Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantifying Escherichia coli Glutaredoxin-3 Substrate Specificity Using Ligand-induced Stability*

Traditionally, quantification of protein-ligand affinity is performed using kinetic or equilibrium measurements. However, if the binding reaction proceeds via a stable covalent complex, these approaches are often limited. By exploiting the fact that the conformational stabilization of a protein is altered upon ligand binding due to specific interactions, and using an array of selectively chosen ligand analogs, one can quantify the contribution individual interactions have on specificity. We have used ligand-induced stability as a basis to dissect the interaction between glutaredoxin-3 (Grx3) and one of its native substrates, the tripeptide glutathione. Taking advantage of the fact that Grx3 can be trapped in a covalent mixed disulfide to glutathione or to selected synthetic glutathione analogs as part of the natural catalytic cycle, individual contributions to binding of specific molecular groups can be quantified by changes in ligand-induced stability. These changes in conformational stability are interpreted in terms of interaction energies (i.e. specificity) of the particular groups present on the ligand analog. Our results illustrate that although Grx3 recognizes glutathione predominantly through independent and additive ionic interactions at the N- and C-terminal of glutathione, van der Waals interactions from the unique γ-glutamate moiety of glutathione also play an important role. This study places us closer to understanding the complex task of accommodating multiple substrate specificities in proteins of the thioredoxin superfamily and underscores the general applicability of ligand-induced stability to probe substrate specificity.
CYP17A1 gene mutations and hypertension variations found in 46, XY females with combined 17α-hydroxylase/17, 20-lyase deficiency

Abstract The aim of this study was to analyze the structural consequences of the mutations in CYP17A1 gene and their relationship with the variations of clinical manifestations in three patients who presented with complete or partial combined 17α-hydroxylase/17,20-lyase deficiency (17OHD). DNA sequences of the coding exons and intron/exon boundaries of the CYP17A1 gene were analyzed for mutations. In silico analysis with computational three-dimensional model of human P450c17 and multiple alignments analysis were performed to evaluate the spatial conformational changes by missense mutations. Five mutations p.S117fs (c.351_352delCT), p.H373L (c.1184 A>T), p.Y329fs (c.985_987delTACinsAA), p.A82D (c.245 C>A) and p.L209P (c.626 T>C) were identified in three patients, respectively. The novel mutation p.S117fs (c.351_352delCT) has not been reported previously. In silico analysis explained the conformational changes by the described mutations, which resulted in different severe 17OHD. Our studies also suggest that molecular data accompanying with in silico analysis of the CYP17A1 gene are much helpful for the diagnosis, management and genetic counseling of 17OHD.
Efficiency and power losses in PM BLDC motor with variable bridge/half-bridge structure electronic commutator

In practice we often meet with electrical drives, where it is necessary to operate with higher speed, while load torque is less than rated torque. This type of operation is called ldquoconstant power operationrdquo and may be defined as second range of natural motor torque-speed characteristic. In case of motors excited with permanent magnets magnetic flux is constant, and while supply voltage remains constant, motor speed is also (approximately) kept constant. In practice, different solutions are attempted in order to achieve increased rotating speed of brushless motors at decreased torque. One of the methods, which make possible PM BLDC motor operation at increased speed and decreased torque, is use of electronic commutator with switchable bridge-half-bridge structure. The investigation presented in the paper has been aimed at estimation of losses and efficiency in the drive consisting of brushless motor operating with variable structure commutator. Results of theoretical analysis, computer simulations and laboratory tests have shown that application of electronic variable structure commutator, which makes possible operation in the second speed range without increasing motor power and supply source power, causes an insignificant decrease in overall drive efficiency.
A reassessment of the lower visual field map in striate-recipient lateral suprasylvian cortex

