Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of essential gene dynamics under antibiotic stress in Streptococcus sanguinis

The paradoxical response of Streptococcus sanguinis to drugs prescribed for dental and clinical practices has complicated treatment guidelines and raised the need for further investigation. We conducted a high throughput study on concomitant transcriptome and proteome dynamics in a time course to assess S. sanguinis behaviour under a sub-inhibitory concentration of ampicillin. Temporal changes at the transcriptome and proteome level were monitored to cover essential genes and proteins over a physiological map of intricate pathways. Our findings revealed that translation was the functional category in S. sanguinis that was most enriched in essential proteins. Moreover, essential proteins in this category demonstrated the greatest conservation across 2774 bacterial proteomes, in comparison to other essential functional categories like cell wall biosynthesis and energy production. In comparison to non-essential proteins, essential proteins were less likely to contain ‘degradation-prone’ amino acids at their N-terminal position, suggesting a longer half-life. Despite the ampicillin-induced stress, the transcriptional up-regulation of amino acid-tRNA synthetases and proteomic elevation of amino acid biosynthesis enzymes favoured the enriched components of essential proteins revealing ‘proteomic signatures’ that can be used to bridge the genotype–phenotype gap of S. sanguinis under ampicillin stress. Furthermore, we identified a significant correlation between the levels of mRNA and protein for essential genes and detected essential protein-enriched pathways differentially regulated through a persistent stress response pattern at late time points. We propose that the current findings will help characterize a bacterial model to study the dynamics of essential genes and proteins under clinically relevant stress conditions.
Quantum information versus black hole physics : deep firewalls from narrow assumptions

The prevalent view that evaporating black holes should simply be smaller black holes has been challenged by the firewall paradox. In particular, this paradox suggests that something different occurs once a black hole has evaporated to one-half its original surface area. Here, we derive variations of the firewall paradox by tracking the thermodynamic entropy within a black hole across its entire lifetime and extend it even to anti-de Sitter space–times. Our approach sweeps away many unnecessary assumptions, allowing us to demonstrate a paradox exists even after its initial onset (when conventional assumptions render earlier analyses invalid). The most natural resolution may be to accept firewalls as a real phenomenon. Further, the vast entropy accumulated implies a deep firewall that goes ‘all the way down’ in contrast with earlier work describing only a structure at the horizon. This article is part of a discussion meeting issue ‘Foundations of quantum mechanics and their impact on contemporary society’.
The Effect of Edge Ratio and Fiber Orientation on Free Vibration Analysis of Laminated Composite Plates on Elastic Foundation

This study presents the effect of edge ratio and fiber orientation on free vibration analysis of simply supported antisymmetric thin and thick laminated composite plates (LCP) on elastic foundation. In the analysis, the foundation is modeled as two parameters Pasternak and Winkler type foundation. The equation of motion for laminated rectangular plates resting on elastic foundation is obtained through Hamilton’s principle. The closed form solutions are obtained by using Navier technique, and then fundamental frequencies are found by solving the results of eigenvalue problems. The numerical results obtained through the present analysis are presented, and compared with the previous studies in the literature.
Ketahanan Komposit Kayu Plastik Polistirena terhadap Serangan Jamur Pelapuk Coklat Tyromyces palustris (Decay Resistance of Wood Polymer Composite (WPC) Against Brown Rot Fungi Tyromyces palustris)

Wood specimens, 50 x 25 x 15 mm were impregnated in styrene and vinil acetate solutions at four concentration levels, using tertbutyl hydroperoxide as acatalyst. The specimens were dried at 60OC for 48 hours after which the solution was polymerized in situ. All specimens, including untreated specimens as control and specimens impregnated with Impralit CKB, were exposed to monoculture a brown rot fungus Tyromyces palustris, a brown rot fungus for 3 months. All wood polymer composite (WPC) specimens obviously showed higher resistance compared with the control. At four concentration levels, WPC of tusam showed excellent result with weight loss value less than specimens treated with Impralit CKB. WPC of karet (Hevea brasiliensis Muell. Arg) and sengon (Paraserianthes falcataria) showed good resistance at high styrene concentration level.
Impaired coordination of nucleophile and increased hydrophobicity in the +1 subsite shift levansucrase activity towards transfructosylation

