gebhart/patrepeval huggingface dataset:
Conformation‐function relationships in LHRH analogs (1993)

Systematic energy calculations were performed for a series of LHRH analogs including five agonists with substitutions of D- or N-Me-amino acid residues in positions 4, 6 and 7, and five antagonists with substitutions of D-, N-Me- or alpha-Me-amino acid residues in positions 1, 2, 3, 6, 7 and 10, as well as a bicyclic LHRH antagonist. The geometrical shapes of the calculated low-energy backbone structures for each compound were compared to those of LHRH itself. It appeared that the beta-II' turn at the Tyr5-Gly6-Leu7-Arg8 central tetrapeptide is the common structure for all LHRH agonists considered. LHRH antagonists also possess a common chain reversal in the central tetrapeptide, but it is different from that for LHRH agonists. The LHRH agonists share a similar low-energy conformer at the level of the entire peptide backbone. A characteristic feature of this conformer is a 'surface' formed by a 'polygon' with hydrophobic moieties of pGlu1, Trp3, Tyr5, Leu7 and Pro9 in the corners and with the side chain of the His2 residue in the middle, the latter being crucial for a manifestation of LHRH agonistic activity. Since the N-terminal tripeptide of LHRH presumably participates in a direct interaction with specific receptors, it is legitimate to suggest that the beta-II' turn in the central tetrapeptide maintains the proper spatial arrangement of the N-terminal tripeptide. On the other hand, LHRH antagonists considered in this study were shown to possess low-energy structures, with the spatial arrangement of the residues in the N-terminal tripeptide similar to that of agonists. This would suggest a new approach to the design of LHRH antagonists, namely by stabilizing this specific arrangement, rather than the beta-II' turn in the central tetrapeptide.
SHCoClust, a scalable similarity-based hierarchical co-clustering method and its application to textual collections (2017)

In comparison with flat clustering methods, such as K-means, hierarchical clustering and co-clustering methods are more advantageous, for the reason that hierarchical clustering is capable to reveal the internal connections of clusters, and co-clustering can yield clusters of data instances and features. Interested in organizing co-clusters in hierarchy and in discovering cluster hierarchies inside co-clusters, in this paper, we propose SHCoClust, a scalable similarity-based hierarchical co-clustering method. Except possessing the above-mentioned advantages in unison, SHCoClust is able to employ kernel functions, thanks to its utilization of inner product. Furthermore, having all similarities between 0 and 1, the input of SHCoClust can be sparsified by threshold values, so that less memory and less time are required for storage and for computation. This grants SHCoClust scalability, i.e, the ability to process relatively large datasets with reduced and limited computing resources. Our experiments demonstrate that SHCoClust significantly outperforms the conventional hierarchical clustering methods. In addition, with sparsifying the input similarity matrices obtained by linear kernel and by Gaussian kernel, SHCoClust is capable to guarantee the clustering quality, even when its input being largely sparsified. Consequently, up to 86% time gain and on average 75% memory gain are achieved.
Tantalum Acetabular Cups Provide Secure Fixation in THA after Pelvic Irradiation at Minimum 5-year Followup (2012)

Level IV, therapeutic study. See Guidelines for Authors for a complete description of levels of evidence.
On the Performance of LoRa-Enabled Backscatter Communication (2022)

&lt;p&gt;The wireless networks of the future are evolving to enable reliable communication for resource-constrained, miniaturized internet of things (IoT) devices, which will place stringent demands on future sixth-generation (6G) mobile networks. These demands include low cost, very low latency, improved spectrum, and power efficiency, higher reliability, and significantly improved data rates. Emphasizing that these devices have limited functionality and may be placed in inaccessible locations, replacing or recharging batteries can be a daunting task, so energy-efficient solutions should be developed to ensure uninterrupted, seamless wireless communication for the power-constrained IoT devices. In this paper, we consider the integration of long-range (LoRa) modulation into backscatter communications (BackCom), and we develop a mathematical framework in order to investigate the error rate performance of the considered system model. In particular, we derive novel exact and approximated closed-form expressions for the symbol error rate (SER), under the assumption of canceled radio-frequency (RF) interference. The obtained analytical results, corroborated by numerical results, confirm the advantages of integrating LoRa into BackCom system as a low-complex technique in order to extend the transmission distance in power-limited backscatter devices. &lt;/p&gt;
Sinusoidal substitution — An integrated parametric tool for enhancement of transform-based perceptual audio coders (2014)

