gebhart/patrepeval huggingface dataset:
Highly potent inhibitors of human cathepsin L identified by screening combinatorial pentapeptide amide collections (2000)

By screening a combinatorial pentapeptide amide collection in an inhibition assay, we systematically evaluated the potential of 19 proteinogenic amino acids and seven nonproteinogenic amino acids to serve as building blocks for inhibitors of human cathepsin L. Particularly efficient were aromatic, bulky, hydrophobic amino-acid residues, especially leucine, and positively charged residues, especially arginine. Building blocks for potential inhibitory peptides were combined by random selection from their activity pattern. This random approach for the design of inhibitors was introduced to compensate for the inaccuracy induced by shifted docking of combinatorial compound collections at the active center of cathepsin L. Thereby, we obtained structurally defined pentapeptide amides which inhibited human cathepsin L at nanomolar concentrations. Among the most potent novel inhibitors, one peptide, RKLLW-NH2, shares the amphiphilic character of the nonamer fragment VMNGLQNRK of the autoinhibitory, substrate-like, but reverse-binding prosegment of human cathepsin L which blocks the active center of the enzyme. Obviously, RKLLW-NH2 carries the functions that are important for enzyme-peptide interaction in a condensed form. This hypothesis was confirmed by structure-activity studies using truncated and modified pentapeptides.
A phase I dose-escalation and pharmacokinetic study of a micellar nanoparticle with entrapped docetaxel (CPC634) in patients with advanced solid tumours (2020)

CPC634 could be administered safely upon pretreatment with dexamethasone. Cumulative skin toxicity was the main DLT. The recommended phase 2 dose was determined at 60 mg/m<sup>2</sup> Q3W with dexamethasone premedication.
1-(1,3-Benzothiazol-2-yl)-3-benzoylthiourea (2007)

The title compound, C(15)H(11)N(3)OS(2), was synthesized from benzoyl thio-cyanate and 2-amino-benzothia-zole in dry acetone. The thio-urea group is in the thio-amide form. The mol-ecules are stabilized by two inter-molecular C-H⋯S and C-H⋯O hydrogen bonds. Intra-molecular N-H⋯O hydrogen bonding results in a pseudo-S(6) planar ring with dihedral angles of 11.23 and 11.91° with the benzothiazole ring system and the phenyl ring, respectively.
The influence of radial RBC distribution, blood velocity profiles, and glycocalyx on coupled NO/O2transport (2005)

The purpose of this investigation was to study the effect of the presence of red blood cells (RBCs) in the plasma layer near the arteriole wall on nitric oxide (NO) and oxygen (O2) transport. To this end, we extended a coupled NO and O2 diffusion-reaction model in the arteriole, developed by our group, to include the effect of the presence of RBCs in the plasma layer and the effect of convection. Two blood flow velocity profiles (plug and parabolic) were tested. The average hematocrit in the bloodstream was assumed to be constant in the central core and decreasing to zero in the boundary layer next to the endothelial surface layer. The effect of the presence or absence of RBCs near the endothelium was studied while varying the endothelial surface layer and boundary layer thickness. With RBCs present in the boundary layer, the model predicts that 1) NO decreases significantly in the endothelium and vascular wall; 2) there is a very small increase in endothelial and vascular wall Po2; 3) scavenging of NO by hemoglobin decreases with increasing thickness of the boundary layer; 4) the shape of the velocity profile influences both NO and Po2 gradients in the bloodstream; and 5) the presence of RBCs in the boundary layer near the endothelium has a much larger effect on NO than on O2 transport.
Enabling Secure Database as a Service using Fully Homomorphic Encryption: Challenges and Opportunities (2013)

The database community, at least for the last decade, has been grappling with querying encrypted data, which would enable secure database as a service solutions. A recent breakthrough in the cryptographic community (in 2009) related to fully homomorphic encryption (FHE) showed that arbitrary computation on encrypted data is possible. Successful adoption of FHE for query processing is, however, still a distant dream, and numerous challenges have to be addressed. One challenge is how to perform algebraic query processing of encrypted data, where we produce encrypted intermediate results and operations on encrypted data can be composed. In this paper, we describe our solution for algebraic query processing of encrypted data, and also outline several other challenges that need to be addressed, while also describing the lessons that can be learnt from a decade of work by the database community in querying encrypted data.
Radiotherapy for HPV-related cancers: prediction of therapeutic effects based on the mechanism of tumor immunity and the application of immunoradiotherapy (2022)

