Miracle-dz/UniFAR-FTUs huggingface dataset:
Direct observation of the actin filament by tip-scan atomic force microscopy

Actin filaments, the actin–myosin complex and the actin–tropomyosin complex were observed by a tip-scan atomic force microscope (AFM), which was recently developed by Olympus as the AFM part of a correlative microscope. This newly developed AFM uses cantilevers of similar size as stage-scan AFMs to improve substantially the spatial and temporal resolution. Such an approach has previously never been possible by a tip-scan system, in which a cantilever moves in the x, y and z directions. We evaluated the performance of this developed tip-scan AFM by observing the molecular structure of actin filaments and the actin–tropomyosin complex. In the image of the actin filament, the molecular interval of the actin subunits (∼5.5 nm) was clearly observed as stripes. From the shape of the stripes, the polarity of the actin filament was directly determined and the results were consistent with the polarity determined by myosin binding. In the image of the actin–tropomyosin complex, each tropomyosin molecule (∼2 nm in diameter) on the actin filament was directly observed without averaging images of different molecules. Each tropomyosin molecule on the actin filament has never been directly observed by AFM or electron microscopy. Thus, our developed tip-scan AFM offers significant potential in observing purified proteins and cellular structures at nanometer resolution. Current results represent an important step in the development of a new correlative microscope to observe nm-order structures at an acceptable frame rate (∼10 s/frame) by AFM at the position indicated by the fluorescent dye observed under a light microscope.
Electrostatics of two-dimensional lateral junctions

The increasing technological control of two-dimensional (2D) materials has allowed the demonstration of 2D lateral junctions exhibiting unique properties that might serve as the basis for a new generation of 2D electronic and optoelectronic devices. Notably, the chemically doped MoS2 homojunction, the WSe2-MoS2 monolayer and MoS2 monolayer/multilayer heterojunctions, have been demonstrated. Here we report the investigation of 2D lateral junction electrostatics, which differs from the bulk case because of the weaker screening, producing a much longer transition region between the space-charge region and the quasi-neutral region, making inappropriate the use of the complete-depletion region approximation. For such a purpose we have developed a method based on the conformal mapping technique to solve the 2D electrostatics, widely applicable to every kind of junctions, giving accurate results for even large asymmetric charge distribution scenarios.
Identification of a novel mutation in FGFR1 gene in patients with Kallmann syndrome by high throughput sequencing

ABSTRACT Kallmann syndrome (KS) is a rare clinical and genetic heterogeneity disease, which is familial or sporadic. KS is known to have three patterns of inheritance: X linked recessive inheritance, autosomal dominant inheritance and rare autosomal recessive inheritance. Here, we report a sibling pedigree with autosomal dominant inheritance of KS, and we identified a novel heterozygous frameshift mutation c. 299_300insCCGCAGACTCCGGCCTCTATGC (p.C101Rfs*17) in FGFR1 gene using whole-exome sequencing (WES). The mutation and affection status were cosegregated. The mutation is not present in the dbSNP, 1000 Genome, ExAC, and gnomAD databases. The discovery of this new mutation in the FGFR1 gene enriches the spectrum of FGFR1 mutations in patients with KS. Abbreviations: FGFR1: fibroblast growth factor receptor 1; HH: hypogonadotropic hypogonadism; KS: Kallmann syndrome; MRI: magnetic resonance imaging; WES: whole–exome sequencing.
Forespore Targeting of SpoVD in Bacillus subtilis Is Mediated by the N-Terminal Part of the Protein

