Miracle-dz/UniFAR-FTUs huggingface dataset:
Deciphering the Resistome of the Widespread Pseudomonas aeruginosa Sequence Type 175 International High-Risk Clone through Whole-Genome Sequencing

ABSTRACT Whole-genome sequencing (WGS) was used for the characterization of the frequently extensively drug resistant (XDR) Pseudomonas aeruginosa sequence type 175 (ST175) high-risk clone. A total of 18 ST175 isolates recovered from 8 different Spanish hospitals were analyzed; 4 isolates from 4 different French hospitals were included for comparison. The typical resistance profile of ST175 included penicillins, cephalosporins, monobactams, carbapenems, aminoglycosides, and fluoroquinolones. In the phylogenetic analysis, the four French isolates clustered together with two isolates from one of the Spanish regions. Sequence variation was analyzed for 146 chromosomal genes related to antimicrobial resistance, and horizontally acquired genes were explored using online databases. The resistome of ST175 was determined mainly by mutational events; resistance traits common to all or nearly all of the strains included specific ampR mutations leading to ampC overexpression, specific mutations in oprD conferring carbapenem resistance, or a mexZ mutation leading to MexXY overexpression. All isolates additionally harbored an aadB gene conferring gentamicin and tobramycin resistance. Several other resistance traits were specific to certain geographic areas, such as a streptomycin resistance gene, aadA13, detected in all four isolates from France and in the two isolates from the Cantabria region and a glpT mutation conferring fosfomycin resistance, detected in all but these six isolates. Finally, several unique resistance mutations were detected in single isolates; particularly interesting were those in genes encoding penicillin-binding proteins (PBP1A, PBP3, and PBP4). Thus, these results provide information valuable for understanding the genetic basis of resistance and the dynamics of the dissemination and evolution of high-risk clones.
Antibiofilm Activities of a Novel Chimeolysin against Streptococcus mutans under Physiological and Cariogenic Conditions

ABSTRACT Streptococcus mutans often survives as a biofilm on the tooth surface and contributes to the development of dental caries. We investigated the efficacy of ClyR, an engineered chimeolysin, against S. mutans biofilms under physiological and cariogenic conditions. Susceptibility tests showed that ClyR was active against all clinical S. mutans isolates tested as well as S. mutans biofilms that displayed resistance to penicillin. The S. mutans biofilms that formed on hydroxyapatite discs under physiological sugar conditions and cariogenic conditions were reduced ∼2 logs and 3 logs after treatment with 100 μg/ml ClyR, respectively. In comparison, only a 1-log reduction was observed in the chlorhexidine gluconate (ChX)-treated group, and no killing effect was observed in the NaF-treated group. A mouse dental colonization model showed that repeated use of ClyR for 3 weeks (5 μg/day) reduced the number of colonized S. mutans cells in the dental plaques significantly (P < 0.05) and had no harmful effects on the mice. Furthermore, toxicity was not noted at concentrations exceeding those used for the in vitro and in vivo studies, and ClyR-specific antibodies could not be detected in mouse saliva after repeated use of ClyR in the oral cavity. Our data collectively demonstrate that ClyR is active against S. mutans biofilms both in vitro and in vivo, thus representing a preventative or therapeutic agent for use against dental caries.
Systematic analysis of a wasp parasitism arsenal

Parasitoid wasps are among the most diverse insects on earth with many species causing major mortality in host populations. Parasitoids introduce a variety of factors into hosts to promote parasitism, including symbiotic viruses, venom, teratocytes and wasp larvae. Polydnavirus‐carrying wasps use viruses to globally suppress host immunity and prevent rejection of developing parasites. Although prior results provide detailed insights into the genes viruses deliver to hosts, little is known about other products. RNAseq and proteomics were used to characterize the proteins secreted by venom glands, teratocytes and larvae from Microplitis demolitor, which carries M. demolitor bracovirus (MdBV). These data revealed that venom glands and teratocytes secrete large amounts of a small number of products relative to ovaries and larvae. Venom and teratocyte products exhibited almost no overlap with one another or MdBV genes, which suggested that M. demolitor effector molecules are functionally partitioned according to their source. This finding was well illustrated in the case of MdBV and teratocytes. Many viral proteins have immunosuppressive functions that include disruption of antimicrobial peptide production, yet this study showed that teratocytes express high levels of the antimicrobial peptide hymenoptaecin, which likely compensates for MdBV‐mediated immunosuppression. A second key finding was the prevalence of duplications among genes encoding venom and teratocyte molecules. Several of these gene families share similarities with proteins from other species, while also showing specificity of expression in venom glands or teratocytes. Overall, these results provide the first comprehensive analysis of the proteins a polydnavirus‐carrying wasp introduces into its host.
Terminal decline of episodic memory and perceptual speed in a biracial population

