Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterizing Escherichia coli’s transcriptional response to different styrene exposure modes reveals novel toxicity and tolerance insights

Abstract The global transcriptional response of Escherichia coli to styrene and potential influence of exposure source was determined by performing RNA sequencing (RNA-seq) analysis on both styrene-producing and styrene-exposed cells. In both cases, styrene exposure appears to cause both cell envelope and DNA damage, to which cells respond by down-regulating key genes/pathways involved in DNA replication, protein production, and cell wall biogenesis. Among the most significantly up-regulated genes were those involved with phage shock protein response (e.g. pspABCDE/G), general stress regulators (e.g. marA, rpoH), and membrane-altering genes (notably, bhsA, ompR, ldtC), whereas efflux transporters were, surprisingly, unaffected. Subsequent studies with styrene addition demonstrate how strains lacking ompR [involved in controlling outer membrane (OM) composition/osmoregulation] or any of tolQ, tolA, or tolR (involved in OM constriction) each displayed over 40% reduced growth relative to wild-type. Conversely, despite reducing basal fitness, overexpression of plsX (involved in phospholipid biosynthesis) led to 70% greater growth when styrene exposed. These collective differences point to the likely importance of OM properties in controlling native styrene tolerance. Overall, the collective behaviours suggest that, regardless of source, prolonged exposure to inhibitory styrene levels causes cells to shift from‘growth mode’ to ‘survival mode’, redistributing cellular resources to fuel native tolerance mechanisms.
White Matter Connectivity in Incident Mild Cognitive Impairment: A Diffusion Spectrum Imaging Study of World Trade Center Responders at Midlife

Background: Individuals who participated in response efforts at the World Trade Center (WTC) following 9/11/2001 are experiencing elevated incidence of mild cognitive impairment (MCI) at midlife. Objective: We hypothesized that white matter connectivity measured using diffusion spectrum imaging (DSI) would be restructured in WTC responders with MCI versus cognitively unimpaired responders. Methods: Twenty responders (mean age 56; 10 MCI/10 unimpaired) recruited from an epidemiological study were characterized using NIA-AA criteria alongside controls matched on demographics (age/sex/occupation/race/education). Axial DSI was acquired on a 3T Siemen’s Biograph mMR scanner (12-channel head coil) using a multi-band diffusion sequence. Connectometry examined whole-brain tract-level differences in white matter integrity. Fractional anisotropy (FA), mean diffusivity (MD), and quantified anisotropy were extracted for region of interest (ROI) analyses using the Desikan-Killiany atlas. Results: Connectometry identified both increased and decreased connectivity within regions of the brains of responders with MCI identified in the corticothalamic pathway and cortico-striatal pathway that survived adjustment for multiple comparisons. MCI was also associated with higher FA values in five ROIs including in the rostral anterior cingulate; lower MD values in four ROIs including the left rostral anterior cingulate; and higher MD values in the right inferior circular insula. Analyses by cognitive domain revealed nominal associations in domains of response speed, verbal learning, verbal retention, and visuospatial learning. Conclusions: WTC responders with MCI at midlife showed early signs of neurodegeneration characterized by both increased and decreased white matter diffusivity in regions commonly affected by early-onset Alzheimer’s disease.
Analysis of the transcriptomic, metabolomic, and gene regulatory responses to Puccinia sorghi in maize