ABSTRACT SpoVD and PBP4b are structurally very similar high-molecular-weight, class B penicillin-binding proteins produced early during sporulation in Bacillus subtilis. SpoVD is known to be essential for endospore cortex synthesis and thereby the production of heat-resistant spores. The role of PBP4b is still enigmatic. Both proteins are synthesized in the cytoplasm of the mother cell. PBP4b remains in the cytoplasmic membrane of the mother cell, whereas SpoVD accumulates in the forespore outer membrane. By the use of SpoVD/PBP4b chimeras with swapped protein domains, we show that the N-terminal part of SpoVD, containing the single transmembrane region, determines the forespore targeting of the protein. IMPORTANCE Beta-lactam-type antibiotics target penicillin-binding proteins (PBPs), which function in cell wall peptidoglycan synthesis. Bacteria of a subset of genera, including Bacillus and Clostridium species, can form endospores. The extreme resistance of endospores against harsh physicochemical conditions is of concern in clinical microbiology and the food industry. Endospore cortex layer biogenesis constitutes an experimental model system for research on peptidoglycan synthesis. The differentiation of a vegetative bacterial cell into an endospore involves the formation of a forespore within the cytoplasm of the sporulating cell. A number of proteins, including some PBPs, accumulate in the forespore. An understanding of the molecular mechanisms behind such subcellular targeting of proteins in bacterial cells can, for example, lead to a means of blocking the process of sporulation.
DHA supplementation improved both memory and reaction time in healthy young adults: a randomized controlled trial.

BACKGROUND Docosahexaenoic acid (DHA) is important for brain function, and its status is dependent on dietary intakes. Therefore, individuals who consume diets low in omega-3 (n-3) polyunsaturated fatty acids may cognitively benefit from DHA supplementation. Sex and apolipoprotein E genotype (APOE) affect cognition and may modulate the response to DHA supplementation. OBJECTIVES We investigated whether a DHA supplement improves cognitive performance in healthy young adults and whether sex and APOE modulate the response. DESIGN Healthy adults (n = 176; age range: 18-45 y; nonsmoking and with a low intake of DHA) completed a 6-mo randomized, placebo-controlled, double-blind intervention in which they consumed 1.16 g DHA/d or a placebo. Cognitive performance was assessed by using a computerized cognitive test battery. For all tests, z scores were calculated and clustered into cognitive domains as follows: episodic and working memory, attention, reaction time (RT) of episodic and working memory, and attention and processing speed. ANCOVA was conducted with sex and APOE as independent variables. RESULTS RTs of episodic and working memory improved with DHA compared with placebo [mean difference (95% CI): -0.18 SD (-0.33, -0.03 SD) (P = 0.02) and -0.36 SD (-0.58, -0.14 SD) (P = 0.002), respectively]. Sex × treatment interactions occurred for episodic memory (P = 0.006) and the RT of working memory (P = 0.03). Compared with the placebo, DHA improved episodic memory in women [0.28 SD (0.08, 0.48 SD); P = 0.006] and RTs of working memory in men [-0.60 SD (-0.95, -0.25 SD); P = 0.001]. APOE did not affect cognitive function, but there were some indications of APOE × sex × treatment interactions. CONCLUSIONS DHA supplementation improved memory and the RT of memory in healthy, young adults whose habitual diets were low in DHA. The response was modulated by sex. This trial was registered at the New Zealand Clinical Trials Registry (http://www.anzctr.org.au/default.aspx) as ACTRN12610000212055.
Identifiability and self-presentation: computer-mediated communication and intergroup interaction.

This research investigated the intergroup properties of hostile 'flaming' behaviour in computer-mediated communication and how flaming language is affected by Internet identifiability, or identifiability by name and e-mail address/geographical location as is common to Internet communication. According to the Social Identity Model of Deindividuation Effects (SIDE; e.g. Reicher, Spears, & Postmes, 1995) there may be strategic reasons for identifiable groups members to act in a more group-normative manner in the presence of an audience, to gain acceptance from the in-group, to avoid punishment from the out-group, or to assert their identity to the out-group. For these reasons, it was predicted that communicators would produce more stereotype-consistent (group-normative) descriptions of out-group members' behaviours when their descriptions were identifiable to an audience. In one archival and three experimental studies, it was found that identifiability to an in-group audience was associated with higher levels of stereotype-consistent language when communicators described anonymous out-group targets. These results extend SIDE and suggest the importance of an in-group audience for the expression of stereotypical views.
Review in formulating the standard form of contract for Industrialized Building System (IBS) construction approach in Malaysia

