gebhart/patrepeval huggingface dataset:
Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP (2016)

Abstract Background Membrane proteins are vastly underrepresented in structural databases, which has led to a lack of computational tools and the corresponding inappropriate use of tools designed for soluble proteins. For membrane proteins, lipid accessibility is an essential property. Even though programs are available for sequence-based prediction of lipid accessibility and structure-based identification of solvent-accessible surface area, the latter does not distinguish between water accessible and lipid accessible residues in membrane proteins. Results Here we present mp_lipid_acc , the first method to identify lipid accessible residues from the protein structure, implemented in the RosettaMP framework and available as a webserver. Our method uses protein structures transformed in membrane coordinates, for instance from PDBTM or OPM databases, and a defined membrane thickness to classify lipid accessibility of residues. mp_lipid_acc is applicable to both α-helical and β-barrel membrane proteins of diverse architectures with or without water-filled pores and uses a concave hull algorithm for classification. We further provide a manually curated benchmark dataset, on which our method achieves prediction accuracies of 90%. Conclusion We present a novel tool to classify lipid accessibility from the protein structure, which is applicable to proteins of diverse architectures and achieves prediction accuracies of 90% on a manually curated database. mp_lipid_acc is part of the Rosetta software suite, available at www.rosettacommons.org . The webserver is available at http://rosie.graylab.jhu.edu/mp_lipid_acc/submit and the benchmark dataset is available at http://tinyurl.com/mp-lipid-acc-dataset . Supplementary information Supplementary information is available at BMC Bioinformatics .
Development of a 7.5kW High Speed Interior Permanent Magnet Synchronous Spindle Motor for CNC Milling Machine (2018)

In this paper, two different type interior permanent magnet (IPM) motor designs are proposed for Computer Numerical Control (CNC) milling machine application as spindle motors. An existing surface mounted permanent magnet motor is used as a reference motor. Both spoke type and v-type Interior Permanent Magnet (IPM) motor alternatives are designed and optimized in detail. The results of the two IPM motors are compared with the reference Surface Permanent Magnet (SPM) motor for the same design requirements. Detailed loss analysis are also performed for the desired motor structure at high speeds. A prototype motor is manufactured and initial experimental tests are performed. Detailed comparison between Finite Element Analysis and test data are also presented. It is shown that it is possible to have an optimized IPM motor for such high speed spindle application.
Multimode illumination for speckle reduction and angle neutrality in millimeter wave active imaging: range and time-resolved mode averaging (2014)

Active illumination is an attractive approach for millimeter and submillimeter wave imaging because of its generally larger signal margins and capacity for range determination. However, the resultant speckle from diffuse targets and the requirement that specular targets have strategic angular alignment are significant shortcomings. As a result, many, if not most, demonstrations of active imaging have involved the use of strategically oriented specular targets. We have previously shown [J. Opt. Soc. Am. A29, 2643 (2012)10.1364/JOSAA.29.002643JOAOD61084-7529] that spatially time-resolved modulated multimode mixing approaches mitigate these issues. In this paper, we extend this work to demonstrate the use of range resolved multimode mixing as an alternative means to provide statistically independent images for speckle reduction averaging. We also demonstrate the use of systematic illumination of spatial modes in a &#x201C;grassy field&#x201D; geometry.
The Systems BaO‐SrO‐TiO 2 , BaO‐CaO‐TiO 2 , and SrO‐CaO‐TiO 2 (1959)

The solid phases formed at 1400°C. in air in the three‐component systems BaO‐SrO‐TiO 2 , BaO‐CaO‐TiO 2 , and SrO‐CaO‐TiO 2 are described. Besides solid solutions of components with known structures, some new ternary compounds have been studied. The dielectric constants and loss factors of a number of specimens are given. Crystallographic data of the compounds BaCaTiO 4 , Ba 3 Ca 2 Ti 2 O 9 , and Ca 3 Ti 2 O 7 and of the solid solution series (Ba, Sr), TiO 4 are presented. The preparation of the new compounds is described in detail.
Butyrylcholinesterase: An Important New Target in Alzheimer’s Disease Therapy (2002)