Abstract Common rust, caused by Puccinia sorghi, is a widespread and destructive disease of maize. The Rp1‐D gene confers resistance to the P. sorghi IN2 isolate, mediating a hypersensitive cell death response (HR). To identify differentially expressed genes (DEGs) and metabolites associated with the compatible (susceptible) interaction and with Rp1‐D‐mediated resistance in maize, we performed transcriptomics and targeted metabolome analyses of P. sorghi IN2‐infected leaves from the near‐isogenic lines H95 and H95:Rp1‐D, which differed for the presence of Rp1‐D. We observed up‐regulation of genes involved in the defence response and secondary metabolism, including the phenylpropanoid, flavonoid, and terpenoid pathways. Metabolome analyses confirmed that intermediates from several transcriptionally up‐regulated pathways accumulated during the defence response. We identified a common response in H95:Rp1‐D and H95 with an additional H95:Rp1‐D‐specific resistance response observed at early time points at both transcriptional and metabolic levels. To better understand the mechanisms underlying Rp1‐D‐mediated resistance, we inferred gene regulatory networks occurring in response to P. sorghi infection. A number of transcription factors including WRKY53, BHLH124, NKD1, BZIP84, and MYB100 were identified as potentially important signalling hubs in the resistance‐specific response. Overall, this study provides a novel and multifaceted understanding of the maize susceptible and resistance‐specific responses to P. sorghi.
Multiphoton dissociation of a diatomic molecule: Laser intensity, frequency, and pulse shape dependence of the fragment momentum distribution

We study by an exact method the infrared multiphoton dissociation of a rotationless diatomic molecule and calculate the fragment relative momentum distribution as a function of the laser intensity and frequency, using either a square or smoothly varying pulse shape. The distribution has peaks due to multiphoton transitions. The nature of the peak structure depends on the laser intensity and whether the laser frequency is comparable to (i.e., within 20%) the ν=0 to ν=1 transition frequency (ω10) of the diatomic: If it is the distribution has bands spaced by the photon energy which contain peaks due to transitions from many bound states; if the laser frequency is not comparable to ω10, the distribution consists of isolated peaks spaced by the photon energy, which result from multiphoton transitions from the ground vibrational state. Changing the pulse shape from smoothly varying to square adds additional structure to the distributions. At sufficiently high intensities (1015 W/cm2) the high momentum peaks in.
Aerobic Exercise Mediates Neural Inefficiency Among Adolescents At Risk for Suicide

This study examined the electroencephalograpy (EEG) coherence and working memory performance effects of a 9-week exercise program on a small group of adolescents at high suicide risk. We randomly assigned 26 adolescents at high suicide risk (based on their scores on the Adolescents Mental Health Inventory- AMHI) into equal sized exercise and no-exercise groups. Before and after the 9-week exercise program, all participants performed the Sternberg working memory task, during which we recorded their EEGs, with electrodes placed at F3, F4, C3, C4, P3, P4, T3, T4, O1, and O2 regions (using the International 10-20 system of EEG electrode placement). We measured working memory performance and inter-hemispheric (F3-F4, C3-C4, T3-T4, P3-P4, O1-O2) and intra-hemispheric (F3-C3, F3-T3, F3-P3, F3-O1, F4-C4, F4-T4, F4-P4, F4-O2) EEG coherence as an index of the participants’ underlying neural efficiency. While we found no significant group differences in working memory performances, the exercise group, relative to the no-exercise group, exhibited lower inter- and intra-hemispheric EEG coherence while performing the working memory task. These EEG differences may reflect a mediating effect of aerobic exercise on these participants’ neural efficiency.
Production and fragmentation of molybdenum oxide ions

The production and fragmentation of molybdenum oxide cluster ions MoxO+/−y have been studied by Fourier transform mass spectrometry. The cluster ions were generated by direct laser vaporization (DLV) and fast‐atom bombardment (FAB) of molybdenum trioxide and molybdenum dioxide. The ionization method has a dramatic effect on ion formation with DLV producing primarily MoxO+y with high oxygen‐to‐metal ratios, while FAB yields Mo+x and MoxO+y with low oxygen‐to‐metal ratios. Direct emission appears to be an important mechanism in laser vaporization of molybdenum oxides, while the FAB results are consistent with ion formation by recombination reactions. For molybdenum dioxide, a comparison is made between DLV with pulsed CO2 and Nd:YAG lasers. The spectra obtained are similar; however, differences in (MoO3)+n, n=1–3, production with the two lasers may be related to sample absorption at the CO2 wavelength of 10.6 μm. The low‐energy collision‐induced dissociation of MoxO+y is dominated by loss of (MoO3)n. In add.
Mask blast with a new chemical logic of amino acids for improved protein function prediction