Industrialised Building System (IBS) is the common term used to represent the prefabrication concept in Malaysia. Based on previous research being done locally and internationally, it is certain that using IBS offers huge benefits in terms of cost, time, productivity and quality. The Malaysian construction industry has been urged to use innovative construction techniques. It is being highlighted under the present Construction Industry Transformation Programme 2016 - 2020 (CITP). These initiatives illustrate the Malaysia government’s commitment in addressing the IBS agenda. Although some efforts have been taken to enhance the IBS adoption in Malaysia, various contract issues have emerged to become major concern amongst the IBS players that have led to delays, disputes, payment and cash flow issues in their projects. Formulating a dedicated standard form of contract for IBS construction approach is necessary to address the concerns. Therefore, the aim of the main research is to formulate the standard form of contract for IBS projects that will assist authorities and IBS industry players in mitigating the issues and challenges from the contractual perspectives. However, this paper will only present the literature reviews and findings from a preliminary survey conducted to establish pertinent contractual issues and challenges on the subject matter.
Effect of conjugated linoleic acid on body fat accretion in overweight or obese children.

BACKGROUND Conjugated linoleic acid (CLA) is a supplemental dietary fatty acid that decreases fat mass accretion in young animals. OBJECTIVE The aim of this study was to determine CLA's efficacy with regard to change in fat and body mass index (BMI; in kg/m(2)) in children. DESIGN We conducted a 7 +/- 0.5-mo randomized, double-blind, placebo-controlled trial of CLA in 62 prepubertal children aged 6-10 y who were overweight or obese but otherwise healthy. The subjects were randomly assigned to receive 3 g/d of 80% CLA (50:50 cis-9,trans-11 and trans-10,cis-12 isomers) or placebo in chocolate milk. RESULTS Fifty-three subjects completed the trial (n = 28 in the CLA group, n = 25 in the placebo group). CLA attenuated the increase in BMI (0.5 +/- 0.8) compared with placebo (1.1 +/- 1.1) (P = 0.05). The percentage change in body fat measured by dual-energy X-ray absorptiometry was smaller (P = 0.001) in the CLA group (-0.5 +/- 2.1%) than in the placebo group (1.3 +/- 1.8%). The change in abdominal body fat as a percentage of total body weight was smaller (P = 0.02) in the CLA group (-0.09 +/- 0.9%) than in the placebo group (0.43 +/- 0.6%). There were no significant changes in plasma glucose, insulin, or LDL cholesterol between groups. Plasma HDL cholesterol decreased significantly more (P = 0.05) in the CLA group (-5.1 +/- 7.3 mg/dL) than in the placebo group (-0.7 +/- 8 mg/dL). Bone mineral accretion was lower (P = 0.04) in the CLA group (0.05 +/- 0.03 kg) than in the placebo group (0.07 +/- 0.03 kg). Reported gastrointestinal symptoms did not differ significantly between groups. CONCLUSIONS CLA supplementation for 7 +/- 0.5 mo decreased body fatness in 6-10-y-old children who were overweight or obese but did not improve plasma lipids or glucose and decreased HDL more than in the placebo group. Long-term investigation of the safety and efficacy of CLA supplementation in children is recommended.
Current Signature and Vibration Analyses to Diagnose an In-Service Wind Turbine Drive Train

The goal of the present paper is to achieve the diagnosis of an in-service 1.5 MW wind turbine equipped with a doubly-fed induction generator through current signature and vibration analyses. Real data from operating machines have rarely been analysed in the scientific literature through current signature analysis supported by vibrations. The wind turbine under study was originally misdiagnosed by the operator, where a healthy component was replaced and the actual failure continued progressing. The chronological evolution of both the electrical current and vibration spectra is presented to conduct an in-depth tracking of the fault. The diagnosis is achieved through spectral analysis of the stator currents, where fault frequency components related to rotor mechanical unbalance are identified. This is confirmed by the vibration analysis, which provides insightful information on the health of the drive train. These results can be implemented in condition monitoring strategies, which is of great interest to optimise operation and maintenance costs of wind farms.
Organic cultivation of Ashwagandha with improved biomass and high content of active Withanolides: Use of Vermicompost