Acetylcholinesterase (AChE) predominates in the healthy brain, with butyrylcholinesterase (BuChE) considered to play a minor role in regulating brain acetylcholine (ACh) levels. However, BuChE activity progressively increases in patients with Alzheimer's disease (AD), while AChE activity remains unchanged or declines. Both enzymes therefore represent legitimate therapeutic targets for ameliorating the cholinergic deficit considered to be responsible for the declines in cognitive, behavioral and global functioning characteristic of AD. The two enzymes differ in substrate specificity, kinetics and activity in different brain regions. Experimental evidence from the use of agents with enhanced selectivity for BuChE (cymserine analogues, MF-8622) and the dual inhibitor of both AChE and BuChE, rivastigmine, indicates potential therapeutic benefits of inhibiting both AChE and BuChE in AD and related dementias. Recent evidence suggests that both AChE and BuChE may have roles in the aetiology and progression of AD beyond regulation of synaptic ACh levels. The development of specific BuChE inhibitors and further experience with the dual enzyme inhibitor rivastigmine will improve understanding of the aetiology of AD and should lead to a wider variety of potent treatment options.
Feed-forward active noise control system using microphone array (2018)

Feedforward active noise control (ANC) system are widely used to reduce the wide-band noise in different application. In feedforward ANC systems, when the noise source is unknown, the misplacement of the reference microphone may violate the causality constraint. We present a performance analysis of the feedforward ANC system under a noncausal condition. The ANC system performance degrades when the degree of noncausality increases. This research applies the microphone array technique to feedforward ANC systems to solve the unknown noise source problem. The generalized cross-correlation (GCC) and steering response power (SRP) methods based on microphone array are used to estimate the noise source location. Then, the ANC system selects the proper reference microphone for a noise control algorithm. The simulation and experiment results show that the SRP method can estimate the noise source direction with 84% accuracy. The proposed microphone array integrated ANC system can dramatically improve the system performance.
Laboratory Observation of a Nonlinear Interaction between Shear Alfvén Waves (2006)

An experimental investigation of nonlinear interactions between shear Alfvén waves in a laboratory plasma is presented. Two Alfvén waves, generated by a resonant cavity, are observed to beat together, driving a pseudomode at the beat frequency. The pseudomode then scatters the Alfvén waves, generating a series of sidebands. The observed interaction is very strong, with the normalized amplitude of the driven pseudomode comparable to the normalized magnetic field amplitude (deltaB/B) of the interacting Alfvén waves.
Formal Modeling and Analysis of Leader Election in MANETs (2015)

The modeling and analysis of mobile ad hoc networks MANETs pose non-trivial challenges to formal methods. Time, geometry, communication delays and failures, mobility, and uni- and bidirectionality can interact in unforeseen ways that are hard to model and analyze by automatic formal methods. In this work we use rewriting logic and Real-Time Maude to address this challenge. We propose a composable formal framework for MANET protocols and their mobility models that can take into account such complex interactions. We illustrate our framework by analyzing a well-studied leader election protocol for MANETs in the presence of both mobility and uni- and bidirectional links.
Preterm Birth in North Carolina (2004)

A 73-year-old woman was referred to a tertiary centre with isolated splenic metastasis from previous pT1aNo stage 1a lung adenocarcinoma. The patient underwent a right lower lobe lobectomy and mediastinal lymph node dissection 2 years ago for invasive adenocarcinoma with no adjuvant therapy. An incidental finding of new splenic cyst was noted on surveillance imaging, which was fluorodeoxyglucose positive on positron emission tomography, and confirmed on cytology to be metastatic lung adenocarcinoma. After multi-disciplinary team's review, the patient underwent splenectomy, with partial excision of diaphragm due to local infiltration. Her postoperative course was eventful, and was complicated by a simple fluid collection in the surgical bed (amylase negative), a left sided pneumonia and atelectasis and left sided pleural effusion, requiring antibiotics and radiological drainage of the abdominal and pleural collection. The patient recovered well and is currently doing well 9 months postoperatively with no evidence of recurrence or metastatic disease.
Robotic hummingbird: design of a control mechanism for a hovering flapping wing micro air vehicle (2014)