With the exponential increase in protein sequence data, there is an urgency to acquire a knowledge of function of the millions of sequences, using automated methods with high reliability. Conventional methods for annotating a protein sequence transfer the function of a homologous sequence with known functions based on evolutionary information. Here, we present a newer way of classifying amino acids based on chemical measures and demonstrate that, when integrated with mask BLAST, the chemical properties identified outperform current classifications of amino acids as well as evolutionary measures in function detection.
Fiber ringdown breathing rate sensor

We describe a new sensor for patient's breathing measurement by using fiber loop ringdown spectroscopy. The sensing system consists of a typical single mode fiber-loop ring-down spectroscopy and a sensor mat which is used to introduce breathing related optical loss. The sensor mat could be put in the chair or embedded in the bed. It is non invasive measurement. The breathing rate sensor is demonstrated with an accuracy of +/-2 breaths per minute and stable sensor output.
Controlling Nonviral Gene Delivery through the Cell-Biomaterial Interface

Cell-biomaterial interactions and the corresponding cellular behaviors are poorly understood. Therefore, in this study, the ability of biomaterial surface properties to control nonviral gene delivery was investigated through surface chemistry and protein adsorption and subsequently correlated to cellular behaviors controlled by cell-biomaterial interactions. Self-assembled monolayers (SAMs) of alkanethiols on gold were used as model biomaterials to investigate the effect of surface properties on nonviral gene transfer to cells adhered to these surfaces. SAMs presenting terminal CH3, OH, COO , and NH3 + functionalities were adsorbed with varying concentrations of FN to determine the amount of FN needed to form an adsorbed monolayer on the surface of SAMs, onto which cells were then seeded and plasmid DNA was delivered via a bolus approach using polymerand lipid-mediated delivery techniques. SAMs without adsorbed FN were used as a comparison, in addition to traditional polystyrene (PS) culture surfaces. SAMs with different surface chemistries that were adsorbed with FN influenced transfection profiles. Additional preliminary studies explored the use of adsorbed bovine serum albumin (BSA) as a blocking agent to fill in open spaces between the adsorbed
Generalized Chernoff Sampling for Active Testing, Active Regression and Structured Bandit Algorithms

Active learning and structured stochastic bandit problems are intimately related to the classical problem of sequential experimental design. This paper studies active learning and best-arm iden-tiﬁcation in structured bandit settings from the viewpoint of active sequential hypothesis testing, a framework initiated by Chernoff (1959). We obtain a novel sample complexity bound for Cher-noff’s original active testing procedure by uncovering non-asymptotic terms that reduce in significance as the allowed error probability δ → 0 . Initially proposed for testing among ﬁnitely many hypotheses, we obtain the analogue of Chernoff sampling for the case when the hypotheses belong to a compact space. This allows us to directly apply it to active learning and structured bandit problems, where the unknown parameter specifying the arm means is often assumed to be an element of Euclidean space. Empirically, we demonstrate the potential of our proposed approach for active learning of neural network models and in linear and non-linear bandit settings, where we observe that our general-purpose approach compares favorably to state-of-the-art methods.
The Sex in Your Violence

In its broadest conceptualization, violence includes everything from physical assault to the creation and maintenance of institutional structures that are discriminatory and exclusionary. However, violence as a topic of biological and archaeological anthropological inquiry has often been limited to malevolent physical assault perpetrated by men against other men. This is due to an outsized focus on the role that men played in the evolutionary history of our species. This conceptualization of violence obscures both the ways that other forms of harm—other violence(s) also often committed by men—structure the daily lives of people who do not have significant social or institutional power and how this harm becomes embodied. In this paper I explore how gendered knowledge production in anthropology has influenced our acceptance of what counts as meaningful harm. I posit that the threat of physical violence and encounters with other violence(s), specifically emotional and structural violence, shape the lives of people who are structurally disadvantaged in ways that are missing from our analyses. When we forgo emphases on war and murder and choose to study other violence(s) that are enacted in families and relationships, we become aware of the kinds of hidden assaults that are often meted out in small doses, eventually accumulating and impacting individual mental and physical health and survivorship.
Quadrotor Attitude Dynamics Identification Based on Nonlinear Autoregressive Neural Network with Exogenous Inputs