Human papillomavirus (HPV)-related cancer is one of the diseases entities for which the applications of radiotherapy have been increasing. Recently, the process of carcinogenesis from HPV infection and the mechanism of tumor immunity that develops during disease progression have been elucidated. In this review, we will describe the mechanism of tumor immunity and how chemoradiotherapy may overcome and improve the efficacy of tumor immunity. We will also discuss the usefulness of proteins involved with tumor immunity as a predictive marker of radiotherapy response, and present an overview of ongoing clinical trials of combinations of immune checkpoint inhibitors and radiotherapy to demonstrate the promising combination therapy that has been currently emerging.
Evaluation of Mental Stress Using Wireless Patch-style Heart Activity Monitoring System (2008)

For evaluation of mental stress, this research gives out the questionnaire and measures the number of hormone through blood test. The activity of autonomic nervous system was evaluated through the analysis of ECG signal measured with wireless patch-style heart monitoring system which is able to measure and record the data.Psychological evaluation was performed for measuring mental stress by questionnaire research. The result of physiological evaluation was acquired through hormone test. Various parameters of frequency and time domain which are relative to psychological and physiological evaluation were extracted from heart rate variability.
A comprehensive guide in prostate MR imaging providing an overview of current, advanced techniques, central pitfalls and correction strategies (2022)

In the other hand, pelvic magnetic resonance imaging (MRI) involves many challenges that are not encountered to the same degree in other body regions. Complications that uniquely affect body MRI include physiologic motion from respiratory and bowel motion. By introducing of technical innovations in MRI, such as the development of phased-array coils, high performance gradients, and methods to reduce motion-related artefacts, body imaging can be obtained with excellent contrast resolution in a reasonable scanning time. In order to optimize prostate MR protocols and improve its efficiency, it is essential for the radiographer to be familiar with basic MR imaging principles and able to minimize the effects of motion artefact. Therefore, the purpose of this review is to discuss the prostate MRI technique and address some challenges that may encounter MR radiographers.
Over-expression of AhR (aryl hydrocarbon receptor) induces neural differentiation of Neuro2a cells: neurotoxicology study (2006)

The excessive activation of AhR resulted in neural differentiation of Neuro2a cells. This result revealed that dioxins may affect the nervous system through the AhR-signaling pathway. Activated AhR may disrupt the strictly regulated brain formation with irregular differentiation occurring rather than cell death.
Image segmentation for uranium isotopic analysis by SIMS: Combined adaptive thresholding and marker controlled watershed approach (2016)

A novel approach to particle identification and particle isotope ratio determination has been developed for nuclear safeguard applications. This particle search approach combines an adaptive thresholding algorithm and marker-controlled watershed segmentation (MCWS) transform, which improves the secondary ion mass spectrometry (SIMS) isotopic analysis of uranium containing particle populations for nuclear safeguards applications. The Niblack assisted MCWS approach (a.k.a. Seeker) developed for this work has improved the identification of isotopically unique uranium particles under conditions that have historically presented significant challenges for SIMS image data processing techniques. Particles obtained from five National Institute of Standards and Technology (NIST) uranium certified reference materials (CRM U129A, U015, U150, U500, and U850) were successfully identified in regions of SIMS image data (1) where a high variability in image intensity existed, (2) where particles were touching or were in close proximity to one another, and/or (3) where the magnitude of ion signal for a given region was count limited. Analysis of the isotopic distributions of uranium containing particles identified by Seeker showed four distinct, accurately identified 235U enrichment distributions, corresponding to the NIST certified 235U/238U isotope ratios for CRM U129A/U015 (not statistically differentiated), U150, U500, and U850. Additionally, comparison of the minor uranium isotope (234U, 235U, and 236U) atom percent values verified that, even in the absence of high precision isotope ratio measurements, Seeker could be used to segment isotopically unique uranium particles from SIMS image data. Although demonstrated specifically for SIMS analysis of uranium containing particles for nuclear safeguards, Seeker has application in addressing a broad set of image processing challenges.
A transition radiation detector based on thin inorganic scintillators (2013)

