gebhart/patrepeval huggingface dataset:
PepSeA: Peptide Sequence Alignment and Visualization Tools to Enable Lead Optimization (2022)

Therapeutic peptides offer potential advantages over small molecules in terms of selectivity, affinity, and their ability to target "undruggable" proteins that are associated with a wide range of pathologies. Despite their importance, current molecular design capabilities that inform medicinal chemistry decisions on peptide programs are limited. More specifically, there are unmet needs for structure-activity relationship (SAR) analysis and visualization of linear, cyclic, and cross-linked peptides containing non-natural motifs, which are widely used in drug discovery. To bridge this gap, we developed PepSeA (<b>Pep</b>tide <b>Se</b>quence <b>A</b>lignment and Visualization), an open-source, freely available package of sequence-based tools (https://github.com/Merck/PepSeA). PepSeA enables multiple sequence alignment of non-natural amino acids and enhanced visualization with the hierarchical editing language for macromolecules (HELM). Via stepwise SAR analysis of a ChEMBL peptide data set, we demonstrate the utility of PepSeA to accelerate decision making in lead optimization campaigns in pharmaceutical setting. PepSeA represents an initial attempt to expand cheminformatics capabilities for therapeutic peptides and to enable rapid and more efficient design-make-test cycles.
Theoretical Investigation into the Ripple Source of External Gear Pumps (2019)

External gear pumps are among the most popular fluid power positive displacement pumps, however they often suffer of excessive flow pulsation transmitted to the downstream circuit. To meet the increasing demand of quiet operation for modern fluid power system, a better understanding of the ripple source of gear pumps is desirable. This paper presents a novel approach for the analysis of the ripple source of gear pumps based on decomposition into a kinematic component and a pressurization component. The pump ripple can be regarded as the superposition of the displacement solution and the pressurization solution. The displacement solution is driven by the kinematic flow, and it can be derived from the kinematic flow theory; instead, the pressurization solution can be approximated by overlapping the pressurization flow for a single displacement chamber. Furthermore, in this way the changes of these two components with modification of the delivery circuit are determined in both analytical and numerical ways. The result of this analysis provides a good interpretation of the pulsation simulated by a detailed lumped-parameter simulation model, thus showing its validity. The result also indicates that the response of two ripple sources to the change of the loading in the downstream hydraulic circuit is very different. These findings reveal the limitation of the traditional experimental method for determining the pump ripple, that new experimental methods which are more physics-based can be potentially formulated based on this work.
Enhanced Gas Sensing Performance of Hydrothermal MoS2 Nanosheets by Post-Annealing in Hydrogen Ambient (2019)

Abstract A two-dimensional (2D) MoS2 is considered as a next-generation gas sensor owing to its high surface-to-mass ratio and excellent selectivity. However, promoting the gas-sensing capability requires increasing the presence of active sites such as edges and S vacancies for gas adsorption. Herein, we report a process of post-annealing in a hydrogen atmosphere to improve NO2 gas-sensing performance of hydrothermally grown MoS2 nanosheets. The effects of the post-treatment on the morphology, chemical state, and resultant gas-sensing performance were investigated by varying the annealing temperature (100–800 °C). The annealing treatment eliminated residual organics formed during the hydrothermal process and increased both the S vacancies and crystallinity, without significant oxidation. A gas-sensing test using a resistive-type sensor indicated that the sensitivity for NO2 gas of 500 ppm at room temperature was enhanced from 258% to 451% (p-type response) as the annealing temperature increased to 700 °C, followed by a rapid decrease at 800 °C, owing to the n-type response. These findings demonstrate that post-annealing in a hydrogen ambient is effective at increasing the defective sites of 2D MoS2, and hence, the gas-sensing performance.
Aquatic design for individuals with disabilities: Upper limb prosthesis (2014)

The overall result of this project was to create a new swim prosthesis that is more flexible than current models and more easily used for a variety of swim techniques. The prosthesis made is comprised of a Polyethylene and Copolymer socket and a Polyethylene hand. Both were made through the processes of vacuum-forming and draping of plastic. The proposed design is a new swim prosthesis that promotes those qualities lacked by current models. The prosthetic swim hand and socket attach through the use of an Aluminum plate that the hand screws into. The difference between this prosthesis and current models is that this one not only fixes the problems left by current models, but also uses custom molding. The final result is a swim prosthesis that passes all verification and validation tests and allows the user to increase their water mobility.
Supplementary Data from Mitochondrial Uncoupling Induces Epigenome Remodeling and Promotes Differentiation in Neuroblastoma (2023)

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Privacy-Preserving Smart Parking System Using Blockchain and Private Information Retrieval (2019)