ABSTRACT We compared trajectories of terminal cognitive decline in older Black (n = 3372) and White (n = 1756) persons from a defined population who completed tests of episodic memory and perceptual speed at 3-year intervals for up to 18 years. During a mean of 9.9 years of observation, 1608 Black persons and 902 White persons died. Preterminal decline of episodic memory did not differ by race. Terminal episodic memory decline began earlier in Black persons (mean of 4.3 years before death) than in White persons (mean = 3.9 years) and progressed more slowly. By contrast, terminal decline of perceptual speed began earlier in White persons (mean = 5.0 years) than in Black persons (mean = 4.5 years). Rate of perceptual speed decline was more rapid in White persons than in Black persons in both the preterminal and terminal periods. The results indicate that terminal cognitive decline occurs in Black persons but suggest that the rate of cognitive decline during the terminal period is less rapid in Black persons than in White persons.
Emerging Adulthood, Emergent Health Lifestyles: Sociodemographic Determinants of Trajectories of Smoking, Binge Drinking, Obesity, and Sedentary Behavior

During the transition to adulthood, many unhealthy behaviors are developed that in turn shape behaviors, health, and mortality in later life. However, research on unhealthy behaviors and risky transitions has mostly focused on one health problem at a time. In this article, we examine variation in health behavior trajectories, how trajectories cluster together, and how the likelihood of experiencing different behavior trajectories varies by sociodemographic characteristics. We use the National Longitudinal Study of Adolescent Health (Add Health) Waves I to IV to chart the most common health behavior trajectories over the transition to adulthood for cigarette smoking, alcohol consumption, obesity, and sedentary behavior. We find that health behavior trajectories cluster together in seven joint classes and that sociodemographic factors (including gender, parental education, and race-ethnicity) significantly predict membership in these joint trajectories.
Android Malware Detection Using Complex-Flows

This paper proposes a new technique to detect mobile malware based on information flow analysis. Our approach examines the structure of information flows to identify patterns of behavior present in them and which flows are related, those that share partial computation paths. We call such flows Complex-Flows, as their structure, patterns, and relations accurately capture the complex behavior exhibited by both recent malware and benign applications. N-gram analysis is used to identify unique and common behavioral patterns present in Complex-Flows. The N-gram analysis is performed on sequences of API calls that occur along Complex-Flows' control flow paths. We show the precision of our technique by applying it to different data sets totaling 7,798 apps. These data sets consist of both recent and older generation benign and malicious apps to demonstrate the effectiveness of our approach across different generations of apps.
Adaptive compression therapy for venous leg ulcers: a clinically effective, patient‐centred approach

A prospective, randomised, 12‐week study was performed to evaluate the efficacy and tolerability of two compression methods for venous leg ulcers (VLUs); a new adaptive compression therapy (ACT) system, combining intermittent and sustained pneumatic compression (n = 38) and a conventional four‐layer bandage system (n = 52). Primary outcomes were ulcer healing and safety. Secondary outcomes were comfort, compliance, ulcer pain, patient‐perceived product performance and quality of life. Ulcer healing rate was similar (31·6% versus 42·3%, respectively, P = 0·30) between the treatments. Adverse events and patient‐rated comfort were also similar. Average daily usage for the dual system was 10·5 and 1·8 hours in the sustained and intermittent modes, respectively, representing its use during 71% of waking hours. Predicted final ulcer pain was also similar (P = 0·68). Performance was subjectively better for adaptive compression and significantly higher for exudate management (P = 0·04), skin protection (P < 0·001), removal ease (P = 0·0007), bathing (P < 0·0001) and sleep comfort (P = 0·0405). The adjusted final quality‐of‐life score was 0·1025 higher for adaptive compression (P = 0·0375). Subjects with healed ulcers attained higher final scores than unhealed subjects (P = 0·0004). This study provides evidence that ACT is comparably efficacious to successfully heal VLUs compared with four‐layer bandage management but is better accepted and achieves higher patient‐reported quality‐of‐life scores in these challenging patients.
Symptoms Suggestive of Acute Coronary Syndrome: When Is Sex Important?