The possibility of designing a prototype of the scintillation transition radiation detector (Sci-TRD) based on a thin (∼200 μm) inorganic scintillator has been investigated. Vacuum and silicon photomultipliers have been used in the measurements with inorganic scintillator samples based on LuBO3:Ce and wavelength shifting fibers. The light collection coefficient has been measured for scintillator prototypes under exposure to X rays, and the quantity of photoelectrons has been experimentally determined by irradiating the Sci-TRD working substance with a 241Am X ray source. The electron-hadron rejection ratio of the proposed Sci-TRD is expected to be ∼30.
A Deep Neural Network Augmented Approach for Fixed Polarity AND-XOR Network Synthesis (2019)

<sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sup> This work is partially supported by the research project sponsored by the Synopsys Inc., USAWith the recent advancements of FPGA (Field Programmable Gate Array), circuits in AND-XOR plane gets its fair share of advantages due to the high testability feature of the AND-XOR networks and independence of the logic-gate area as well as delays on FPGA. Minimization of the product terms for such networks is an NP-hard problem. In this paper, we have proposed a Binary Particle Swarm Optimization (BPSO) based technique to solve the optimization problem accurately and accelerate the same using a Deep Neural Network. With the proposed technique, after testing it against various MCNC benchmark circuits, the results were very promising in terms of product terms, while utilizing significantly lesser CPU-time.
COHERENT THERMAL EMISSION IN MID INFRARED FROM A BILAYER STRUCTURE (2010)

International audience
EVELOPMENT OF AN ENVIRONMENTALLY BENIGN MICROBIAL INHIBITOR TO CONTROL INTERNAL PIPELINE CORROSION (2004)

The overall program objective is to develop and evaluate environmentally benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is to develop one or more environmentally benign (a.k.a. ''green'') products that can be applied to maintain the structure and dependability of the natural gas infrastructure. Previous testing of pepper extracts resulted in preliminary data indicating that some pepper extracts inhibit the growth of some corrosion-associated microorganisms. This quarter additional tests were performed to more specifically investigate the ability of three pepper extracts to inhibit the growth, and to influence the metal corrosion caused by two microbial species: Desulfovibrio vulgaris, and Comomonas denitrificans. All three pepper extracts rapidly killed Desulfovibrio vulgaris, but did not appear to inhibit Comomonas denitrificans. While corrosion rates were at control levels in experiments with Desulfovibrio vulgaris that received pepper extract, corrosion rates were increased in the presence of Comomonas denitrificans plus pepper extract. Further testing with a wider range of pure bacterial cultures, and more importantly, with mixed bacterial cultures should be performed to determine the potential effectiveness of pepper extracts to inhibit MIC.
Purification and Characterization of an Exo-1,5-.ALPHA.-L-Arabinanase from Aspergillus sojae (2005)

An exo-1,5-α-L-arabinanase was purified as an electrophoretically homogenous protein from a liquid culture of Aspergillus sojae. The molecular mass of the purified enzyme was estimated to be 41 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and 43 kDa by gel filtration chromatography. The isoelectric point of the enzyme was 3.7. The maximum velocity of carboxymethyl (CM)-linear arabinan degradation by the exo-arabinanase was attained at 50°C and at pH 5.0. The purified enzyme was stable in a range from pH 6.0 to 8.0 and up to 45°C. The activity of the enzyme was significantly inhibited by Ag+ (1 mM) and Cr2+ (1 mM), and stimulated by SDS (5 mM). The Km value for the 1,5-arabinan from beet was 5.8 mg/mL. The sequence of amino-terminus (25 residues) of the exo-arabinanase from A. sojae exhibits extensive identity (69%) with that of Penicillium chrysogenum. After the hydrolysis of 1,5-arabinan from beet, the major product was arabinobiose, and no liberation of arabinose was observed in the reaction mixture.
Motion-compensated layered video coding for playback scalability (2001)