Searching for available parking spaces is a major problem for drivers in crowded cities, causing traffic congestion, air pollution, and wasting drivers' time. Smart parking systems enable drivers to solicit real-time parking information and book parking slots. However, current smart parking systems require drivers to disclose their sensitive information, such as their desired destinations. Moreover, existing schemes are centralized, which makes them vulnerable to bottlenecks and single point of failure problems and privacy breaches by service providers. In this paper, we propose a privacy-preserving smart parking system using blockchain and private information retrieval. First, a consortium blockchain is created by different parking lot owners to ensure security, transparency, and availability of the parking offers. Then, to preserve the drivers' location privacy, we adopt private information retrieval technique to privately retrieve parking offers from blockchain nodes. In addition, a short randomizable signature is used to allow drivers to authenticate for reserving available parking slots from parking owners anonymously. Our evaluations demonstrate that our proposed scheme preserves drivers' privacy with low communication and computation overheads.
The effect of berberine nanomicelles on hepatic cirrhosis in bile duct-ligated rats (2018)

Objective (s): The anti-fibrotic effect of chronic berberine (BBR) had demonstrated previously in a rat model of bile duct ligation (BDL). The aim of present study was to investigate hepatoprotective effect of BBR nanomicelles on liver cirrhosis induced by BDL in male rats.Materials and methods: After 21 days of drugs’ treatments, the serum and tissue levels of hepatic markers were measured and pathologic evaluations performed.Results: BDL could markedly increase aspartate aminotransferase (AST), alanine aminotransferase (ALT), LDH, and total bilirubin (TBIL) serum levels and tissue tumor necrosis factor-alpha (TNF-α) level along with reductions in tissue levels of key antioxidants glutathione (GSH) and superoxide dismutase (SOD) as well as total protein. On the other hand, silymarin (100 mg/kg, p.o.), BBR (100 mg/kg) and BBR nanomicelles (50 mg/kg, p.o.) markedly decreased AST and ALT while enhanced GSH. In addition, BBR nanomicelles (50 mg/kg, p.o.), silymarin (100 mg/kg, p.o.) and BBR (100 mg/kg, p.o.) groups showed a considerable increase in SOD. BBR nanomicelles (50 mg/kg, po.) significantly lowered TNF-α. In addition, nanoBBR treatment prevented liver cirrhosis in histopathologic analysis.Conclusion: Formulation of BBR may represent a worthy approach to enhance the effect of it in liver injuries.
Combining neural-based approaches and linguistic knowledge for text recognition in multimedia documents (2013)

This thesis focuses on the recognition of textual clues in images and videos. In this context, OCR (optical character recognition) systems, able to recognize caption texts as well as natural scene texts captured anywhere in the environment have been designed. Novel approaches, robust to text variability (differentfonts, colors, sizes, etc.) and acquisition conditions (complex background, non uniform lighting, low resolution, etc.) have been proposed. In particular, two kinds of methods dedicated to text recognition are provided:- A segmentation-based approach that computes nonlinear separations between characters well adapted to the localmorphology of images;- Two segmentation-free approaches that integrate a multi-scale scanning scheme. The first one relies on a graph model, while the second one uses a particular connectionist recurrent model able to handle spatial constraints between characters.In addition to the originalities of each approach, two extra contributions of this work lie in the design of a character recognition method based on a neural classification model and the incorporation of some linguistic knowledge that enables to take into account the lexical context.The proposed OCR systems were tested and evaluated on two datasets: a caption texts video dataset and a natural scene texts dataset (namely the public database ICDAR 2003). Experiments have demonstrated the efficiency of our approaches and have permitted to compare their performances to those of state-of-the-art methods, highlighting their advantages and limits.
Temporal Patterns of Activity in Neural Networks (1987)

Patterns of activity over real neural structures are known to exhibit time-dependent behavior. It would seem that the brain may be capable of utilizing temporal behavior of activity in neural networks as a way of performing functions which cannot otherwise be easily implemented. These might include the origination of sequential behavior and the recognition of time-dependent stimuli. A model is presented here which uses neuronal populations with recurrent feedback connections in an attempt to observe and describe the resulting time-dependent behavior. Shortcomings and problems inherent to this model are discussed. Current models by other researchers are reviewed and their similarities and differences discussed.
The Human V<sub>H</sub>Repertoire: A Restricted Set of V<sub>H</sub>Genes May be the Target of Immune Regulation (1992)

During the development of the immune system, a restricted set of VH gene segments provides the bulk of the immunoglobulin heavy chain repertoire. Most of these VH genes have been found later in life encoding autospecificities either in normals or in patients with autoimmune diseases. Additionally, there is considerable evidence that the fetal/neonatal B-cell repertoire is autoreactive and idiotypically connected. In the course of sequencing the heavy chain of a panel of human autoantibodies mainly derived from patients with autoimmune diseases, we found that one of the VH families, and more specifically one single VH gene contributes to a large extent to the adult autoimmune repertoire in restricted as well as unrestricted responses. This VH gene segment is not particularly overexpressed in the fetus. Since the only common element to these autoreactive responses is the region encoded by the VH gene itself, these observations may provide an important insight into B-cell regulation.
The role of the renal afferent and efferent nerve fibers in heart failure (2015)