Transform-based audio coders are the preferred technique for music data compression. However, at low bitrates, traditional coders based on Modified Discrete Cosine Transform are prone to strong warbling and roughness artifacts originating from sparsely coded tonal components. Parametric coders, in turn, suffer from an unpleasantly artificial sound and do not scale well up to perceptual transparency. Hybrid transform-based and parametric coding could potentially overcome the limits of the individual approaches. Yet, existing hybrid coders are hampered by the lack of integrative interplay between both techniques. We outline our ideas how to tightly integrate transform-based coding and parametric coding to obtain an enhanced perceptual quality and scalability. Also, we provide listening test results which demonstrate the benefits of our hybrid coder design.
Pharmacokinetics of a Lidocaine Patch 5% in Dogs (2006)

Lidocaine is increasingly used in transdermal drug delivery systems for different pain conditions in human medicine whereby several pharmacokinetic studies have demonstrated minimal systemic absorption in men. In the present study, the pharmacokinetics of a lidocaine patch 5% was studied in six dogs. In the first experiment, one single lidocaine patch was applied for 12 h to the lateral side of the thorax after removing the hair either by clipping or by the application of a depilatory agent, according to a two-way crossover design. No potential adverse effects induced by the patches were observed in either group. In dogs with clipped hair, a mean peak plasma lidocaine concentration of 62.94 ng/ml was obtained after 10.67 h. In the depilatory group, a mean peak plasma concentration of 103.55 ng/ml was reached after 9.27 h. Significant differences in the AUC(0 --> infinity), C(max), k(a) and T(1/2a) were noticed between the two groups. No significant differences were found for the elimination parameters and for T(max). In the second experiment, the patches were applied for 60 h to the clipped skin in order to study the absorption kinetics after a prolonged application period. There, the mean peak lidocaine plasma concentration was 45.18 ng/ml achieved after 24 h and a final concentration of 29.37 ng/ml was obtained at 60 h. In conclusion, all dogs tolerated the transdermal lidocaine patch well. The results of this study suggest that there is an overall minimal absorption from the lidocaine patch. However, the application of a depilatory agent leads to a more rapid and increased absorption of lidocaine.
Gallium Maltolate Disrupts Tumor Iron Metabolism and Retards the Growth of Glioblastoma by Inhibiting Mitochondrial Function and Ribonucleotide Reductase (2018)

Gallium, a metal with antineoplastic activity, binds transferrin (Tf) and enters tumor cells via Tf receptor1 (TfR1); it disrupts iron homeostasis leading to cell death. We hypothesized that TfR1 on brain microvascular endothelial cells (BMEC) would facilitate Tf-Ga transport into the brain enabling it to target TfR-bearing glioblastoma. We show that U-87 MG and D54 glioblastoma cell lines and multiple glioblastoma stem cell (GSC) lines express TfRs, and that their growth is inhibited by gallium maltolate (GaM) <i>in vitro</i> After 24 hours of incubation with GaM, cells displayed a loss of mitochondrial reserve capacity followed by a dose-dependent decrease in oxygen consumption and a decrease in the activity of the iron-dependent M2 subunit of ribonucleotide reductase (RRM2). IHC staining of rat and human tumor-bearing brains showed that glioblastoma, but not normal glial cells, expressed TfR1 and RRM2, and that glioblastoma expressed greater levels of H- and L-ferritin than normal brain. In an orthotopic U-87 MG glioblastoma xenograft rat model, GaM retarded the growth of brain tumors relative to untreated control (<i>P</i> = 0.0159) and reduced tumor mitotic figures (<i>P</i> = 0.045). Tumors in GaM-treated animals displayed an upregulation of TfR1 expression relative to control animals, thus indicating that gallium produced tumor iron deprivation. GaM also inhibited iron uptake and upregulated TfR1 expression in U-87 MG and D54 cells <i>in vitro</i> We conclude that GaM enters the brain via TfR1 on BMECs and targets iron metabolism in glioblastoma <i>in vivo,</i> thus inhibiting tumor growth. Further development of novel gallium compounds for brain tumor treatment is warranted. <i>Mol Cancer Ther; 17(6); 1240-50. ©2018 AACR</i>.
Data from The Phosphoinositide 3-Kinase Regulatory Subunit p85α Can Exert Tumor Suppressor Properties through Negative Regulation of Growth Factor Signaling (2023)