Background: Studies have identified sex differences in symptoms of acute coronary syndrome (ACS); however, retrospective designs, abstraction of symptoms from medical records, and variations in assessment forms make it difficult to determine the clinical significance of sex differences. Objective: The aim of this study is to determine the influence of sex on the occurrence and distress of 13 symptoms for patients presenting to the emergency department for symptoms suggestive of ACS. Methods: A total of 1064 patients admitted to 5 emergency departments with symptoms triggering a cardiac evaluation were enrolled. Demographic and clinical variables, symptoms, comorbid conditions, and functional status were measured. Results: The sample was predominantly male (n = 664, 62.4%), white (n = 739, 69.5%), and married (n = 497, 46.9%). Women were significantly older than men (61.3 ± 14.6 vs 59.5 ± 13.6 years). Most patients were discharged with a non-ACS diagnosis (n = 590, 55.5%). Women with ACS were less likely to report chest pain as their chief complaint and to report more nausea (odds ratio [OR], 1.56; confidence interval [CI], 1.00–2.42), shoulder pain (OR, 1.76; CI, 1.13–2.73), and upper back pain (OR, 2.92; CI, 1.81–4.70). Women with ACS experienced more symptoms (6.1 vs 5.5; P = .026) compared with men. Men without ACS had less symptom distress compared with women. Conclusions: Women and men evaluated for ACS reported similar rates of chest pain but differed on other classic symptoms. These findings suggest that women and men should be counseled that ACS is not always accompanied by chest pain and multiple symptoms may occur simultaneously.
Heat resistance of radiation crosslinked poly(ε-caprolactone)

Polycaprolactone (PCL) was gamma-irradiated at different phases such as solid state at 30 to 55°C, molten state, and supercooled state, under vacuum or air atmosphere, to elucidate its crosslinking behavior. Irradiation in the molten state (80°C) gave higher gel content compared to room temperature. The resulting gel, however, contains many voids due to the gas evolved during irradiation. Conversely, irradiation of PCL in the supercooled state led to the highest gel content among the three irradiation conditions and it was free of voids. Based on these findings, to evaluate heat resistibility of crosslinked PCL prepared by irradiation in supercooled state, the crosslinked PCL was hot pressed at 200°C to form a film. Unirradiated PCL melted at 60°C. The film prepared from 160 kGy irradiated PCL (crosslinked sample) under an applied load of 0.667 MPa, at a temperature of 110°C did not break even after 3 h. At a temperature of 120°C, the film has a tensile strength of 3 MPa. Furthermore, the film extended by hot pressing is transparent and has high heat shrinkability. © 1998 John Wiley & Sons, Inc. J Appl Polym Sci 68: 581–588, 1998
Toxicity and Binding Studies of Bacillus thuringiensis Cry1Ac, Cry1F, Cry1C, and Cry2A Proteins in the Soybean Pests Anticarsia gemmatalis and Chrysodeixis (Pseudoplusia) includens

