these sophisticated kits generally precludes penetration testers from simply obtaining such exploits – so an alternative approach is needed to understand what exploits an attacker will most likely purchase and how to defend against them. In this paper, we introduce a data-driven security game framework to model an attacker and provide policy recommendations to the defender. In addition to providing a formal framework and algorithms to develop strategies, we present experimental results from applying our framework, for various system configurations, on realworld exploit market data actively mined from the darknet.