&lt;div&gt;Abstract&lt;p&gt;Phosphoinositide 3-kinase (PI3K) plays a critical role in tumorigenesis, and the PI3K p85 regulatory subunit exerts both positive and negative effects on signaling. Expression of &lt;i&gt;Pik3r1&lt;/i&gt;, the gene encoding p85, is decreased in human prostate, lung, ovarian, bladder, and liver cancers, consistent with the possibility that p85 has tumor suppressor properties. We tested this hypothesis by studying mice with a liver-specific deletion of the Pik3r1 gene. These mice exhibited enhanced insulin and growth factor signaling and progressive changes in hepatic pathology, leading to the development of aggressive hepatocellular carcinomas with pulmonary metastases. Liver tumors that arose exhibited markedly elevated levels of phosphatidylinositol (3,4,5)-trisphosphate, along with Akt activation and decreased PTEN expression, at both the mRNA and protein levels. Together, these results substantiate the concept that the p85 subunit of PI3K has a tumor-suppressive role in the liver and possibly other tissues. Cancer Res; 70(13); 5305–15. ©2010 AACR.&lt;/p&gt;&lt;/div&gt;
Response : A Truncated Erythropoietin Receptor and Cell Death (1993)

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Characterization of a new potential virulence factor of Microsporum canis, the secreted subtilisin Sub6 (2011)

Background: Microsporum canis is a dermatophyte responsible for cutaneous superficial mycoses in domestic carnivores and humans. The pathogenesis of dermatophytoses, including M. canis infections, remains poorly understood. Secreted proteases including members of the subtilisin family are thought to be involved in the infection process. In particular the subtilisin Sub6 could represent a major virulence factor.Objective: The aim of this work was to (i) isolate the M. canis SUB6 genomic DNA and cDNA (ii) produce Sub6 as a recombinant protease (rSub6) and (iii) produce a specific anti-Sub6 polyclonal serum. Material and methods: Genomic SUB6 was amplified by PCR using specific primers and M. canis IHEM 21239 DNA as a target. The SUB6 cDNA was obtained by reverse transcriptase (RT)-PCR using total RNA extracted from the same M. canis strain grown in liquid medium containing feline keratin as unique nitrogen source. Both SUB6 cDNA and genomic DNA were sequenced. The SUB6 cDNA was cloned in pPICZA to produce recombinant Sub6 (rSub6) in Pichia pastoris KM71. This protease rSub6 was produced in methanol medium at a yield of 30 mg ml)1 and purified by anion exchange chromatography using a DEAE-sepharose column. Polyclonal antibodies against purified rSub6 were produced in a rabbit using a standard immunization procedure with saponin as the adjuvant. Seventy days after the first immunization, serum was collected and IgG were purified by affinity chromatography.Results: The coding sequence for M. canis SUB6 from genomic DNA contains 1410 bp and 3 introns, while the cDNA contains a 1221 bp open reading frame. Deduced amino acid sequence analysis revealed that Sub6 is synthesized as a 406 amino acids preproprotein. The predicted catalytic domain has 286 amino acids, a molecular mass of 29.1 kDa and five potential N-glycosylation sites. SDS-PAGE of rSub6 revealed a single polypeptide chain with an apparent molecular mass of 37 kDa. Purified rabbit IgG were shown to be specific for Sub6 using ELISA.Conclusion: We have characterized for the first time Sub6 from a dermatophyte species as a recombinant secreted active enzyme and purified it until homogeneity. Active rSub6 and Sub6 specific antiserum will be used to further study the role of M. canis Sub6 protease in pathogenesis, notably the pattern of in vivo Sub6 secretion in different host species.
Network Utility Aware Traffic Loading Balancing in Backhaul-constrained Cache-enabled Small Cell Networks with Hybrid Power Supplies (2014)