We propose a multilayered video coding scheme based on motion estimation which enables a decoder to dynamically change its temporal and spatial resolution during playback. In the proposed scheme, a new motion-prediction structure with a temporal hierarchy of frames is adopted to afford temporal resolution scalability and the wavelet decomposition with a new intra-update algorithm is used to offer spatial scalability. Experimental results show that the proposed scheme exhibits a higher compression ratio than conditional replenishment schemes because it further reduces the temporal redundancy using motion estimation. Also the proposed intra-update technique enables adaptation to dynamic change of spatial resolution with the effective follow-up of prediction in the decoder while preventing the large peaks in bit rate. Therefore, the proposed scheme is expected to be effectively used in heterogeneous environments such as the Internet, ATM, and wireless networks where dynamic scalability and interoperability are required.
Structural characterization of dissolved organic matter: a review of current techniques for isolation and analysis (2014)

Current approaches to isolation and structural characterization of natural dissolved organic matter are presented and evaluated for strengths and weaknesses.
Assessing the mechanical properties of tissue-mimicking phantoms at different depths as an approach to measure biomechanical gradient of crystalline lens (2013)

We demonstrate the feasibility of using the dominant frequency of the sample surface response to a mechanical stimulation as an effective indicator for sensing the depthwise distribution of elastic properties in transparent layered phantom samples simulating the cortex and nucleus of the crystalline lens. Focused ultrasound waves are used to noninvasively interrogate the sample surface. A phase-sensitive optical coherence tomography system is utilized to capture the surface dynamics over time with nanometer scale sensitivity. Spectral analysis is performed on the sample surface response to ultrasound stimulation and the dominant frequency is calculated under particular loading parameters. Pilot experiments were conducted on homogeneous and layered tissue-mimicking phantoms. Results indicate that the mechanical layers located at different depths introduce different frequencies to the sample surface response, which are correlated with the depth-dependent elasticity of the sample. The duration and the frequency of the ultrasound excitation are also investigated for their influences on this spectrum-based detection. This noninvasive method may be potentially applied for localized and rapid assessment of the depth dependence of the mechanical properties of the crystalline lens.
Augmented reality as a tool to enrich educational settings (2020)

Augmented (AR) is an important technology that allows an interactive experience with the real world, where the objects in the real world are enhanced by computer-generated perceptual information. This information can be perceived as a natural part of the environment through different sensory modalities including visual, auditory, haptic, olfactory, and somatosensory. The term augmented reality was coined in 1992 and has received different definitions since then. however, a simple and broadly accepted definition describes AR as technology that overlays virtual objects over the real world. This technology has experienced a rapid growth since 2010, due in part to improvements in mobile computing power and tablets. This technology has potential to positively influence different aspects os our daily lives. It can change the way we think, the way we entertain, the way we work, the way we communicate and, more importantly, the way we learn...
Correction: Whole Cell Screen for Inhibitors of pH Homeostasis in Mycobacterium tuberculosis (2013)

Bacterial pathogens like Mycobacterium tuberculosis (Mtb) encounter acidic microenvironments in the host and must maintain their acid-base homeostasis to survive. A genetic screen identified two Mtb strains that cannot control intrabacterial pH (pH IB ) in an acidic environment; infection with either strain led to severe attenuation in mice. To search for additional proteins that Mtb requires to survive at low pH, we introduced a whole-cell screen for compounds that disrupt pH IB , along with counter-screens that identify ionophores and membrane perturbors. Application of these methods to a natural product library identified four compounds of interest, one of which may inhibit novel pathway(s). This approach yields compounds that may lead to the identification of pathways that allow Mtb to survive in acidic environments, a setting in which Mtb is resistant to most of the drugs currently used to treat tuberculosis.
Probing key elements of teixobactin–lipid II interactions in membranes (2018)