Withania somnifera (Ashwagandha) has recently been studied extensively for its health-supplementing and therapeutic activities against a variety of ailments. Several independent studies have experimentally demonstrated pharmaceutical potential of its active Withanolides, Withaferin A (Wi-A), Withanone (Wi-N) and Withanolide A (Wil-A). However, to promote its use in herbal industry, an environmentally sustainable cultivation and high yield are warranted. In modern agriculture strategies, there has been indiscriminate use of chemical fertilizers to boost the crop-yield, however the practice largely ignored its adverse effect on the quality of soil and the environment. In view of these, we attempted to recruit Vermicompost (Vcom, 20–100%) as an organic fertilizer of choice during the sowing and growing phases of Ashwagandha plants. We report that (i) pre-soaking of seeds for 12 h in Vermicompost leachate (Vcom-L) and Vermicompost tea (Vcom-T) led to higher germination, (ii) binary combination of pre-soaking of seeds and cultivation in Vcom (up to 80%) resulted in further improvement both in germination and seedling growth, (iii) cultivated plants in the presence of Vcom+Vcom-L showed higher leaf and root mass, earlier onset of flowering and fruiting and (iv) leaves from the Vcom+Vcom-L cultivated plants showed higher level of active Withanolides, Withanone (Wi-N), Withanolide A (Wil-A) and Withaferin A (Wi-A) and showed anticancer activities in cell culture assays. Taken together, we report a simple and inexpensive method for improving the yield and pharmaceutical components of Ashwagandha leaves.
Tunable optical coherence tomography in the infrared range using visible photons

Optical coherence tomography (OCT) is an appealing technique for bio-imaging, medicine, and material analysis. For many applications, OCT in mid- and far-infrared (IR) leads to significantly more accurate results. Reported mid-IR OCT systems require light sources and photodetectors which operate in mid-IR range. These devices are expensive and need cryogenic cooling. Here, we report a proof-of-concept demonstration of a wavelength tunable IR OCT technique with detection of only visible range photons. Our method is based on the nonlinear interference of frequency correlated photon pairs. The nonlinear crystal, introduced in the Michelson-type interferometer, generates photon pairs with one photon in the visible and another in the IR range. The intensity of detected visible photons depends on the phase and loss of IR photons, which interact with the sample under study. This enables us to characterize sample properties and perform imaging in the IR range by detecting visible photons. The technique possesses broad wavelength tunability and yields a fair axial and lateral resolution, which can be tailored to the specific application. The work contributes to the development of versatile 3D imaging and material characterization systems working in a broad range of IR wavelengths, which do not require the use of IR-range light sources and photodetectors.
Connecting the dots: linking nitrogen cycle gene expression to nitrogen fluxes in marine sediment mesocosms

Connecting molecular information directly to microbial transformation rates remains a challenge, despite the availability of molecular methods to investigate microbial biogeochemistry. By combining information on gene abundance and expression for key genes with quantitative modeling of nitrogen fluxes, we can begin to understand the scales on which genetic signals vary and how they relate to key functions. We used quantitative PCR of DNA and cDNA, along with biogeochemical modeling to assess how the abundance and expression of microbes responsible for two steps in the nitrogen cycle changed over time in estuarine sediment mesocosms. Sediments and water were collected from coastal Massachusetts and maintained in replicated 20 L mesocosms for 45 days. Concentrations of all major inorganic nitrogen species were measured daily and used to derive rates of nitrification and denitrification from a Monte Carlo-based non-negative least-squares analysis of finite difference equations. The mesocosms followed a classic regeneration sequence in which ammonium released from the decomposition of organic matter was subsequently oxidized to nitrite and then further to nitrate, some portion of which was ultimately denitrified. Normalized abundances of ammonia oxidizing archaeal ammonia monoxoygenase (amoA) transcripts closely tracked rates of ammonia oxidation throughout the experiment. No such relationship, however, was evident between denitrification rates and the normalized abundance of nitrite reductase (nirS and nirK) transcripts. These findings underscore the complexity of directly linking the structure of the microbial community to rates of biogeochemical processes.
Identification of nocturnal movements during sleep using the non-contact under mattress bed sensor