Explosive data traffic growth leads to a continuous surge in capacity demands across mobile networks. In order to provision high network capacity, small cell base stations (SCBSs) are widely deployed. Owing to the close proximity to mobile users, SCBSs can effectively enhance the network capacity and offloading traffic load from macro BSs (MBSs). However, the cost-effective backhaul may not be readily available for SCBSs, thus leading to backhaul constraints in small cell networks (SCNs). Enabling cache in BSs may mitigate the backhaul constraints in SCNs. Moreover, the dense deployment of SCBSs may incur excessive energy consumption. To alleviate brown power consumption, renewable energy will be explored to power BSs. In such a network, it is challenging to dynamically balance traffic load among BSs to optimize the network utilities. In this paper, we investigate the traffic load balancing in backhaul-constrained cache-enabled small cell networks powered by hybrid energy sources. We have proposed a network utility aware (NUA) traffic load balancing scheme that optimizes user association to strike a tradeoff between the green power utilization and the traffic delivery latency. On balancing the traffic load, the proposed NUA traffic load balancing scheme considers the green power utilization, the traffic delivery latency in both BSs and their backhaul, and the cache hit ratio. The NUA traffic load balancing scheme allows dynamically adjusting the tradeoff between the green power utilization and the traffic delivery latency. We have proved the convergence and the optimality of the proposed NUA traffic load balancing scheme. Through extensive simulations, we have compared performance of the NUA traffic load balancing scheme with other schemes and showed its advantages in backhaul-constrained cache-enabled small cell networks with hybrid power supplies.
Traceback Framework against Botmaster by Sharing Network Communication Pattern Information (2011)

In order to exterminate a botnet, we have to trace a botnet and arrest its botmaster. In this paper, we make a model of communication pattern of a C&C server that sends/receives packets to/from the botmaster. Then we discuss how botmaster trace back can be achieved. We describe which communication patterns we should focus on to find the botmaster or upper C&C servers. Furthermore, we propose a framework for botmaster trace back. In this framework, owners of servers which become to C&C server will collaborate and share the communication patterns for trace back. To do this, we propose the information sharing using communication pattern monitoring tools with the servers.
Ring-by-Ring Femtosecond Inscription of a Multilayer Single-mode Bragg Grating in Sapphire Optical Fiber (2022)

A multilayer Bragg grating was inscribed in sapphire optical fiber using a femtosecond laser. The grating was single-mode at 1550 nm with a ~0.3 nm bandwidth, showing potential for multi-point high-temperature sensing.
Neuronal Dynamics (2014)

What happens in our brain when we make a decision? What triggers a neuron to send out a signal? What is the neural code? This textbook for advanced undergraduate and beginning graduate students provides a thorough and up-to-date introduction to the fields of computational and theoretical neuroscience. It covers classical topics, including the Hodgkin-Huxley equations and Hopfield model, as well as modern developments in the field such as Generalized Linear Models and decision theory. Concepts are introduced using clear step-by-step explanations suitable for readers with only a basic knowledge of differential equations and probabilities, and are richly illustrated by figures and worked-out examples. End-of-chapter summaries and classroom-tested exercises make the book ideal for courses or for self-study. The authors also give pointers to the literature and an extensive bibliography, which will prove invaluable to readers interested in further study.
Photonic effects in the deactivation of ion implanted arsenic (1998)

Observation has been made of a photonic enhancement effect during optical rapid thermal annealing (RTA) of high dose, As implants in Si. Arsenic implant activation using optical radiation heating from tungsten–halogen lamps, λpeak=0.8 μm, was compared with annealing in a continuously heated rapid thermal vertical furnace, λpeak=2 μm. Energetic photons assist in the rapid deactivation of electrically active As+ to its equilibrium value in less than 5 s at the annealing temperature of 1000 °C. A model is presented for rapid As deactivation which is based upon the lowering of reaction energies through electron/hole recombination events. Transient-enhanced diffusion is observed in the RTA sample but not in the furnace-annealed sample. Rapid deactivation by recombination-enhanced processes causes the generation of excess self-interstitials of sufficient concentrations to contribute to the growth of end-of-range dislocation loops at the original amorphous/crystalline interface. After deactivation ends and the excess self-interstitials dissipate, the loops are able to dissolve and coarsen, thereby emitting self-interstitials which cause As transient-enhanced diffusion (TED) in the lower concentration portions of the RTA-annealed As profile. By contrast, end-of-range loops in samples similarly annealed in the vertical furnace are somewhat smaller but of higher density, and a 1000 °C, 15 s anneal results in As deactivation overshoot where [As+] drops below the electrical solubility limit. No As TED was observed in this sample due to the absorption of excess self-interstitials by the growing loops over the duration of the anneal.
A low-profile spiral termination helical antenna (2017)