Renal nerves contain afferent, sensory and efferent, sympathetic nerve fibers. In heart failure (HF) there is an increase in renal sympathetic nerve activity (RSNA), which can lead to renal vasoconstriction, increased renin release and sodium retention. These changes are thought to contribute to renal dysfunction, which is predictive of poor outcome in patients with HF. In contrast, the role of the renal afferent nerves remains largely unexplored in HF. This is somewhat surprising as there are multiple triggers in HF that have the potential to increase afferent nerve activity, including increased venous pressure and reduced kidney perfusion. Some of the few studies investigating renal afferents in HF have suggested that at least the sympatho-inhibitory reno-renal reflex is blunted. In experimentally induced HF, renal denervation, both surgical and catheter-based, has been associated with some improvements in renal and cardiac function. It remains unknown whether the effects are due to removal of the efferent renal nerve fibers or afferent renal nerve fibers, or a combination of both. Here, we review the effects of HF on renal efferent and afferent nerve function and critically assess the latest evidence supporting renal denervation as a potential treatment in HF.
Total Ionizing Dose Impact on 22-nm FD-SOI Ring Oscillator Current and Frequency (2022)

Total ionizing dose (TID) has a significant effect on silicon-on-insulator (SOI) circuits, manifesting primarily as a front-gate threshold voltage ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$V_{t}$ </tex-math></inline-formula> ) shift. This article presents data on ring oscillator (RO) responses of 22-nm fully depleted (FD-SOI) thin oxide (core logic) devices to gamma-ray doses above 1 Mrad(Si). We show large current and frequency TID response differences between ROs comprised of different logic gates. Moreover, the extensive experimental results presented here show that these responses vary significantly with <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$V_{t}$ </tex-math></inline-formula> and well type. The measurements show that depending on the expected dose and transistor <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$V_{t}$ </tex-math></inline-formula> used, TID-induced standby current ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$I_{\mathrm {SB}}$ </tex-math></inline-formula> ) increases may have a substantial impact on overall power in spaceborne integrated circuits (ICs) using this fabrication process. The TID impact on digital circuit timing margins is also discussed.
Tripartite relationship between gut microbiota, intestinal mucus and dietary fibers: towards preventive strategies against enteric infections (2020)

The human gut is inhabited by a large variety of microorganims involved in many physiological processes and collectively referred as to gut microbiota. Disrupted microbiome has been associated with negative health outcomes and especially could promote the onset of enteric infections. To sustain their growth and persistence within the human digestive tract, gut microbes and enteric pathogens rely on two main polysaccharide compartments, namely dietary fibers and mucus carbohydrates. Several evidences suggest that the three-way relationship between gut microbiota, dietary fibers and mucus layer could unravel the capacity of enteric pathogens to colonise the human digestive tract and ultimately lead to infection. The review starts by shedding light on similarities and differences between dietary fibers and mucus carbohydrates structures and functions. Next, we provide an overview of the interactions of these two components with the third partner, namely, the gut microbiota, under health and disease situations. The review will then provide insights into the relevance of using dietary fibers interventions to prevent enteric infections with a focus on gut microbial imbalance and impaired-mucus integrity. Facing the numerous challenges in studying microbiota-pathogen-dietary fiber-mucus interactions, we lastly describe the characteristics and potentialities of currently available in vitro models of the human gut.
An extended-gate CMOS sensor array with enzyme-immobilized microbeads for redox-potential glucose detection (2014)

An extended-gate CMOS sensor array with enzyme-immobilized microbeads for redox-potential glucose detection is demonstrated for the first time. Redox-potential detection has the possibility to achieve high accuracy because it is not affected by the buffer conditions. Despite this high-accuracy property, redox-potential detection requires a sufficient amount of enzyme, which leads to increased cost. In order to reduce the enzyme consumption while maintaining the detection capability, we have introduced enzyme-immobilized microbeads. By using the microbeads, the enzyme can be efficiently positioned and reused several times. Thus, the required amount of enzyme can be reduced dramatically. To verify the proposed concept, we have developed and measured a prototype with a 0.6-μm CMOS test chip including the microfluidics. Measurements successfully demonstrate glucose detection with a sensitivity of -61.6 mV/decade while reusing identical enzyme-immobilized microbeads.
Hydrogen-bonded chains of rings in 3-iodobenzaldehyde 2,4-dinitrophenylhydrazone and 4-iodobenzaldehyde 2,4-dinitrophenylhydrazone, and a three-dimensional framework in 4-iodobenzaldehyde 4-nitrophenylhydrazone generated by the combination of N—H...O and C—H...O hydrogen bonds with iodo–nitro interactions (2003)