ABSTRACT Anticarsia gemmatalis (velvetbean caterpillar) and Chrysodeixis includens (soybean looper, formerly named Pseudoplusia includens) are two important defoliating insects of soybeans. Both lepidopteran pests are controlled mainly with synthetic insecticides. Alternative control strategies, such as biopesticides based on the Bacillus thuringiensis (Bt) toxins or transgenic plants expressing Bt toxins, can be used and are increasingly being adopted. Studies on the insect susceptibilities and modes of action of the different Bt toxins are crucial to determine management strategies to control the pests and to delay outbreaks of insect resistance. In the present study, the susceptibilities of both soybean pests to the Bt toxins Cry1Ac, Cry1Fa, Cry1Ca, and Cry2Aa have been investigated. Bioassays performed in first-instar larvae showed that both insects are susceptible to all these toxins. Competition-binding studies carried out with Cry1Ac and Cry1Fa 125-iodine labeled proteins demonstrated the presence of specific binding sites for both of them on the midgut brush border membrane vesicles (BBMVs) of both A. gemmatalis and C. includens. Competition-binding experiments and specific-binding inhibition studies performed with selected sugars and lectins indicated that Cry1Ac and Cry1Fa share some, but not all, binding sites in the midguts of both insects. Also, the Cry1Ac- or Cry1Fa-binding sites were not shared with Cry1Ca or Cry2Aa in either soybean pest. This study contributes to the knowledge of Bt toxicity and midgut toxin binding sites in A. gemmatalis and C. includens and sheds light on the cross-resistance potential of Cry1Ac, Cry1Fa, Cry1Ca, and Cry2Aa Bt proteins as candidate proteins for Bt-pyramided crops. IMPORTANCE In the present study, the toxicity and the mode of action of the Bacillus thuringiensis (Bt) toxins Cry1Ac, Cry1Fa, Cry1Ca, and Cry2Aa in Anticarsia gemmatalis and Chrysodeixis includens (important defoliating pests of soybeans) have been investigated. These studies are crucial for determining management strategies for pest control. Bioassays showed that both insects were susceptible to the toxins. Competition-binding studies demonstrated the presence of Cry1Fa- and Cry1Ac-specific binding sites in the midguts of both pests. These results, together with the results from binding inhibition studies performed with sugars and lectins, indicated that Cry1Ac and Cry1Fa share some, but not all, binding sites, and that they were not shared with Cry1Ca or Cry2Aa in either soybean pest. This study contributes to the knowledge of Bt toxicity in A. gemmatalis and C. includens and sheds light on the cross-resistance potential of Cry1Ac, Cry1Fa, Cry1Ca, and Cry2Aa Bt proteins as candidate proteins for Bt-pyramided crops.
Marker Exchange Mutagenesis of mxaF, Encoding the Large Subunit of the Mxa Methanol Dehydrogenase, in Methylosinus trichosporium OB3b

ABSTRACT Methanotrophs have remarkable redundancy in multiple steps of the central pathway of methane oxidation to carbon dioxide. For example, it has been known for over 30 years that two forms of methane monooxygenase, responsible for oxidizing methane to methanol, exist in methanotrophs, i.e., soluble methane monooxygenase (sMMO) and particulate methane monooxygenase (pMMO), and that expression of these two forms is controlled by the availability of copper. Specifically, sMMO expression occurs in the absence of copper, while pMMO expression increases with increasing copper concentrations. More recently, it was discovered that multiple forms of methanol dehydrogenase (MeDH), Mxa MeDH and Xox MeDH, also exist in methanotrophs and that the expression of these alternative forms is regulated by the availability of cerium. That is, expression of Xox MeDH increases in the presence of cerium, while Mxa MeDH expression decreases in the presence of cerium. As it had been earlier concluded that pMMO and Mxa MeDH form a supercomplex in which electrons from Mxa MeDH are back donated to pMMO to drive the initial oxidation of methane, we speculated that Mxa MeDH could be rendered inactive through marker-exchange mutagenesis but growth on methane could still be possible if cerium was added to increase the expression of Xox MeDH under sMMO-expressing conditions. Here we report that mxaF, encoding the large subunit of Mxa MeDH, could indeed be knocked out in Methylosinus trichosporium OB3b, yet growth on methane was still possible, so long as cerium was added. Interestingly, growth of this mutant occurred in both the presence and the absence of copper, suggesting that Xox MeDH can replace Mxa MeDH regardless of the form of MMO expressed.
Effects of environmental enrichment on activity and lameness in commercial broiler production