Abstract Bacterial levansucrases produce β(2,6)-linked levan-type polysaccharides using sucrose or sucrose analogs as donor/acceptor substrates. However, the dominant reaction of Bacillus megaterium levansucrase (Bm-LS) is hydrolysis. Single domain levansucrases from Gram-positive bacteria display a wide substrate-binding pocket with open access to water, challenging engineering for transfructosylation-efficient enzymes. We pursued a shift in reaction specificity by either modifying the water distribution in the active site or the coordination of the catalytic acid/base (E352) and the nucleophile (D95), thus affecting the fructosyl-transfer rate and allowing acceptors other than water to occupy the active site. Two serine (173/422) and two water-binding tyrosine (421/439) residues located in the first shell of the catalytic pocket were modified. Library variants of S173, Y421 and S422, which coordinate the position of D95 and E352, show increased transfructosylation (30–200%) and modified product spectra. Substitutions at position 422 have a higher impact on sucrose affinity, while changes at position 173 and 421 have a strong effect on the overall catalytic rate. As most retaining glycoside hydrolases (GHs) Bm-LS catalyzes hydrolysis and transglycosylation via a double displacement reaction involving two-transition states (TS1 and TS2). Hydrogen bonds of D95 with the side chains of S173 and S422 contribute a total of 2.4 kcal mol−1 to TS1 stabilization, while hydrogen bonds between invariant Y421, E352 and the glucosyl C-2 hydroxyl-group of sucrose contribute 2.15 kcal mol−1 stabilization. Changes at Y439 render predominantly hydrolytic variants synthesizing shorter oligosaccharides.
Climbing the hill of left main coronary artery revascularization: percutaneous coronary intervention or coronary artery bypass graft?

Unprotected left main coronary artery (ULMCA) disease can be found in 3–10% of patients undergoing coronary angiography and has an impact on prognosis (1). Surgical myocardial revascularization by means of coronary artery bypass graft (CABG) has traditionally represented the standard therapeutic procedure for ULMCA disease (2) mainly because up to 80% of left main (LM) lesions involve the bifurcation and up to 80% of patients with ULMCA disease also have multivessel coronary artery disease.
Genetic Structure of Chinese Indigenous Goats and the Special Geographical Structure in the Southwest China as a Geographic Barrier Driving the Fragmentation of a Large Population

Background China has numerous native domestic goat breeds, however, extensive studies are focused on the genetic diversity within the fewer breeds and limited regions, the population demograogic history and origin of Chinese goats are still unclear. The roles of geographical structure have not been analyzed in Chinese goat domestic process. In this study, the genetic relationships of Chinese indigenous goat populations were evaluated using 30 microsatellite markers. Methodology/Principal Findings Forty Chinese indigenous populations containing 2078 goats were sampled from different geographic regions of China. Moderate genetic diversity at the population level (HS of 0.644) and high population diversity at the species level (HT value of 0.737) were estimated. Significant moderate population differentiation was detected (FST value of 0.129). Significant excess homozygosity (FIS of 0.105) and recent population bottlenecks were detected in thirty-six populations. Neighbour-joining tree, principal components analysis and Bayesian clusters all revealed that Chinese goat populations could be subdivided into at least four genetic clusters: Southwest China, South China, Northwest China and East China. It was observed that the genetic diversity of Northern China goats was highest among these clusters. The results here suggested that the goat populations in Southwest China might be the earliest domestic goats in China. Conclusions/Significance Our results suggested that the current genetic structure of Chinese goats were resulted from the special geographical structure, especially in the Western China, and the Western goat populations had been separated by the geographic structure (Hengduan Mountains and Qinling Mountains-Huaihe River Line) into two clusters: the Southwest and Northwest. It also indicated that the current genetic structure was caused by the geographical origin mainly, in close accordance with the human’s migration history throughout China. This study provides a fundamental genetic profile for the conservation of these populations and better to understand the domestication process and origin of Chinese goats.
The role of perceived barrier in the postpartum women's health promoting lifestyle: A partial mediator between self-efficacy and health promoting lifestyle

