Miracle-dz/UniFAR-FTUs huggingface dataset:
Stabilizing the subtilisin BPN' pro‐domain by phage display selection: How restrictive is the amino acid code for maximum protein stability?

We have devised a procedure using monovalent phage display to select for stable mutants in the pro‐domain of the serine protease, subtilisin BPN'. In complex with subtilisin, the pro‐domain assumes a compact structure with a four‐stranded antiparallel β‐sheet and two three‐turn α‐helices. When isolated, however, the pro‐domain is 97% unfolded. These experiments use combinatorial mutagenesis to select for stabilizing amino acid combinations at a particular structural locus and determine how many combinations are close to the maximum protein stability. The selection for stability is based on the fact that the independent stability of the pro‐domain is very low and that binding to subtilisin is thermodynamically linked to folding. Two libraries of mutant pro‐domains were constructed and analyzed to determine how many combinations of amino acids at a particular structural locus result in the maximum stability. A library comprises all combinations of four amino acids at a structural locus. Previous studies using combinatorial genetics have shown that many different combinations of amino acids can be accommodated in a selected locus without destroying function. The present results indicate that the number of sequence combinations at a structural locus, which are close to the maximum stability, is small. The most striking example is a selection at an interior locus of the pro‐domain. After two rounds of phagemid selection, one amino acid combination is found in 40% of sequenced mutants. The most frequently selected mutant has a δGunfolding = 4 kcal/mol at 25°C, an increase of 6 kcal/mol relative to the naturally occurring sequence. Some implications of these results on the amount of sequence information needed to specify a unique tertiary fold are discussed. Apart from possible implications on the folding code, the phage display selection described here should be useful in optimizing the stability of other proteins, which can be displayed on the phage surface.
Thyroid hormones induce doxorubicin chemosensitivity through enzymes involved in chemotherapy metabolism in lymphoma T cells

Thyroid hormones (THs) – 3,3′,5-triiodo-L-thyronine (T3) and L-thyroxine (T4) – are important regulators of the metabolism and physiology of most normal tissues. Cytochrome P450 family 3A members are drug metabolizing enzymes involved in the activation and detoxification of several drugs. CYP3A4 is the major enzyme involved in the metabolism of chemotherapeutic drugs. In this work, we demonstrate that THs induce a significant increase in CYP3A4 mRNA levels, protein expression and metabolic activity through the membrane receptor integrin αvβ3 and the activation of signalling pathways through Stat1 and NF-κB. We reasoned that TH-induced CYP3A4 modulation may act as an important regulator in the metabolism of doxorubicin (Doxo). Experiments in vitro demonstrated that in CYP3A4-knocked down cells, no TH-mediated chemosensitivity to Doxo was observed. We also found that THs modulate these functions by activating the membrane receptor integrin αvβ3. In addition, we showed that the thyroid status can modulate CYP450 mRNA levels in tumor and liver tissues, and the tumor volume in response to chemotherapy in vivo. In fact, Doxo treatment in hypothyroid mice was associated with lower tumors, displaying lower levels of CYP enzymes, than euthyroid mice. However, higher mRNA levels of CYP enzymes were found in livers from Doxo treated hypothyroid mice respect to control. These results present a new mechanism by which TH could modulate chemotherapy response. These findings highlight the importance of evaluating thyroid status in patients during application of T-cell lymphoma therapeutic regimens.
β-Hemolytic Streptococcus anginosus subsp. anginosus causes streptolysin S-dependent cytotoxicity to human cell culture lines in vitro