This paper describes the calculation of statistical, spatial and spatiotemporal features from a novel non-contact technology for sleep monitoring, the Under Mattress Bed Sensor (UMBS). Data was collected from two relatively healthy adults with a possible sleep disorder in a clinical setting. Methods for the extraction of statistical data describing overall bed restlessness, a spatial description of movement (centre and spread of pressure) and a spatiotemporal description of each in-bed body movement over the entire sleeping episode are discussed using the pressure sensing grid. These provide a quantitative description of sleep and restlessness throughout the night.
Thermalization near Integrability in a Dipolar Quantum Newton's Cradle

Isolated quantum many-body systems with integrable dynamics generically do not thermalize when taken far from equilibrium. As one perturbs such systems away from the integrable point, thermalization sets in, but the nature of the crossover from integrable to thermalizing behavior is an unresolved and actively discussed question. We explore this question by studying the dynamics of the momentum distribution function in a dipolar quantum Newton's cradle consisting of highly magnetic dysprosium atoms. This is accomplished by creating the first one-dimensional Bose gas with strong magnetic dipole-dipole interactions. These interactions provide tunability of both the strength of the integrability-breaking perturbation and the nature of the near-integrable dynamics. We provide the first experimental evidence that thermalization close to a strongly interacting integrable point occurs in two steps: prethermalization followed by near-exponential thermalization. Exact numerical calculations on a two-rung lattice model yield a similar two-timescale process, suggesting that this is generic in strongly interacting near-integrable models. Moreover, the measured thermalization rate is consistent with a parameter-free theoretical estimate, based on identifying the types of collisions that dominate thermalization. By providing tunability between regimes of integrable and nonintegrable dynamics, our work sheds light both on the mechanisms by which isolated quantum many-body systems thermalize, and on the temporal structure of the onset of thermalization.
Accelerated discovery of metallic glasses through iteration of machine learning and high-throughput experiments

Coupling artificial intelligence with high-throughput experimentation accelerates discovery of amorphous alloys. With more than a hundred elements in the periodic table, a large number of potential new materials exist to address the technological and societal challenges we face today; however, without some guidance, searching through this vast combinatorial space is frustratingly slow and expensive, especially for materials strongly influenced by processing. We train a machine learning (ML) model on previously reported observations, parameters from physiochemical theories, and make it synthesis method–dependent to guide high-throughput (HiTp) experiments to find a new system of metallic glasses in the Co-V-Zr ternary. Experimental observations are in good agreement with the predictions of the model, but there are quantitative discrepancies in the precise compositions predicted. We use these discrepancies to retrain the ML model. The refined model has significantly improved accuracy not only for the Co-V-Zr system but also across all other available validation data. We then use the refined model to guide the discovery of metallic glasses in two additional previously unreported ternaries. Although our approach of iterative use of ML and HiTp experiments has guided us to rapid discovery of three new glass-forming systems, it has also provided us with a quantitatively accurate, synthesis method–sensitive predictor for metallic glasses that improves performance with use and thus promises to greatly accelerate discovery of many new metallic glasses. We believe that this discovery paradigm is applicable to a wider range of materials and should prove equally powerful for other materials and properties that are synthesis path–dependent and that current physiochemical theories find challenging to predict.
Attitudes towards the Use of Violence against Police among Occupy Wall Street Protesters

Although many social movement participants claim to embrace non-violent civil disobedience strategies, protesters tend to have heterogeneous views on the morality and utility of engaging in violence. In particular, protesters sometimes view violence against the police as warranted, especially if they perceive that police have treated them or their peers in a procedurally unjust or excessively forceful manner. This article examines the nature and correlates of attitudes towards the use of violence against police officers among Occupy Wall Street (OWS) protesters in New York City. Data were drawn from in-person surveys of 302 OWS participants on the 6-month anniversary of the movement in March 2012. Our findings reveal that in this context, respondents who perceive that police use unjust force against protesters are significantly more likely to endorse the use of violence against police.