The use of drones, also called unmanned aerial vehicles (UAVs), is increasing every day. These aircraft are piloted either remotely by a human pilot or completely autonomously by an on-board computer. UAVs are typically equipped with a video camera providing a live video feed to the operator. While they were originally developed mainly for military purposes, many civil applications start to emerge as they become more affordable. Micro air vehicles are a subgroup of UAVs with a size and weight limitation; many are designed also for indoor use. Designs with rotary wings are generally preferred over fixed wings as they can take off vertically and operate at low speeds or even hover. At small scales, designs with flapping wings are being explored to try to mimic the exceptional flight capabilities of birds and insects. The objective of this thesis is to develop a control mechanism for a robotic hummingbird, a bio-inspired tail-less hovering flapping wing MAV. The mechanism should generate moments necessary for flight stabilization and steering by an independent control of flapping motion of each wing. The theoretical part of this work uses a quasi-steady modelling approach to approximate the flapping wing aerodynamics. The model is linearised and further reduced to study the flight stability near hovering, identify the wing motion parameters suitable for control and finally design a flight controller. Validity of this approach is demonstrated by simulations with the original, non-linear mathematical model. A robotic hummingbird prototype is developed in the second, practical part. Details are given on the flapping linkage mechanism and wing design, together with tests performed on a custom built force balance and with a high speed camera. Finally, two possible control mechanisms are proposed: the first one is based on wing twist modulation via wing root bars flexing; the second modulates the flapping amplitude and offset via flapping mechanism joint displacements. The performance of the control mechanism prototypes is demonstrated experimentally.
Colour Perception on Facial Expression towards Emotion (2012)

This study is to investigate human perceptions on pairing of facial expressions of emotion with colours. A group of 27 subjects consisting mainly of younger and Malaysian had participated in this study. For each of the seven faces, which expresses the basic emotions neutral, happiness, surprise, anger, disgust, fear and sadness, a single colour is chosen from the eight basic colours for the “match” of best visual look to the face accordingly. The different emotions appear well characterized by a single colour. The approaches used in this experiment for analysis are psychology disciplines and colours engineering. These seven emotions are being matched by the subjects with their perceptions and feeling. Then, 12 male and 12 female data are randomly chosen from among the previous data to make a colour perception comparison between genders. The successes or failures in running of this test depend on the possibility of subjects to propose their every single colour for each expression. The result will translate into number and percentage as a guide for colours designers and psychology field. DOI:  http://dx.doi.org/10.11591/telkomnika.v10i4.862
Work-family Conflict and Job Outcomes: The Moderating Effects of Flexitime Use in a New Zealand Organization (2008)

The influence of work-family practices on the outcomes of work-family conflict has received little attention in New Zealand. The present study of 100 New Zealand employees found work-family conflict held a significant negative relationship with job satisfaction and organizational commitment, while the moderating effects of current and future use of flexitime were mixed. Current flexitime use moderated work-family conflict’s relationship with both job satisfaction and organizational commitment with the negative influence of work-family conflict on these outcomes increasing when conflict was high. However, future flexitime use held a significant buffering effect towards work-family conflict and job satisfaction, with respondents reporting future flexitime use reporting increased job satisfaction when work-family conflict was high. The implications for research are discussed.
Synthesis of 1,3-Dioxane-Bridged Pyropheophorbide-Diimide and Pyropheophorbide Dimer and Their Intramolecular Electron and Energy Transfer (1995)