ABSTRACT Background: Streptococcus anginosus subsp. anginosus (SAA) is one of the opportunistic pathogens in humans that inhabits the oral cavity. The type strain of SAA, NCTC10713T, showed clear β-hemolysis on blood agar plates, and the sole β-hemolytic factor revealed two streptolysin S (SLS) molecules. SLS is well known as the peptide hemolysin produced from the human pathogen S. pyogenes and shows not only hemolytic activity on erythrocytes but also cytotoxic activity in cell culture lines in vitro and in vivo, such as in a mouse infection model. However, no cytotoxic activity of SLS produced from β-hemolytic SAA (β-SAA) has been reported so far. Objective and Design: In this study, the SLS-dependent cytotoxicity of the β-SAA strains including the genetically modified strains was investigated in vitro. Results: The SLS-producing β-SAA showed cytotoxicity in human cell culture lines under the co-cultivation condition and it was found that this cytotoxicity was caused by the SLS secreted into the extracellular milieu. Conclusion: The results from this study suggest that the SLS produced from β-SAA might indicate the cytotoxic potential similar to that of the SLS from S. pyogenes and the SLS-producing β-SAA would be recognized as “a wolf in sheep’s clothing” More attention will be paid to the pathogenicity of β-hemolytic Anginosus group streptococci.
α1A-Adrenergic receptor prevents cardiac ischemic damage through PKCδ/GLUT1/4-mediated glucose uptake

Abstract While α1-adrenergic receptors (ARs) have been previously shown to limit ischemic cardiac damage, the mechanisms remain unclear. Most previous studies utilized low oxygen conditions in addition to ischemic buffers with glucose deficiencies, but we discovered profound differences if the two conditions are separated. We assessed both mouse neonatal and adult myocytes and HL-1 cells in a series of assays assessing ischemic damage under hypoxic or low glucose conditions. We found that α1-AR stimulation protected against increased lactate dehydrogenase release or Annexin V+ apoptosis under conditions that were due to low glucose concentration not to hypoxia. The α1-AR antagonist prazosin or nonselective protein kinase C (PKC) inhibitors blocked the protective effect. α1-AR stimulation increased 3H-deoxyglucose uptake that was blocked with either an inhibitor to glucose transporter 1 or 4 (GLUT1 or GLUT4) or small interfering RNA (siRNA) against PKCδ. GLUT1/4 inhibition also blocked α1-AR-mediated protection from apoptosis. The PKC inhibitor rottlerin or siRNA against PKCδ blocked α1-AR stimulated GLUT1 or GLUT4 plasma membrane translocation. α1-AR stimulation increased plasma membrane concentration of either GLUT1 or GLUT4 in a time-dependent fashion. Transgenic mice overexpressing the α1A-AR but not α1B-AR mice displayed increased glucose uptake and increased GLUT1 and GLUT4 plasma membrane translocation in the adult heart while α1A-AR but not α1B-AR knockout mice displayed lowered glucose uptake and GLUT translocation. Our results suggest that α1-AR activation is anti-apoptotic and protective during cardiac ischemia due to glucose deprivation and not hypoxia by enhancing glucose uptake into the heart via PKCδ-mediated GLUT translocation that may be specific to the α1A-AR subtype.
Extraction of motion individuality in sports and its application to motion of characters with different figures

We propose a method to extract motion individuality from the form of a sport expert and to apply it to figures that have different segment lengths. For this purpose, a standard motion is established by removing the subjective motion from an actor who conducts a sport skillfully, and the surface features (angular velocity and torque of the joint) are extracted for each joint angle difference in each animation frame between the original motion of the sports expert and the standard motion. The surface features and relative timing in the deep structure are transmitted to the characters having different segment lengths by applying them to a standard motion of the characters, which is also made by removing subjective motion in advance.
Current and Emerging Legionella Diagnostics for Laboratory and Outbreak Investigations

SUMMARY Legionnaires' disease (LD) is an often severe and potentially fatal form of bacterial pneumonia caused by an extensive list of Legionella species. These ubiquitous freshwater and soil inhabitants cause human respiratory disease when amplified in man-made water or cooling systems and their aerosols expose a susceptible population. Treatment of sporadic cases and rapid control of LD outbreaks benefit from swift diagnosis in concert with discriminatory bacterial typing for immediate epidemiological responses. Traditional culture and serology were instrumental in describing disease incidence early in its history; currently, diagnosis of LD relies almost solely on the urinary antigen test, which captures only the dominant species and serogroup, Legionella pneumophila serogroup 1 (Lp1). This has created a diagnostic “blind spot” for LD caused by non-Lp1 strains. This review focuses on historic, current, and emerging technologies that hold promise for increasing LD diagnostic efficiency and detection rates as part of a coherent testing regimen. The importance of cooperation between epidemiologists and laboratorians for a rapid outbreak response is also illustrated in field investigations conducted by the CDC with state and local authorities. Finally, challenges facing health care professionals, building managers, and the public health community in combating LD are highlighted, and potential solutions are discussed.
Parthenogenetic and nuclear transfer rabbit embryo development and apoptosis after activation treatments