INTRODUCTION: In recent decades, the focuses of health studies were mostly in middle-aged women, and few studies have investigated the lifestyle of women after delivery. The aim of this study was to determine the effects of both self-efficacy and perceived barriers on Iranian women health-promoting lifestyle (HPL) in the first 1 year after childbirth. MATERIALS AND METHODS: Using a cross-sectional design, 310 women at first-year postpartum were surveyed in Zanjan (Iran) in 2016. The proportionate stratified random sampling method was carried out to select a participant. HPL has assessed with HPL profile II questionnaire. Self-efficacy was assessed using self-rated abilities for health practices scale. Perceived barriers were assessed by Barriers to Health-promoting Activities for Disabled Person scale. A meditational model was used to examine whether perceived barriers mediates between perceived self-efficacy and HPL. RESULTS: The participants mean age was 29.82 (5.1) years, 53.9% were primiparous, and most of them were homemakers (82.9%). The mean total score of HPL was 2.50 (0.29). The relationship between HPL and self-efficacy was mediated by perceived barriers partially. DISCUSSION: Self-efficacy, not only promotes women's HPL but also indirectly affect the women's lifestyle by reducing perceived barriers.
Six-Phase Soft-Switching Interleaved Boost Converter Based on SiC Semiconductor and Coupled Inductor for Fuel Cell Vehicles

This paper deals with the design of a DC/DC boost converter aimed at Fuel Cell Vehicle (FCV) application. In this study, a six-phase Interleaved Boost Converter (IBC) is chosen to extend the FC lifespan and to increase the reliability, efficiency and power density. Then, in order to further decrease the power losses of the system, power switches based on Silicon Carbide semiconductors and simple auxiliary circuits for soft- switching have been adopted. At last, coupled inductors have been utilized for purpose of reducing total volume and weight of the proposed converter. Integral Sliding- Mode Variable Structure Control (ISMVSC) has been chosen as the control strategy to satisfy the requirements of this non-linear system.
Who takes the medicine? Adherence to antiretroviral therapy in Southern Ethiopia

Background Treatment adherence is critical for the success of antiretroviral therapy (ART) for people living with HIV. There is limited representative information on ART drug adherence and its associated factors from Southern Ethiopia. We aimed at estimating the level of adherence to ART among people living with HIV and factors associated with it in 20 randomly selected ART clinics of Southern Ethiopia. Methods In this cross-sectional study, we interviewed consecutive HIV patients on first-line antiretroviral regimen attending the clinics in June 2014 using a pretested and structured questionnaire. For measuring adherence, we used 4-day recall method based on “The AIDS Clinical Trial Group adherence assessment tool”. Patients were classified as “Incomplete adherence” if they missed any of the doses in the last 4 days. Data were singly entered using EpiData and descriptive analysis, and unadjusted odds ratios were calculated using EpiDataStat software. Multivariate logistic regression analysis was performed using Stata v12.0. Results Of 974 patients interviewed, 539 (56%) were females, and mean age was 35 years. The proportion of patients with incomplete adherence was 13% (95% confidence interval: 11%–15%). In multivariate analysis, factors significantly associated with incomplete adherence included young age, being Protestant Christian, consuming alcohol, being single, and being a member of an HIV association. Psychosocial factors like stigma, depression, and satisfaction to care were not associated with incomplete adherence in the current context. Conclusion The overall adherence to ART was good. However, there were certain subgroups with incomplete adherence who need special attention. The health care providers (especially counselors) need to be aware of these subgroups and tailor their counseling to improve adherence among these groups. Exploratory qualitative studies may help uncover the exact reasons for incomplete adherence.
Virtual fiber configuration method for dynamic lightpath establishment in large-scaled WDM networks