Molecules of 3- and 4-iodobenzaldehyde 2,4-dinitrophenylhydrazone, C(13)H(9)IN(4)O(4), are both effectively planar. In the crystal structure of each compound, molecules are linked by a combination of N-H...O and C-H...O hydrogen bonds into complex chains of rings, containing four and three different ring motifs, respectively; neither compound contains any iodo-nitro interactions. In 3-iodobenzaldehyde 4-nitrophenylhydrazone, C(13)H(10)IN(3)O(2), where the iodinated aryl ring is disordered over two sets of sites, the hydrogen bonds generate a chain of rings, while two independent I...O interactions generate a three-dimensional framework.
Further SAR Studies of Piperidine-Based Analogues of Cocaine. 2. Potent Dopamine and Serotonin Reuptake Inhibitors (2000)

The synthesis and monoamine transporter activity of additional members of a series of 3,4-disubstituted piperidines (truncated analogues of the WIN series) are described. All members of this series were prepared from arecoline hydrobromide in optically pure form and were evaluated for their ability to inhibit high affinity uptake of dopamine (DA), serotonin (5-HT) and norepinephrine (NE) into rat brain nerve endings (synaptosomes). Most of the compounds prepared in this series are reasonably potent DAT inhibitors (K(i) values of 4-400 nM) and have selectivity for the 5-HT transporter relative to both the NE transporter (3-9-fold) and to the DAT ( approximately 25-fold). In the present series, (-)-methyl 1-methyl-4beta-(2-naphthyl)piperidine-3beta-carboxylate (6) was found to be the most potent piperidine-based ligand, exhibiting K(i)'s of 21 nM and 7.6 nM at the DAT and 5-HTT, respectively. While the 5-HTT activity of compound 6 is comparable to that of the antidepressant medication fluoxetine, it is less selective. As is apparent from the data presented, the naphthyl substituted piperidines 6-9, which differ in their stereochemistry, show different degrees of selectivity for the three transporters. Consistent with results reported in the literature for the tropane analogues, removal of the methyl group from the nitrogen atom of 9 leads to a further enhancement in 5-HTT activity. To examine the in vivo effects of these piperidines, preliminary behavioral screening was carried out on piperidine 14. Despite its 2.5-fold greater DAT activity compared to cocaine, piperidine 14 was found to be about 2. 5-fold less potent in increasing distance traveled in mice. However, consistent with its DAT activity, piperidine 14 was found to be about 2.5-fold more potent than cocaine in enhancing stereotypic movements. Further studies of these piperidine-based ligands may provide valuable insights into the pharmacological mechanisms underlying the enhancement in distance traveled versus stereotypic movements. The present results have important implications for better understanding the structural motifs required in the design of agents with specific potency and selectivity at monoamine transporters.
Biology-guided adaptive radiation therapy – presence or future? (2010)

The present issue of Acta Oncologica contains a large number of publications from the 2010 Acta Oncologica Symposium held in Aarhus, Denmark May 26 – 28, 2010. The symposium was dedicated to aspects of Biology-Guided Adaptive Radiation Therapy (BiGART). A broad faculty of distinguished international scientists presented state-of-the-art of the research fi eld, and a record number of abstracts were received for the proffered paper sessions. It is our hope that both the meeting and the papers in the current issue will provide new insight into the bio
Elevated ganglioside GM2 activator (GM2A) in human brain tissue reduces neurite integrity and spontaneous neuronal activity (2022)

The techniques and data herein introduce a system for modeling neuronal vulnerability in response to factors in the human brain and provide insights into proteins potentially contributing to AD pathogenesis.
Scalable, resource and locality-aware selection of active scatterers in Geometry-based stochastic channel models (2021)

In this paper we adopt and modify a well-known locality-aware hashing scheme to the problem of active stochastic scatterer selection in vehicular non-stationary geometry-based stochastic channel models (GSCM). We show, how under relaxed assumptions on the query set an efficient selection of active stochastic scatterers during simulation is computationally feasible. The proposed approach enables real-time simulation and emulation of large-scale GSCMs by restricting the active stochastic scatterer set to meet given resource constraints. We showcase our approach by introducing a GSCM that is boot-strapped via OpenStreetMap data. The stochastic scatterers are placed automatically along buildings, traffic signs and vegetation. We validate and investigate the impact of the proposed approach on the accuracy of a GSCM by means of second order statistics of the time- and frequency-varying fading process. For validation and performance evaluation we parameterize our GSCM using a vehicular wireless channel measurement campaign conducted in the inner city of Vienna. The impact of selecting only a subset of scatterers is then evaluated using the calibrated GSCM.