Teixobactin (Txb) is a recently discovered antibiotic against Gram-positive bacteria that induces no detectable resistance. The bactericidal mechanism is believed to be the inhibition of cell wall biosynthesis by Txb binding to lipid II and lipid III. Txb binding specificity likely arises from targeting of the shared lipid component, the pyrophosphate moiety. Despite synthesis and functional assessment of numerous chemical analogs of Txb, and consequent identification of the Txb pharmacophore, the detailed structural information of Txb-substrate binding is still lacking. Here, we use molecular modeling and microsecond-scale molecular dynamics simulations to capture the formation of Txb-lipid II complexes at a membrane surface. Two dominant binding conformations were observed, both showing characteristic lipid II phosphate binding by the Txb backbone amides near the C-terminal cyclodepsipeptide (d-Thr8-Ile11) ring. Additionally, binding by Txb also involved the side chain hydroxyl group of Ser7, as well as a secondary phosphate binding provided by the side chain of l-<i>allo</i>-enduracididine. Interestingly, those conformations differ by swapping two groups of hydrogen bond donors that coordinate the two phosphate moieties of lipid II, resulting in opposite orientations of lipid II binding. In addition, residues d-<i>allo</i>-Ile5 and Ile6 serve as the membrane anchors in both Txb conformations, regardless of the detailed phosphate binding interactions near the cyclodepsipeptide ring. The role of hydrophobic residues in Txb activity is primarily for its membrane insertion, and subsidiarily to provide non-polar interactions with the lipid II tail. Based on the Txb-lipid II interactions captured in their complexes, as well as their partitioning depths into the membrane, we propose that the bactericidal mechanism of Txb is to arrest cell wall synthesis by selectively inhibiting the transglycosylation of peptidoglycan, while possibly leaving the transpeptidation step unaffected. The observed "pyrophosphate caging" mechanism of lipid II inhibition appears to be similar to some lantibiotics, but different from that of vancomycin or bacitracin.
Validation study of a novel method for the 3D reconstruction of coronary bifurcations (2020)

Quantitative Coronary Angiography (QCA) is an important tool in the study of coronary artery disease. Validation of this technique is crucial for their ongoing development and refinement although it is difficult due to several factors such as potential sources of error. The present work aims to a further validation of a new semi-automated method for three-dimensional (3D) reconstruction of coronary bifurcations arteries based on X-Ray Coronary Angiographies (CA). In a dataset of 40 patients (79 angiographic views), we used the aforementioned method to reconstruct them in 3D space. The validation was based on the comparison of these 3D models with the true silhouette of 2D models annotated by an expert using specific metrics. The obtained results indicate a good accuracy for the most parameters (≥ 90 %). Comparison with similar works shows that our new method is a promising tool for the 3D reconstruction of coronary bifurcations and for application in everyday clinical use.
Gene expression of lactobacilli in murine forestomach biofilms (2014)

Lactobacilli populate the gastro-intestinal tract of vertebrates, and are used in food fermentations and as probiotics. Lactobacilli are also major constituents of stable biofilms in the forestomach of rodents. In order to investigate the lifestyle of these biofilm lactobacilli in C57BL/6 mice, we applied metatranscriptomics to analyse gene expression (assessed by mRNA) and community composition (assessed by rRNA). Lactobacillales were the major biofilm inhabitants (62-82% of rRNA reads), followed by Clostridiales (8-31% of rRNA reads). To identify mRNA transcripts specific for the forestomach, we compared forestomach and hindgut metatranscriptomes. Gene expression of the biofilm microbiota was characterized by high abundance of transcripts related to glucose and maltose utilization, peptide degradation, and amino acid transport, indicating their major catabolic and anabolic pathways. The microbiota transcribed genes encoding pathways enhancing oxidative stress (glutathione synthesis) and acid tolerance. Various pathways, including metabolite formation (urea degradation, arginine pathway, γ-aminobutyrate) and cell wall modification (DltA, cyclopropane-fatty-acyl-phospholipid synthase), contributed to acid tolerance, as judged from the transcript profile. In addition, the biofilm microbiota expressed numerous genes encoding extracellular proteins involved in adhesion and/or biofilm formation (e.g. MucBP, glycosyl hydrolase families 68 and 70). This study shed light on the lifestyle and specific adaptations of lactobacilli in the murine forestomach that might also be relevant for lactobacilli biofilms in other vertebrates, including humans.