Recently, progress has been made in the Gen- eralized Multi-Protocol Label Switching (GMPLS) and Au- tomatic Switched Optical Networks (ASON) standardizations. These technologies realize construction of large-scaled optical networks, interconnection between single-domain Wavelength Division Multiplexing (WDM) networks, and direct commu- nication over multi-domain WDM networks. Meanwhile, it is known that the topology of the Internet exhibits the power-law attribute. Since the topology of the Internet, which is constructed by interconnecting ASs, exhibits the power- law, there is a possibility that large-scale WDM networks, which are constructed by interconnecting WDM networks, will also exhibit the power-law attribute. One of the structural properties of a topology that adheres to the power-law is that most nodes have just a few links, although some have a tremendous number of them. Another property is that the average distance between nodes is smaller than in a mesh-like network. A natural question is how such a structural property performs in WDM networks. In this paper, we first investigate the property of the power- law attribute of physical topologies for WDM networks. We compare the performances of WDM networks with mesh-like and power-law topologies, and show that links connected to high-degree nodes are bottlenecks in power-law topologies. To relax this, we introduce a concept of virtual fiber which consists of two or more fibers and propose its configuration method to utilize wavelength resources more effectively. We compare performances of power-law networks with and without our method by computer simulations. The results show that our method reduces the blocking probabilities by more than one order of magnitude.
Assessing Employee Wellbeing in Schools Using a Multifaceted Approach: Associations with Physical Health, Life Satisfaction, and Professional Thriving

Purpose: Drawing on recent advances in the field of positive psychology, we conducted a pilot evaluation of employee wellbeing using Seligman's (2011) multidimensional PERMA (positive emotion, engagement, relationships, meaning, and accomplishment) model of flourishing. We analyzed associations between multiple aspects of employee wellbeing and three outcomes: phys- ical health, life satisfaction, and professional thriving. Method: Employees (N = 153) from a large private school in Australia completed a survey with items theoretically relevant to the PERMA theory. Factor analyses recovered the expected five PERMA components and a negative emotion factor. Regression analyses estimated cross-sectional associations between the wellbeing factors and self-reported physical health, life satisfaction, and professional thriving (job satisfaction and organizational commitment). Results: Differential associations support the multidimensional ap- proach to defining and measuring wellbeing. For example, staff with higher engagement and bet- ter relationships reported greater job satisfaction and organizational commitment. Conclusions: Multidimensional wellbeing assessments can help school administrators understand and improve staff wellbeing, supporting policy and practice designs that ultimately will promote wellness for all stakeholders in the education system.
Scan-based Side-channel Attack against HMAC-SHA-256 Circuits Based on Isolating Bit-transition Groups Using Scan Signatures

: A scan chain is used by scan-path test, one of design-for-test techniques, which can control and observe internal registers in an LSI chip. On the other hand, a scan-based side-channel attack is focused on which can restore secret information by exploiting the scan data obtained from a scan chain inside the crypto chip during cryptographic processing. In this paper, we propose a scan-based attack method against a hash generator circuit called HMAC-SHA-256. Our proposed method is composed of three steps; Firstly, we isolate 64 bit-transition groups from a scan data using scan signatures based on the property of the HMAC-SHA-256 algorithm. Secondly, we classify these 64 bit-transition groups into 32 pairs. Lastly, we ﬁnd out the correspondence between the scan data and the internal registers in the target HMAC-SHA-256 circuit. Our proposed method restores the secret information by the three steps above, even if the scan chain includes registers other than the target hash generator circuit and hence it becomes too long. Experimental results show that our proposed method successfully restores two secret keys of the HMAC-SHA-256 circuit using up to 425 input messages in 7.5 hours.
A fine-tuned vector-parasite dialogue in tsetse's cardia determines peritrophic matrix integrity and trypanosome transmission success