ABSTRACT In the case of quadrotors, system identification is a challenging task because quadrotors are inherently unstable exhibit nonlinear behavior and significant coupling. In addition to this, quadrotors’ behavior is greatly influenced by characteristics and coefficients, which are very hard to measure directly or determine analytically. However, all the difficulties listed above are known to be successfully overcome by the use of artificial intelligence. In this paper, two system identification techniques were applied and compared to model quadrotor attitude dynamics. These techniques are Nonlinear Autoregressive Network with Exogenous Inputs (NARX) and continuous-time transfer function.
Preparations of Optically Active Homocysteine and Homocystine by Asymmetric Transformation of (RS)-1,3-Thiazane-4-carboxylic Acid

DL-Homocysteine [DL-Hcy] from (RS)-homocysteine thiolactone hydrochloride [(RS)-HTL·HCl] was subjected to reaction with formaldehyde in acetic acid to give (RS)-1,3-thiazane-4-carboxylic acid monohydrate [(RS)-THA·H2O]. An asymmetric transformation of (RS)-THA·H2O was achieved via salt formation with optically active tartaric acid in the presence of salicylaldehyde in acetic acid. The (R)- and (S)-THA obtained, respectively, from the salt of (R)-THA with (2R, 3R)-tartaric acid and its enantiomeric salt were treated with hydroxylamine hydrochloride to give D- and L-Hcy of 100% optical purity, respectively, in 50% yield from (RS)-HTL·HCl. Oxidation of D- and L-Hcy with hydrogen peroxide gave D- and L-homocystine, respectively, in 47% yield.
Morphological change of solid ammonium sulfate particles below the deliquescence relative humidity: Experimental reproduction of atmospheric sulfate particle shapes

Abstract Atmospheric aerosols containing ammonium sulfate have several morphological types in the solid phase. Laboratory experiments were used to reproduce the particle shapes commonly found in atmospheric samples to elucidate factors affecting these different particle shapes. Ammonium sulfate particles and mixed particles with oxalate were prepared under different relative humidity (RH) conditions and were observed using transmission electron microscopy (TEM). Most ammonium sulfate particles dried using a diffusion dryer after generation from aqueous solution were spherical or clusters of spherical units. However, after exposure of the TEM samples to 59% RH and 75% RH at atmospheric pressure, some particles changed to a rotundate-rectangular shape with parallel straight lines as the particle perimeter. Number fractions of particles that had changed to rotundate-rectangular shape from a spherical shape at 59% RH and 75% RH were, respectively, 6% and 52% at 3 h, and 18% and 66% at 1 day. Morphological changes during the experiment suggest that ammonium sulfate crystallization occurred under metastable RH. Morphological changes to rotundate-rectangular shapes were also found for ammonium sulfate co-existing with oxalate. These results indicate that spherical or complexly shaped sulfate-containing aerosols can change gradually to shapes having more regular structures according to a particle’s experienced RH condition. Both spherical and rotundate-rectangular shapes of sulfate particles have often been found in atmospheric aerosol samples. The morphological change of ammonium sulfate found in this study will be useful to infer the optical properties of atmospheric particles and the thermodynamic process on a solid particle surface.
SMEs' heterogeneity at the extensive margin and within the intensive margin of trade

ABSTRACT In this paper, we contribute to the literature on firm-heterogeneity and trade, by looking not only at the firm-level determinants of trade participation (i.e. extensive margin) but also at differences between firms with different levels of trade intensity (i.e. intensive margin). Further, we compare firms that are born ‘local’ and display different scales of international exposure to firms that are born ‘global’, i.e. access international markets soon after their birth. Using a large World Bank dataset of SMEs from 112 countries and qualitative dependent variable models, our analysis uncovers the heterogeneity of SMEs not only at the extensive margin but also within the intensive margin of trade. Born local and born global firms present different characteristics.
One step mechanosynthesis of graphene oxide directly from graphite