Previous studies mainly evaluated the effect of culture conditions on preimplantation embryo apoptosis. In order to inhibit apoptosis of nuclear transfer (NT) embryos, putative apoptosis inhibitors were used to treat donor cells. However, little is known about the effect of activation treatments on embryo apoptosis. We firstly investigated the effect of various parthenogenetic activation (PA) treatments on embryo development, blastocyst cell number, and apoptosis, and then one of these activation treatments proved to be most efficient was selected for activation rabbit NT embryos. The activation by electrical pulses and 30 min later, electroporation with 25 μM D‐myoinositol 1,4,5‐trisphosphate (IP3) in Ca2+‐ and Mg2+‐free PBS, then exposure to 2.0 mM 6‐dimethylaminopurine (6‐DMAP) for 3 hr effectively activated rabbit oocytes, and resulted in significantly a higher blastocyst development rate (72.7%) and total cell number (175 ± 14.1), and markedly lower apoptosis level of blastocyst (4.3 ± 0.5) than all the other groups. When the same activation protocol was applied in NT embryo activation, we found that exposure of the embryos to 6‐DMAP for 3 hr could decrease the apoptosis level of blastocyst and increase blastocyst rate and cell number. The results demonstrate that oocyte activation affects not only embryo development and quality but also embryo apoptosis. Mol. Reprod. Dev. © 2005 Wiley‐Liss, Inc.
Students with brain tumors: their post-treatment perceptions of teachers, peers, and academics and retrospective views on school during treatment

The purpose of this pilot study was: (1) to determine how students surviving brain tumors (BTs) perceive their teachers’ responses to them, their own academic performance, and their interactions with peers at school using a new measure; and (2) to describe students’ retrospective perceptions of schooling while undergoing treatment. Using a sample of 22 students treated for a BT (ages 9—18) and 22 comparison (ages 8—19), no significant BT-control group differences regarding perceptions of teacher response, academic performance, and interactions with peers at school were found. Generally, students with BTs reported positive school experiences during treatment including favorable perceptions of their teachers’ effectiveness, enjoyment of schoolwork, and the quality of their schooling. Additionally, they felt that completing schoolwork during treatment was important. The results of this study may provide insight into the perceived psychosocial adjustment and academic performance of students with BTs during and after treatment.
Robust Estimation of Derivatives Using Locally Weighted Least Absolute Deviation Regression

In nonparametric regression, the derivative estimation has attracted much attention in recent years due to its wide applications. In this paper, we propose a new method for the derivative estimation using the locally weighted least absolute deviation regression. Different from the local polynomial regression, the proposed method does not require a finite variance for the error term and so is robust to the presence of heavy-tailed errors. Meanwhile, it does not require a zero median or a positive density at zero for the error term in comparison with the local median regression. We further show that the proposed estimator with random difference is asymptotically equivalent to the (infinitely) composite quantile regression estimator. The proposed method is also extended to estimate the derivatives at the boundaries and to estimate the higher-order derivatives. For the equidistant design, we derive theoretical results for the proposed estimators, including the asymptotic bias and variance, consistency, and asymptotic normality. Finally, we conduct simulation studies to demonstrate that the proposed method has better performance than the existing methods in the presence of outliers and heavy-tailed errors.
Identifying Structural Features of Audio

This study tested the ability of nine different auditory structural features to elicit orienting responses from radio listeners. It further tested the effect of the orienting response on listeners' memory for information presented immediately following the orienting- eliciting structural feature. Results show that listeners do have significant decelerating cardiac patterns suggestive of orienting for eight of the nine features. Taken as a categorical whole, these features also increase recognition memory for the information presented after their onset compared to information presented immediately before.
Scalable Service Placement in the Fog Computing Environment for the IoT-Based Smart City