Arthropod vectors have multiple physical and immunological barriers that impede the development and transmission of parasites to new vertebrate hosts. These include the peritrophic matrix (PM), a chitinious barrier that separates the blood bolus from the midgut epithelia and modulates the vector-microbiota interactions. In tsetse flies, a sleeve-like PM is continuously produced by the cardia organ located at the fore- and midgut junction. During their development in tsetse, African trypanosomes have to bypass the PM twice: first to colonize the midgut and then to reach the salivary glands (SG). However, not all flies with midgut infections develop mammalian transmissible SG infections - the reasons for which are unclear. Here, we used transcriptomics, microscopy and functional genomics analyses to dissect the factors that regulate parasite migration from midgut to SG. In flies with midgut infections only, parasites are cleared at the cardia by reactive oxygen intermediates (ROIs) at the expense of collateral cytotoxic damage to the cardia. In flies with midgut and SG infections, gene expression for components of the PM is reduced and structural integrity of the barrier is compromised. Under these circumstances trypanosomes traverse through the layers of the PM by aggregating into cyst-like bodies. The process of PM attrition that enables the parasites to reenter into the midgut lumen to move forward to SG is apparently mediated by components of the parasites residing in the cardia. Thus, a fine-tuned dialogue between tsetse and trypanosomes at the cardia determines the outcome of PM integrity and trypanosome transmission success. Author summary Insects are responsible for transmission of parasites that cause deadly diseases in humans and animals. Understanding the key factors that enhance or interfere with parasite transmission processes can result in new control strategies. Here, we report that a proportion of tsetse flies with African trypanosome infections in their gut can prevent the parasites from migrating to the salivary glands, albeit at the expense of collateral damage. In a subset of flies with gut infections, the parasites manipulate the integrity of the gut barrier, called the peritrophic matrix, and reach the salivary glands for transmission to the next mammal. Either targeting parasite manipulative processes or enhancing peritrophic matrix integrity could reduce parasite transmission.
Analysis of Genetic Variation in Brevipalpus yothersi (Acari: Tenuipalpidae) Populations from Four Species of Citrus Host Plants

We studied species diversity and genetic variation among populations of Brevipalpus mites from four species of citrus host plants. We sampled mites on orange, lime, grapefruit and mandarin trees from orchards at six localities distributed in the five most important citrus producing states in Mexico. Genetic variation among citrus host plants and localities were assessed by analysis of nucleotide sequence data from fragments of the mitochondrial cytochrome oxidase subunit I (COI). Both Brevipalpus yothersi and B. californicus were found at these sites, and B. yothersi was the most abundant species found on all citrus species and in all localities sampled. B. californicus was found mainly on orange and mandarin and only in two of the states sampled. AMOVA and haplotype network analyses revealed no correlation between B. yothersi genetic population structure and geographical origin or citrus host plant species. Considering that a previous study reported greater genetic diversity in B. yothersi populations from Brazil than we observed in Mexico, we discuss the possibility that the Mexican populations may have originated in the southern region of America.
Investigating simple shear mechanics of bovine cartilage using a triaxial shear test machine

Objective: Articular cartilage is a non-homogeneous tissue with complex structure-function relationships. Damage to articular cartilage leads to traditionally irreparable conditions such as osteoarthritis, a disease that is both painful and debilitating to a large human population. The objective in this thesis is to perform triaxial mechanical tests on articular cartilage that are quasi-static and large-shear strains, in order to understand tissue mechanical behavior. Methods: Cartilage explants were taken from three healthy adult bovine femurs. Specimens were categorized by joint contact and contact stress regions with respect to the femoral condyle. Specimens were subject to applied shear parallel and perpendicular to the split line direction at 5 %, 10 %, 15 % and 20 % while submerged in phosphate buffered saline at 37 ◦C. Force and displacement were measured, and the shear stress and dissipation energy were calculated. Results: Joint contact region, governed by degrees of flexion, and thickness have significant effects on articular cartilage stiffness and the dissipation energy. There were no significant differences in results obtained from shearing parallel to the split line direction versus perpendicular, nor between high and low stress load-bearing regions. At 5% applied shear strain, G = 412 kPa, which is comparable to reported values for bovine by other groups.