Abstract A fast method for the synthesis of graphene oxide directly from a graphitic material via a one-step mechanochemical process without adding solvent, acid or oxidizing agents, is presented. Chemical, structural and morphological characterization of such material was carried on by Raman, FT-IR and UV/vis spectroscopies, Atomic Force Microscopy, X-ray Diffraction, Scanning Electron Microscopy and Energy-Dispersive X-ray Spectroscopy. Functional groups present in the material are similar to those of materials produced via methods related to that of Hummers or by mechanical milling. Although its interlayer spacing is lower than in the former, it allowed its exfoliation via sonication. Oxygen content of up to 11.1% is comparable to what is reported for materials synthesized by mechanical milling, nevertheless, this process was carried on in less time and without using added oxidizing agents or inert atmospheres. This oxidation is achieved decreasing rotational speed (1060 rpm) but increasing the degrees of freedom (5) of milling jars. When comparing against past reports, it is evident that degrees of freedom affects reaction times more than rotational speed.
Leveraging 3D Printing Technologies: The Case of Mexico’s Footwear Industry

Overview: Traditional manufacturing techniques, new trends in global consumer behavior, and agile competition necessitate change in the fashion footwear industry, one of the world’s oldest and most prestigious sectors. 3D printing may be precisely what the fashion footwear industry needs. By 2029, 3D printing in the fashion footwear industry is forecast to grow into a USD $6 billion revenue opportunity globally. We applied a mixed-method approach to study the adoption of 3D printing in Mexico’s prominent footwear cluster, which comprises all manufacturers, suppliers, and associated industry contributors in the Guanajuato region. We discuss the state of the art of 3D printing and share local adoption behavior and global best practices. Our findings offer a guide on how companies in the footwear industry—and other traditional industries—can leverage 3D printing.
Spatial Distribution and Epidemiological Characteristics of Foodborne Disease in Zhejiang Province, China

Foodborne Disease (FBD) is the most common disease around the world. Based on the surveillance data of FBD in Zhejiang Province from Jan 1, 2013 to Dec 31, 2015, including 26721 illness cases, 1591 hospitalizations and 6 deaths. We conducted exploratory data analysis to evaluate eidemiological characteristics. The spatial autocorrelation analysis was performed to detect the clusters at county level. The results show that the high peaks usually occurred in summer and autumn, and high-high pattern areas were mainly concentrated in the southwest counties. Most likely clusters were mainly located in the northern counties over the period from May to October, which deserved public's attention. Incidence rates of illness and hospitalization for males were higher than females. People in 18-35 group were suspected to FBD and the elderly over 60 had a highest hospitalized percentage. Peasants and children accounted for about 40% of illness cases, and over 50% of hospitalized cases were peasants (especially in spring and winter). Norovirus was the major cause in spring and winter, while Vibrio parahaemolyticus and Salmonella were the top two pathogens in summer and autumn.
Trust and Distrust based Cross-domain Recommender System

ABSTRACT A recommender system (RS) provides assistance for users to filter out items of their interest in the presence of millions of available items. The reason is to find out the likewise user with the assumption that if users have shared similar interest in the past then they may share the same in future. Collaborative filtering (CF) is the widely used recommendation algorithm due to its ease of use but suffers with the problems of sparsity and cold start problem. In this paper, we propose a trust and distrust-based cross domain context aware recommender system in the multi-agent environment which tries to reduce the problem of data sparsity in collaborative-filtering recommender system and improves coverage. Cross Domain Recommender System (CDRS) utilizes data from multiple domains to reduce the problem of sparsity. Moreover, the combination of trust and distrust in recommendation help to improve trustworthiness of generated recommendation. Distrust provides higher accuracy in recommendation by incorporating knowledge about the malicious users. Prototype of the system is developed using JADE and Java technology for the tourism domain consisting of restaurant, hotel, travel places and shopping places as sub-domains. The performance of the proposed trust and distrust-based cross domain recommender system is compared with the traditional approach of recommendation along with the cross domain approach and trust-based cross-domain approach in terms of accuracy and coverage. The results show that the proposed system outperforms in terms of both accuracy and coverage.