Abstract 1,3-Dioxane-bridged pyropheophorbide–diimide dyads and pyropheophorbide dimer were synthesized by simple acid-catalyzed reactions of methyl pyropheophorbide d with diimide-substituted diols and with pentaerythritol, respectively. 1,3-Dioxane-bridged bacteriopyropheophorbide–diimide was similarly prepared from bacteriopyropheophorbide a. Intramolecular electron-transfer and energy-transfer reactions in these models have been studied by picosecond fluorescence measurements.
Seating of TightRope RT Button Under Direct Arthroscopic Visualization in Anterior Cruciate Ligament Reconstruction to Prevent Potential Complications (2012)

The ACL TightRope RT (Arthrex, Naples, FL) is a recently introduced fixation device. The adjustable graft loop allows the surgeon some freedom in terms of the length of the femoral socket, eliminates the need for bothersome intraoperative calculations for selecting loop length, ensures that the socket is completely filled with graft, and provides the possibility of tensioning the graft even after graft fixation. However, the device can be associated with the same complications that have been described with EndoButton (Smith & Nephew Endoscopy, Andover, MA) fixation. For example, in our experience, sometimes the button of the TightRope RT may not flip, may become jammed inside the femoral canal, or may flip in the substance of the vastus lateralis. To prevent this, we have introduced 2 additional steps in our procedure: (1) direct visualization of the TightRope RT button in the femoral socket with the arthroscope during its passage and (2) a controlled push directly on the button with the help of a guide pin. Thus proper seating of the button is ensured by direct visualization and the crucial push helps in flipping and seating of the button.
Performance Evaluation of Time-Based and Hop-Based TTL Schemes in Partially Connected Ad Hoc Networks (2006)

We characterize the resource usage of an upload application for partially connected ad hoc networks. Time-based (TB) and hop-based (HB) TTL schemes are proposed and evaluated via both analysis and simulation. A HB(b, 2) scheme is near optimal, where 2 and b denote depth and breadth of the data dissemination tree. b is chosen such that the probability of message delivery approaches one. We also consider feedback schemes to notify mobile nodes to purge message replicas upon successful message delivery. With feedback, we obtain a 100-fold and 5-fold cost reduction for TB and HB schemes, respectively.
prtH2 , Not prtH , Is the Ubiquitous Cell Wall Proteinase Gene in Lactobacillus helveticus (2009)

Lactobacillus helveticus strains possess an efficient proteolytic system that releases peptides which are essential for lactobacillus growth in various fermented dairy products and also affect textural properties or biological activities. Cell envelope proteinases (CEPs) are bacterial enzymes that hydrolyze milk proteins. In the case of L. helveticus, two CEPs with low percentages of amino acid identity have been described, i.e., PrtH and PrtH2. However, the distribution of the genes that encode CEPs still remains unclear, rendering it difficult to further control the formation of particular peptides. This study evaluated the diversity of genes that encode CEPs in a collection of strains of L. helveticus isolated from various biotopes, both in terms of the presence or absence of these genes and in terms of nucleotide sequence, and studied their transcription in dairy matrices. After defining three sets of primers for both the prtH and prtH2 genes, we studied the distribution of the genes by using PCR and Southern blotting experiments. The prtH2 gene was ubiquitous in the 29 strains of L. helveticus studied, whereas only 18 of them also exhibited the prtH gene. Sequencing of a 350-bp internal fragment of these genes revealed the existence of intraspecific diversity. Finally, expression of these two CEP-encoding genes was followed during the growth in dairy matrices of two strains, ITG LH77 and CNRZ32, which possess one and two CEP-encoding genes, respectively. Both genes were shown to be expressed by L. helveticus at each stage of growth in milk and at different stages of mini-Swiss-type cheese making and ripening.
Frequency-Domain sEMG Classification Using a Single Sensor (2022)