The Internet of Things (IoT) is one of the main enablers for situation awareness needed in accomplishing smart cities. IoT devices, especially for monitoring purposes, have stringent timing requirements which may not be met by cloud computing. This deficiency of cloud computing can be overcome by fog computing for which fog nodes are placed close to IoT devices. Because of low capabilities of fog nodes compared to cloud data centers, fog nodes may not be deployed with all the services required by IoT devices. Thus, in this article, we focus on the issue of fog service placement and present the recent research trends in this issue. Most of the literature on fog service placement deals with determining an appropriate fog node satisfying the various requirements like delay from the perspective of one or more service requests. In this article, we aim to effectively place fog services in accordance with the pre-obtained service demands, which may have been collected during the prior time interval, instead of on-demand service placement for one or more service requests. The concept of the logical fog network is newly presented for the sake of the scalability of fog service placement in a large-scale smart city. The logical fog network is formed in a tree topology rooted at the cloud data center. Based on the logical fog network, a service placement approach is proposed so that services can be placed on fog nodes in a resourceeffective way.
DNA polymerase III of Gram-positive eubacteria is a zinc metalloprotein conserving an essential finger-like domain.

DNA polymerase III (pol III) of Gram-positive eubacteria is a catalytically bifunctional DNA polymerase:3'-5' exonuclease [Low, R. L. , Rashbaum, S. A. , and Cozzarelli, N. R. (1976) J. Biol.Chem. 251, 1311-1325]. The pol III protein conserves, between its exonuclease and dNTP binding sites, a 35-residue segment of primary structure with the potential to form a zinc finger-like structure [Berg, J. M. (1990) Ann. Rev. Biochem. 19, 405-421]. This paper describes results of experiments which probe the capacity of this segment to bind zinc and the role of this segment in enzyme function. The results of metal and mutational analysis of a model pol III derived from Bacillus subtilis indicate that (i) the Gram-positive pol III is a metalloprotein containing tightly bound zinc in a stoichiometry of 1, (ii) the zinc atom is bound within the 35-residue segment, likely in one of two probable finger-like structures, and (iii) the integrity of the zinc-bound structure is specifically critical to the formation and/or function of the enzyme's polymerase site.
Block Sparse Signals Recovery Algorithm for Distributed Compressed Sensing Reconstruction

Distributed compressed sensing (DCS) states that we can recover the sparse signals from very few linear measurements. Various studies about DCS have been carried out recently. In many practical applications, there is no prior information except for standard sparsity on signals. The typical example is the sparse signals have block-sparse structures whose non-zero coefficients occurring in clusters, while the cluster pattern is usually unavailable as the prior information. To discuss this issue, a new algorithm, called backtracking-based adaptive orthogonal matching pursuit for block distributed compressed sensing (DCSBBAOMP), is proposed. In contrast to existing block methods which consider the single-channel signal reconstruction, the DCSBBAOMP resorts to the multi-channel signals reconstruction. Moreover, this algorithm is an iterative approach, which consists of forward selection and backward removal stages in each iteration. An advantage of this method is that perfect reconstruction performance can be achieved without prior information on the block-sparsity structure. Numerical experiments are provided to illustrate the desirable performance of the proposed method.
Usefulness of chromic oxide as an internal standard for balance studies in formula-fed patients and for assessment of colonic function.

In 35 patients maintained solely on liquid formula diets, chromic oxide has been evaluated as an internal standard for balance studies that require stool collections. In 28 patients the excretion of chromic oxide was ideal: steady states were attained in which mean daily output was 90% (or more) of mean daily intake. In these patients corrections for fecal flow could validly be applied.In patients who excreted the marker ideally, the availability of chromic oxide balance data made possible the calculation of pool sizes and turnover rates of unexcreted intestinal content. These indexes bore little relationship to the usual clinical descriptions of bowel habits. In some patient who had daily bowel movements, pool sizes were very large and daily turnover was small, i.e., a large proportion of the colonic contents was not excreted for surprisingly long periods. It is critically important for investigators to recognize this possibility when carrying out balance studies for fecal constituents that may be altered by bacterial action within the gut lumen: for instance, in 6 patients a significant inverse correlation was found between daily fecal turnover and degradative losses of large amounts of dietary beta-sitosterol.7 of 35 patients failed to attain the ideal steady state of chromic oxide excretion. These patients would not have been singled out if an internal standard had not been used. In such patients balance studies that require analysis of fecal constituents must be interpreted with great caution, since the constituents in question may be handled in the same nonideal fashion as the internal standard.
Understanding Android App Piggybacking