The spiral termination helical antenna is proposed in this paper. To reduce axial length, the number of helical turns is selected to be two turns and the pitch angle is selected to be 2.5°. The axial length of the proposed antenna is 0.15 λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> (46 mm). It is reduced to 80% of conventional low-profile helical antenna. The gain of proposed antenna is 9.6 dB and 3 dB axial ratio bandwidth is 10%.
Torsional properties of implant grade titanium (1991)

The purpose of this research was to evaluate the torsional strength and ductility of CP titanium in the as received condition, heat treated below the alpha----beta transition temperature, and glass bead blasted. Results were compared to as-received samples of implant quality 316L stainless steel. Little or no effect of any of the treatments was noted. The torsional strength of all titanium samples was comparable to 316L stainless and the torsional ductility of the titanium was significantly greater than 316L stainless (p less than .01). These results are significantly different than those obtained when torsion testing bone screws of the same material. A hypothesis is proposed for the differences in these results.
Genome-Wide Identification of WRKY Genes in Artemisia annua: Characterization of a Putative Ortholog of AtWRKY40 (2020)

<i>Artemisia annua</i> L. is well-known as the plant source of artemisinin, a sesquiterpene lactone with effective antimalarial activity. Here, a putative ortholog of the <i>Arabidopsis thaliana</i> WRKY40 transcription factor (TF) was isolated via reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends in <i>A. annua</i> and named <i>AaWRKY40</i>. A putative nuclear localization domain was identified in silico and experimentally confirmed by using protoplasts of <i>A. annua</i> transiently transformed with <i>AaWRKY40-GFP</i>. A genome-wide analysis identified 122 <i>WRKY</i> genes in <i>A. annua</i>, and a manually curated database was obtained. The deduced proteins were categorized into the major WRKY groups, with group IIa containing eight WRKY members including AaWRKY40. Protein motifs, gene structure, and promoter regions of group IIa WRKY TFs of <i>A. annua</i> were characterized. The promoter region of <i>AaWRKY</i> group IIa genes contained several abiotic stress <i>cis</i>-acting regulatory elements, among which a highly conserved W-box motif was identified. Expression analysis of <i>AaWRKY40</i> compared to <i>AaWRKY1</i> in <i>A. annua</i> cell cultures treated with methyl jasmonate known to enhance artemisinin production, suggested a possible involvement of <i>AaWRKY40</i> in terpenoid metabolism. Further investigation is necessary to study the role of AaWRKY40 and possible interactions with other TFs in <i>A. annua</i>.
Cytostasis of different tumours by a murine PPD-reactive CD4+ T lymphocyte clone is mediated by interferon-gamma and tumour necrosis factor alone or synergistically (1990)

We have shown that a murine CD4+ PPD-reactive T lymphocyte clone was weakly cytotoxic towards the syngeneic tumour B16 melanoma and MC6A fibrosarcoma which had been coated with PPD using a monoclonal antibody-PPD heteroconjugate. Cell-free supernatants produced by PPD-stimulated T lymphocyte clones were however highly cytostatic for the two tumour targets when assayed over 48-72 h. In this study we have demonstrated good titres of tumour necrosis factor (TNF) and interferon-gamma (IFN-gamma) in the supernatants, which accounted for their observed cytostatic activity on the tumour targets. The high level of cytostasis seen with the B16 melanoma using the supernatants could be attributed to their sensitivity to the cytostatic activity of IFN-gamma; the lower levels of cytostasis seen with the IFN-gamma-resistant MC6A target was the result of IFN-gamma increasing the sensitivity of this target to TNF. Antibodies to IFN-gamma were able to neutralize the majority of the cytostatic activity of the supernatants on both targets, consistent with the role demonstrated for this lymphokine.