Working towards the development of robust motion recognition systems for assistive technology control, the widespread approach has been to use a plethora of, often times, multi-modal sensors. In this paper, we develop single-sensor motion recognition systems. Utilising the peripheral nature of surface electromyography (sEMG) data acquisition, we optimise the information extracted from sEMG sensors. This allows the reduction in sEMG sensors or provision of contingencies in a system with redundancies. In particular, we process the sEMG readings captured at the trapezius descendens and platysma muscles. We demonstrate that sEMG readings captured at one muscle contain distinct information on movements or contractions of other agonists. We used the trapezius and platysma muscle sEMG data captured in able-bodied participants and participants with tetraplegia to classify shoulder movements and platysma contractions using white-box supervised learning algorithms. Using the trapezius sensor, <i>shoulder raise</i> is classified with an accuracy of 99%. Implementing subject-specific multi-class classification, <i>shoulder raise</i>, <i>shoulder forward</i> and <i>shoulder backward</i> are classified with a 94% accuracy amongst <i>object raise</i> and <i>shoulder raise-and-hold</i> data in able bodied adults. A three-way classification of the platysma sensor data captured with participants with tetraplegia achieves a 95% accuracy on <i>platysma contraction</i> and <i>shoulder raise</i> detection.
u-Synthesis Control with PI Augmentation (2006)

The mu-synthesis approach has been successfully applied to both single-stage and dual-stage disk drive servo control. There is a problem, however, in that it is not easy to get tight control over the low frequency properties of the controller (such as integral action). Moreover, this problem is exacerbated by the fact that the plant is essentially a double integrator at low frequencies, which can cause significant numerical problems for the associated algorithms. In this paper we show how to address this problem, and develop a decoupled design approach which allows tight a-priori specification of the low frequency controller, while allowing for the mu-synthesis approach to handle the mid/high frequency regions. Moreover, by pulling the low frequency control out of the associated H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">infin</sub> -synthesis problem, we alleviate the numerical issues described above
Efficient Simulation of DEDS by Means of Standard Clock Techniques: Queueing and Integrated Radio Network Examples (1993)

In this report we discuss the application of the Standard Clock (SC) approach to the simulation of several examples of discrete event dynamic systems (DEDS), and demonstrate the improved efficiency that can be achieved by using this approach. In SC simulation, a common clock (event time, event type) sequence is used by a large number of simulations running in parallel, thereby resulting in a significant decrease in the most costly aspect of the simulation process, namely the generation of events. In studies of the M/M/1/K queue, we quantify the time spent in the various aspects of the simulation, and compare predicted performance improvement with that which is actually measured. This approach scales well when applied to larger problems, including queueing networks and multihop radio networks. We develop a SC simulation model for a multihop, integrated voice/data radio network, and demonstrate its use for the determination of admission control policies. Ordinal optimization techniques are shown to provide good, although not optimal, control policies on the basis of short simulation runs. Simulation, Voice/data integration, Discrete event dynamic systems, Standard clock, Communications network
The mitochondrial inner membrane protein Mitofilin exists as a complex with SAM50, metaxins 1 and 2, coiled‐coil‐helix coiled‐coil‐helix domain‐containing protein 3 and 6 and DnaJC11 (2007)

A monoclonal antibody (mAb) has been produced which reacts with human mitofilin, a mitochondrial inner membrane protein. This mAb immunocaptures its target protein in association with six other proteins, metaxins 1 and 2, SAM50, CHCHD3, CHCHD6 and DnaJC11, respectively. The first three are outer membrane proteins, CHCHD3 has been assigned to the matrix space, and the other two proteins have not been described in mitochondria previously. The functional role of this new complex is uncertain. However, a role in protein import related to maintenance of mitochondrial structure is suggested as mitofilin helps regulate mitochondrial morphology and at least four of the associated proteins (metaxins 1 and 2, SAM50 and CHCHD3) have been implicated in protein import, while DnaJC11 is a chaperone-like protein that may have a similar role.