The Android packaging model offers adequate opportunities for attackers to inject malicious code into popular benign apps, attempting to develop new malicious apps that can then be easily spread to a large user base. Despite the fact that the literature has already presented a number of tools to detect piggybacked apps, there is still lacking a comprehensive investigation on the piggybacking processes. To fill this gap, in this work, we collect a large set of benign/piggybacked app pairs that can be taken as benchmark apps for further investigation. We manually look into these benchmark pairs for understanding the characteristics of piggybacking apps and eventually we report 20 interesting findings. We expect these findings to initiate new research directions such as practical and scalable piggybacked app detection, explainable malware detection, and malicious code location.
Inhibitory Control Differentiates Rare Target Search Performance in Children

Age-related differences in rare-target search are primarily explained by the speed-accuracy trade-off, primed responses, or decision making. The goal was to examine how motor inhibition influences visual search. Children pressed a key when a rare target was detected. On no-target trials, children withheld reactions. Response time (RT), hits, misses, correct rejection, and false alarms were measured. Tapping tests assessed motor control. Older children tapped faster, were more sensitive to rare targets (higher d'), and reacted more slowly than younger ones. Girls outperformed boys in search sensitivity but not in RT. Motor speed was closely associated with hit rate and RT. Results suggest that development of inhibitory control plays a key role in visual detection. The potential implications for cognitive-motor development and individual differences are discussed.
Temperature and Voltage Measurement for Field Test Using an Aging-Tolerant Monitor

Measuring temperature and voltage (T&V) in a current VLSI is very important in guaranteeing its reliability, because a large variation of temperature or voltage in field will reduce a delay margin and makes the chip behavior unreliable. This paper proposes a novel method of T&V measurement, which can be used for variety of applications, such as field test, online test, or hot-spot monitoring. The method counts frequencies of more than one ring oscillator (RO), which composes an aging-tolerant monitor. Then, the T&V are derived from the frequencies using a multiple regression analysis. To improve the accuracy of measurement, three techniques of an optimal selection of RO types, their calibration, and hierarchical calculation are newly introduced. In order to make sure the proposed method, circuit simulation in 180-, 90-, and 45-nm CMOS technologies is performed. In the 180-nm CMOS technology, the temperature accuracy is within 0.99 °C, and the voltage accuracy is within 4.17 mV. Furthermore, some experimental results using fabricated test chips with 180-nm CMOS technology confirm its feasibility.
A Low Phase Noise Quadrature Injection Locked Frequency Synthesizer for MM-Wave Applications

This paper proposes a 60 GHz quadrature PLL frequency synthesizer for the IEEE802.15. 3c with wide tuning range and low phase noise. The synthesizer is constructed using a 20 GHz PLL that is coupled with a Quadrature Injection Locked Oscillator (QILO) as a frequency tripler to generate the 60 GHz signal. The 20 GHz PLL generates a signal with a phase noise that is lower than -105 dBc/Hz using tail feedback to improve the phase noise while having a 17% tuning range. The proposed 60 GHz QILO uses a combination of parallel and tail injection to enhance the locking range by improving the QILO injection efficiency at the moment of injection and has a 12% tuning range. Both the 20 GHz PLL and the QILO were fabricated as separate chips using a 65 nm CMOS process and measurement results show a phase noise that is less than -95 dBc/Hz@1 MHz at 60 GHz while consuming 80 mW from a 1.2 V supply. To the author's knowledge this phase noise is about 20 dB better than recently reported QPLLs and about 10 dB compared to differential PLLs operating at a similar frequency and at a similar offset.