ABSTRACT The aim of this pilot study was to investigate the effects of commercially applied environmental enrichments on behavior and lameness in broilers. Two consecutive flocks of broilers were observed at 16 days and 30 days of age to investigate differences between enriched (peat, bales of lucerne hay, and elevated platforms) and control birds with regards to behavioral activities and lameness. More running (p < .001), worm running (p = .006), play fighting (p = .015), dust bathing (p = .009), and ground pecking while standing (p < .001) were observed at 16 days than at 30 days. Across both ages, enriched birds showed more wing flapping (p = .016), wing stretching (p = .002), body shaking (p = .002), ground scratching (p < .001), and ground pecking while standing (p < .001) and lying (p = .003) compared with control birds. Even when no enrichments were close, enriched birds showed more body shaking (p = .008) and ground pecking while standing (p < 0.001) and lying (p = .010) than birds in comparable locations in control pens. There was a tendency for a lower gait score (i.e., reduced lameness) with the enriched treatment (p = .077). In conclusion, enriched birds showed higher levels of several activities compared with control birds, and demonstrated higher levels in areas where no enrichments were present.
Respiratory and Ocular Symptoms Among Employees at Swedish Indoor Swimming Pools

Background: This study investigated trichloramine exposure and prevalence of respiratory and ocular symptoms among Swedish indoor swimming pool workers. Methods: Questionnaires were distributed to pool workers and referents. Lung function and fraction of exhaled nitric oxide (FeNO) were measured before and after work. Exposure to trichloramine and trihalomethanes was measured over work shifts. Results: The mean personal trichloramine exposure was 36 &mgr;g/m3. Significantly more exposed workers reported ocular and nasal symptoms. There were significant differences between groups in FeNO change following work, with exposed showing increased FeNO, which grew when analyses included only nonsmokers. Conclusions: The findings indicate that indoor swimming pool environments may have irritating effects on mucous membranes. FeNO data also indicate an inflammatory effect on central airways, but the clinical relevance is unclear. Low trichloramine levels found in this study were not associated with health effects.
Deficiency of RgpG Causes Major Defects in Cell Division and Biofilm Formation, and Deficiency of LytR-CpsA-Psr Family Proteins Leads to Accumulation of Cell Wall Antigens in Culture Medium by Streptococcus mutans

ABSTRACT Streptococcus mutans is known to possess rhamnose-glucose polysaccharide (RGP), a major cell wall antigen. S. mutans strains deficient in rgpG, encoding the first enzyme of the RGP biosynthesis pathway, were constructed by allelic exchange. The rgpG deficiency had no effect on growth rate but caused major defects in cell division and altered cell morphology. Unlike the coccoid wild type, the rgpG mutant existed primarily in chains of swollen, “squarish” dividing cells. Deficiency of rgpG also causes significant reduction in biofilm formation (P < 0.01). Double and triple mutants with deficiency in brpA and/or psr, genes coding for the LytR-CpsA-Psr family proteins BrpA and Psr, which were previously shown to play important roles in cell envelope biogenesis, were constructed using the rgpG mutant. There were no major differences in growth rates between the wild-type strain and the rgpG brpA and rgpG psr double mutants, but the growth rate of the rgpG brpA psr triple mutant was reduced drastically (P < 0.001). Under transmission electron microscopy, both double mutants resembled the rgpG mutant, while the triple mutant existed as giant cells with multiple asymmetric septa. When analyzed by immunoblotting, the rgpG mutant displayed major reductions in cell wall antigens compared to the wild type, while little or no signal was detected with the double and triple mutants and the brpA and psr single mutants. These results suggest that RgpG in S. mutans plays a critical role in cell division and biofilm formation and that BrpA and Psr may be responsible for attachment of cell wall antigens to the cell envelope. IMPORTANCE Streptococcus mutans, a major etiological agent of human dental caries, produces rhamnose-glucose polysaccharide (RGP) as the major cell wall antigen. This study provides direct evidence that deficiency of RgpG, the first enzyme of the RGP biosynthesis pathway, caused major defects in cell division and morphology and reduced biofilm formation by S. mutans, indicative of a significant role of RGP in cell division and biofilm formation in S. mutans. These results are novel not only in S. mutans, but also other streptococci that produce RGP. This study also shows that the LytR-CpsA-Psr family proteins BrpA and Psr in S. mutans are involved in attachment of RGP and probably other cell wall glycopolymers to the peptidoglycan. In addition, the results also suggest that BrpA and Psr may play a direct role in cell division and biofilm formation in S. mutans. This study reveals new potential targets to develop anticaries therapeutics.