Abstract Lateral suprasylvian visual cortex in the cat has been studied extensively, but its retinotopic organization remains controversial. Although some investigators have divided this region into many distinct areas, others have argued for a simpler organization. A clear understanding of the region’s retinotopic organization is important in order to define distinct areas that are likely to subserve unique visual functions. We therefore reexamined the map of the lower visual field in the striate-recipient region of lateral suprasylvian cortex, a region we refer to as the lateral suprasylvian area, LS. A dual mapping approach was used. First, receptive fields were plotted at numerous locations along closely spaced electrode penetrations; second, different anterograde tracers were injected at retinotopically identified sites in area 17, yielding patches of label in LS. To visualize the resulting data, suprasylvian cortex was flattened with the aid of a computer. Global features of the map reported in many earlier studies were confirmed. Central visual field was represented posteriorly, and elevations generally shifted downward as one moved anteriorly. Often (though not always) there was a progression from peripheral locations towards the vertical meridian as the electrode moved down the medial suprasylvian bank. The map had some remarkable characteristics not previously reported in any map in the cat. The vertical meridian’s representation was split into two pieces, separated by a gap, and both pieces were partially internalized within the map. Horizontal meridian occupied the gap. The area centralis usually had a dual representation along the posterior boundary of the lower field representation, and other fragments of visual field were duplicated as well. Finally, magnification appeared to change abruptly and unexpectedly, so that compressed regions of representation adjoined expanded regions. Despite its complexity, we found the map to be more orderly than previously thought. There was no clearcut retinotopic basis on which to subdivide LS’s lower field representation into distinct areas.
Geometry-based mapping of vector data and DEM based on hierarchical Longitude/Latitude Grids

Mapping of vector and DEM is one of main methods for ascertaining spatial object locations in 3D dimension space. What's more, mapping technology has been widely used in the analysis and management of virtual landscape. Various methods of mapping vector data and DEM on the plane have been approached. However, when those methods are used for mapping global-scale vector data set and DEM model, they do have some significant drawbacks, such as improper matching in geometry-based mapping, heavy texture distortion in texture-based mapping etc. To overcome these deficiencies, a new geometry-based method based on hierarchical Longitude/Latitude Grid, which is the simplest and most useful one of global discrete grids, is developed in this paper. Our approaches start with dividing longitude/latitude grids on the spherical surface hierarchically. Then, constructing global DEM model base on this structure is presented in brief. Next, the detailed geometry-based mapping algorithm is introduced. In the end, the experiment is made to test the algorithms and methods by using GTOPO30 and Chinese county boundary data. The result indicates: the methods and algorithms discussed in this paper are feasibility and effective.
Cloning of full‐length zebrafish dcc and expression analysis during embryonic and early larval development

Members of the DCC family play key roles in axon guidance in vertebrates as well as invertebrates. In zebrafish, only a short partial sequence of the dcc gene has been reported to date. Here, we report the cloning of full‐length zebrafish dcc. Zebrafish DCC shares the typical structure of the DCC subgroup of the immunoglobulin superfamily, consisting of four immunoglobulin and six fibronectin‐type III repeats in the extracellular domain, a single transmembrane domain, and an intracellular domain with three conserved motifs. As a first step toward studying the function of dcc, we analyzed its sequence and characterized its expression pattern during embryonic and larval development. dcc is expressed highly in brain and spinal cord, but distinct staining was also observed in developing pectoral fins, pancreas, intestine, and heart. Thus, dcc may play roles not only in axon guidance, but in morphogenesis and functioning of these organs as well. Developmental Dynamics 234:732–739, 2005. © 2005 Wiley‐Liss, Inc.
Online decision of foot placement using singular LQ preview regulation

In this paper, we introduce an online decision method of foot placement for legged robots that manages unknown external forces. It consists of a fast trajectory generation method and an optimization method of foot placement. The fast trajectory generation method is based on an explicit solution for singular LQ preview regulation problem of an inverted pendulum model. By using the regulator problem, the conditions of target ZMP trajectory that will not make the COM trajectory diverge and a fast generation method of the COM trajectory which satisfies the target ZMP trajectory are obtained. An online optimization of foot placement is realized by using the fast trajectory generation method. An experiment of the online decision method of foot placement that manages unknown external force shows the performance of the proposed method.
Impact of wind generation variability on small signal stability of power systems

Power systems are shifting toward utilizing higher penetration of renewable energy sources (RESs) and especially wind generation because of the need to reduce carbon emissions over the next several decades. Small signal stability can be influenced with increasing penetration of wind generation in power systems. Poor damping of low frequency electromechanical oscillations are a threat to secure operation of power systems. In this paper, we investigate the sensitivity of the small signal stability of a two area test system on wind generation variability, mainly focusing on the stability of inter-area oscillation mode. Margins that determine the minimum amount of wind generation for a stable system for different tie-line power values are derived. Static load models are used and the impact of different flexibility levels from loads on the stability margins are studied. Furthermore, the impact of the proximity of flexible load to wind generation is also studied.
Simultaneously Learning DNA Motif Along with Its Position and Sequence Rank Preferences Through Expectation Maximization Algorithm

Although de novo motifs can be discovered through mining over-represented sequence patterns, this approach misses some real motifs and generates many false positives. To improve accuracy, one solution is to consider some additional binding features (i.e., position preference and sequence rank preference). This information is usually required from the user. This article presents a de novo motif discovery algorithm called SEME (sampling with expectation maximization for motif elicitation), which uses pure probabilistic mixture model to model the motif's binding features and uses expectation maximization (EM) algorithms to simultaneously learn the sequence motif, position, and sequence rank preferences without asking for any prior knowledge from the user. SEME is both efficient and accurate thanks to two important techniques: the variable motif length extension and importance sampling. Using 75 large-scale synthetic datasets, 32 metazoan compendium benchmark datasets, and 164 chromatin immunoprecipitation sequencing (ChIP-Seq) libraries, we demonstrated the superior performance of SEME over existing programs in finding transcription factor (TF) binding sites. SEME is further applied to a more difficult problem of finding the co-regulated TF (coTF) motifs in 15 ChIP-Seq libraries. It identified significantly more correct coTF motifs and, at the same time, predicted coTF motifs with better matching to the known motifs. Finally, we show that the learned position and sequence rank preferences of each coTF reveals potential interaction mechanisms between the primary TF and the coTF within these sites. Some of these findings were further validated by the ChIP-Seq experiments of the coTFs. The application is available online.
The value of cytokeratins 20 and 7 in discriminating metastatic adenocarcinomas from pleural mesotheliomas

Immunohistochemistry is a useful method in the differential diagnosis between pleural mesotheliomas and metastatic adenocarcinomas to the pleura. Cytokeratin (CK) 5‐6 is one of the most specific mesothelioma‐associated antibodies. Cytokeratin 20 and CK7 have been used successfully in studies determining primary location of adenocarcinomas from metastases. In the current study, the value of these CKs in differential diagnosis of malignant pleural lesions was examined.
Sequence analysis and recombinant expression of a 28-kilodalton Treponema pallidum subsp. pallidum rare outer membrane protein (Tromp2)

In this study, we report the cloning, sequencing, and expression of the gene encoding a 28-kDa Treponema pallidum subsp. pallidum rare outer membrane protein (TROMP), designated Tromp2. The tromp2 gene encodes a precursor protein of 242 amino acids including a putative signal peptide of 24 amino acids ending in a type I signal peptidase cleavage site of Leu-Ala-Ala. The mature protein of 218 amino acids has a calculated molecular weight of 24,759 and a calculated pI of 7.3. The predicted secondary structure of Tromp2 shows nine transmembrane segments of amphipathic beta-sheets typical of outer membrane proteins. Recombinant Tromp2 (rTromp2) was expressed with its native signal peptide, using a tightly regulated T7 RNA polymerase expression vector. Under high-level expression conditions, rTromp2 fractionated exclusively with the Escherichia coli outer membrane. Antiserum raised against rTromp2 was generated and used to identify native Tromp2 in cellular fractionations. Following Triton X-114 extraction and phase separation of T. pallidum, the 28-kDa Tromp2 protein was detected prominently in the detergent phase. Alkali and high-salt treatment of purified outer membrane from T. pallidum, conditions which remove peripherally associated membrane proteins, demonstrated that Tromp2 is an integral membrane protein. Whole-mount immunoelectron microscopy of E. coli cells expressing rTromp2 showed specific surface antibody binding. These findings demonstrate that Tromp2 is a membrane-spanning outer membrane protein, the second such protein to be identified for T. pallidum.
Anterior Cruciate Ligament Injuries in Female Athletes

Female athletes have a 4 to 6 times higher incidence of anterior cruciate ligament injury than do male athletes participating in the same landing and pivoting sports. This greater risk of anterior cruciate ligament injury, coupled with a geometric increase in participation (doubling each decade), has led to a significant rise in anterior cruciate ligament injuries in female athletes. The gender gap in anterior cruciate ligament injury, combined with evidence that the underpinnings of this serious health problem are neuromuscular in nature, leads to the development of neuromuscular interventions designed to prevent injury. A systematic review of the published literature yielded 6 published interventions targeted toward anterior cruciate ligament injury prevention in female athletes. Four of 6 significantly reduced knee injury incidence, and 3 of 6 significantly reduced anterior cruciate ligament injury incidence in female athletes. A meta-analysis of these 6 studies demonstrates a significant effect of neuromuscular training programs on anterior cruciate ligament injury incidence in female athletes (test for overall effect, Z = 4.31, P< .0001). Examination of the similarities and differences between the training regimens gives insight into the development of more effective and efficient interventions. The purpose of this “Current Concepts” review is to highlight the relative effectiveness of these interventions in reducing anterior cruciate ligament injury rates and to evaluate the common training components between the training studies. In addition, the level of rigor of these interventions, the costs and the difficulty of implementation, the compliance with these interventions, and the performance benefits are discussed. This review summarizes conclusions based on evidence from the common components of the various interventions to discuss their potential to reduce anterior cruciate ligament injury risk and assess their potential for combined use in more effective and efficient intervention protocols.
c-Axiszig-zag polarization inverted ScAlN multilayer for FBAR transformer rectifying antenna

Energy harvesting from surrounding electromagnetic wave can satisfy the increasing demand of trillions of wireless sensors for IoT. RF energy harvesting is generally achieved by RF-DC conversion using a rectifying antenna (called rectenna). For weak RF signal, however, RF-DC conversion efficiency significantly decreases because weak RF signal cannot activate the diode in the rectenna. Therefore, in order to obtain high conversion efficiency for a weak signal, a Dickson charge pump[1] is generally used to increase the RF voltage. However, their low efficiency, poor impedance matching, and large size are the problem. In this study, to overcome this problem, we introduce the RF energy harvester consisting of a new type of polarization inverted FBAR transformer and rectenna. As shown in Fig.1 (a), RF input signal can be increased 7 times when 8 polarization inversion layered FBAR transformer is used. We previously reported various polarization inverted structure such as (0001)/(000-1) ScAlN films [2] and (−1–120)/(11–20) AlN films [3]. We here reports the eight layer of c-axis zig-zag polarization inverted ScAlN stack transformer resonator. [1] A. Parks, et al. Proc. IEEE WiSNET, (2013). [2] M. Suzuki, T. Yanagitani, and H. Odagawa, Appl. Phys. Lett. (2014) [3] M. Suzuki, T. Yanagitani, IUS 2011, 4C-2 (2011).
Use of Angiotensin II Receptor Blockers and the Risk of Acute Pancreatitis: A Nested Case-Control Study

Background: There is no specific treatment against acute pancreatitis (AP). A protective effect by angiotensin II receptor blockers (ARB) on AP has been suggested experimentally, but clinical evidence is scarce. Methods: We conducted a population-based case-control study using The Health Improvement Network in the United Kingdom, comprising about 167,000 hypertensive patients in the study period 1996–2005. In multivariate logistic regression analysis, odds ratios were calculated with 95% confidence intervals (CI). Adjustments included sex, age, calendar year, body mass index, tobacco smoking, alcohol, general practitioner visits per year, and various antihypertensive medications with regard to exposure to ARB, and risk of AP. Results: Among 633,281 person-years at risk, 265 new cases of AP were identified. Current users of ARB had a 37% statistically non-significant reduced risk of developing AP as compared to non-users (OR 0.63, 95% CI 0.38–1.02). No clear association was found between use of other antihypertensive drugs and risk of AP. Conclusion: Our study adds some support to previous experimental findings. Use of ARB might be associated with a reduced risk of AP. More research is needed to elucidate the potential role of ARB in the development of AP in the clinical setting.
Determination of glycerol turnover by stable-isotope technique in humans: a new [1,1,2,3,3-2H5]glycerol derivative for mass-spectrometry analysis.

The stable isotope-labeled [1,1,2,3,3-2H5]glycerol analyzed by negative-ion chemical ionization (NCI) mass spectrometry has been proven a valid tracer for studying glycerol kinetics in humans. Because of its high technical complexity, NCI mass spectrometry is available to only a few laboratories. Thus, the aim of our study was to create an alternative method for measuring [1,1,2,3,3-2H5]glycerol enrichment in plasma with a new derivative and positive-ion chemical ionization (PCI) mass spectrometry. It could be demonstrated that the trisacetyl[1,1,2,3,3-2H5]glycerol derivative was able to produce a fragment at m/z = 164 with sufficient intensity. Application of [1,1,2,3,3-2H5]glycerol in seven healthy volunteers resulted in reproducible measurements of basal glycerol turnover rates. The mean glycerol flux rate of 3.02 +/- 0.37 mumol.kg-1 body wt.min-1 after an overnight fast was similar to values reported from studies with comparable protocols. Physiological changes of lipolysis rates after 48 h of fasting followed by infusion of 4 mg.kg-1 body wt.min-1 glucose could also be adequately studied in one subject. Fast-induced elevated glycerol turnover at 7.56 mumol.kg-1 body wt.min-1, was substantially suppressed to 1.13 mumol.kg-1 body wt.min-1, when glucose was administered. The easily performed trisacetyl[1,1,2,3,3-2H5]glycerol derivative analyzed by PCI mass spectrometry is suitable for studying glycerol kinetics in humans.
Comparison of primary balloon angioplasty with bailout stenting strategy to primary coronary stenting strategy in the treatment of patients with ST-segment elevation myocardial infarction (STEMI).

BACKGROUND In recent years significant progress has been made in invasive treatment of patients with acute myocardial infarction (AMI). Primary coronary stenting is currently a routine strategy which replaced primary balloon angioplasty with bailout stenting preferred in the past. Studies comparing these two strategies of stenting in AMI are scarce. AIM To compare the immediate and long-term outcomes after primary angioplasty strategy and bailout stenting versus primary stent placement strategy in patients with AMI. METHODS We analysed data from a single-centre registry of consecutive patients with ST segment elevation myocardial infarction admitted between January 1998 and October 2003. In our centre in years 1998-2000 stenting was used only after failed or suboptimal balloon angioplasty. Starting from year 2001 we used routine primary stenting strategy. We compared these two angioplasty strategies applied in different time intervals with regard to in-hospital outcome and long-term mortality. Patients with cardiogenic shock at admission were excluded. RESULTS Out of a total of 1602 patients treated invasively for AMI (cardiogenic shock excluded) 479 underwent primary balloon angioplasty strategy with bailout stenting - group 1 (years 1998-2000) and 1123 were treated with primary stenting strategy - group 2 (years 2001-2003). In group 1 bailout stenting occurred in 34.4% of patients whereas in group 2 stents were implanted in 83% of patients. Patients in the balloon angioplasty group were younger, had shorter time from the onset of symptom to hospital arrival and more frequently underwent rescue coronary intervention after failed thrombolysis. In-hospital mortality was 2.9 vs. 2.4% in groups 1 and 2, respectively (p=NS). Twenty-four month mortality rate was 9.8% in group 1 and 10.06% in group 2 (p=NS). CONCLUSIONS 1. Effectiveness of coronary angioplasty is high and comparable in both groups. 2. In-hospital and long-term mortality and procedure-related complication rate are all low and comparable with both stenting strategies. 3. Independent factors increasing long-term mortality include: culprit vessel reocclusion, multivessel coronary disease, older age and hypertension. 4. Patients with complete patency of culprit vessel restored and with higher left ventricular ejection fraction presented lower 2-year mortality rate. 5. Bailout stenting did not increase 2-year mortality.