Miracle-dz/UniFAR-FTUs huggingface dataset:
PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens

Abstract Background Antibiotic resistance is a major health problem, as drugs that were once highly effective no longer cure bacterial infections. WGS has previously been shown to be an alternative method for detecting horizontally acquired antimicrobial resistance genes. However, suitable bioinformatics methods that can provide easily interpretable, accurate and fast results for antimicrobial resistance associated with chromosomal point mutations are still lacking. Methods Phenotypic antimicrobial susceptibility tests were performed on 150 isolates covering three different bacterial species: Salmonella enterica, Escherichia coli and Campylobacter jejuni. The web-server ResFinder-2.1 was used to identify acquired antimicrobial resistance genes and two methods, the novel PointFinder (using BLAST) and an in-house method (mapping of raw WGS reads), were used to identify chromosomal point mutations. Results were compared with phenotypic antimicrobial susceptibility testing results. Results A total of 685 different phenotypic tests associated with chromosomal resistance to quinolones, polymyxin, rifampicin, macrolides and tetracyclines resulted in 98.4% concordance. Eleven cases of disagreement between tested and predicted susceptibility were observed: two C. jejuni isolates with phenotypic fluoroquinolone resistance and two with phenotypic erythromycin resistance and five colistin-susceptible E. coli isolates with a detected pmrB V161G mutation when assembled with Velvet, but not when using SPAdes or when mapping the reads. Conclusions PointFinder proved, with high concordance between phenotypic and predicted antimicrobial susceptibility, to be a user-friendly web tool for detection of chromosomal point mutations associated with antimicrobial resistance.
Thermionic junction devices utilizing phonon blocking

Controlling electron and phonon flows through a solid junction enables novel on-chip cooling and sensing functionalities. Electrothermal elements are used in various energy harvesters, coolers, and radiation detectors. The optimal operation of these elements relies on mastering two competing boundary conditions: the maximization of the electrothermal response and the blockade of lattice (phonon) thermal conduction. In this work, we propose and demonstrate that efficient electrothermal operation and phonon blocking can be achieved in solid-state thermionic junctions, paving the way for new phonon-engineered high-efficiency refrigerators and sensors. Our experimental demonstration uses semiconductor-superconductor (Sm-S) junctions where the electrothermal response arises from the superconducting energy gap and the phonon blocking results from the acoustic transmission bottleneck at the junction. We demonstrate a cooling platform where a silicon chip, suspended only from the Sm-S junctions, is cooled by ~40% from the bath temperature. We also show how the observed effect can be used in radiation detectors and multistage electronic refrigerators suitable for cooling of quantum technology devices.
An observation-constrained assessment of the climate sensitivity and future trajectories of wetland methane emissions

Observation-driven model shows that natural CH4 emissions may increase by 50% to 80% in 2100 without action to reduce emissions. Wetlands are a major source of methane (CH4) and contribute between 30 and 40% to the total CH4 emissions. Wetland CH4 emissions depend on temperature, water table depth, and both the quantity and quality of organic matter. Global warming will affect these three drivers of methanogenesis, raising questions about the feedbacks between natural methane production and climate change. Until present the large-scale response of wetland CH4 emissions to climate has been investigated with land-surface models that have produced contrasting results. Here, we produce a novel global estimate of wetland methane emissions based on atmospheric inverse modeling of CH4 fluxes and observed temperature and precipitation. Our data-driven model suggests that by 2100, current emissions may increase by 50% to 80%, which is within the range of 50% and 150% reported in previous studies. This finding highlights the importance of limiting global warming below 2°C to avoid substantial climate feedbacks driven by methane emissions from natural wetlands.
Educational Intervention of Intention Change for Consumption of Junk Food among School Adolescents in Birgunj Metropolitan City, Nepal, Based on Theory of Planned Behaviors

Consumption of junk food among adolescents has been recognized as a serious health problem in the world. Therefore, this study aims to assess the effectiveness of an educational intervention program (interactive lecture) based on the theory of planned behavior (TPB) for reducing junk food consumption among school adolescents in Birgunj Metropolitan City, Nepal. A structured questionnaire was deployed for collecting the data from four government schools. Pretest and Posttest group study design and simple random sampling techniques were used. A multiple linear regression model and a paired t-test were used to assess the effectiveness of an educational intervention program. The theory of planned behavior indicates that behavioral intention of junk food consumption was different in pretest and posttest [5.43 ± 1.3 and 7.96 ± 0.3]. Furthermore, the average score of attitude toward junk food consumption was 11.9 ± 1.5 and 16.3 ± 1.6. Meanwhile, perceived behavior control (PBC) toward junk food was also different after intervention [2.42 ± 0.50 and 3.13 ± 0.58]. The interactive lecture method was proved an effective education program for changing the intentions of adolescent students and preventing them from consuming junk food which were statistically significant (<0.05). In addition, behavioral intention of junk food consumption, attitude toward junk food consumption, and perceived behavioral control toward junk food were statistically significant (<0.05). Therefore, study concluded that the intervention program has positive influence on the perceived behavior without control group of school-going adolescents.
The Use of Bedside Ultrasound in Cardiac Arrest

BACKGROUND: The decision to terminate resuscitative measures in the setting of cardiac arrest is based on several criteria, some of which are subjective. Ultrasound in the emergency department has potentially added an objective data point to assist in this decision. OBJECTIVE: We sought to determine if emergency physicians who were trained in the use of ultrasound use it in cardiac arrest scenarios and if so, what effect they believe it has on the duration of the resuscitative event. Our hypothesis was that emergency physicians terminate resuscitative efforts sooner with visualization of cardiac standstill and feel more comfortable in doing so. METHODS: The ultrasound training program at Los Angeles County + University of Southern California Medical Center began in 1995. We surveyed all graduates of the residency program since that date about their use of ultrasound in cardiac arrest. RESULTS: Surveys were mailed to 154 practicing emergency physicians. One hundred and sixteen surveys (75%) surveys were returned. During residency, the majority of individuals (68%) reported that they had used ultrasound during at least 10 cardiac arrests. It was used to search for a reversible cause of cardiac arrest (pericardial effusion) or for documentation of cardiac standstill. Ninety-one percent of individuals used the ultrasound result as an aid in deciding when to terminate resuscitative efforts and 59% believed it shortened their resuscitation time. After graduation, only 53% of individuals in this study have ultrasound available in their daily clinical practice. For these individuals, 60% use it in more than 50% of their cardiac arrest situations. Ultrasound was used to shorten the code time (63%) as well as to reassure and confirm the presence of cardiac standstill for the physician (88%) and the resuscitation team (59%). CONCLUSION: Most emergency physicians in this cohort who have access to ultrasound use it in cardiac arrest cases and believe that it shortens code times.
Affective Modulation after High-Intensity Exercise Is Associated with Prolonged Amygdalar-Insular Functional Connectivity Increase

Acute moderate exercise has been shown to induce prolonged changes in functional connectivity (FC) within affect and reward networks. The influence of different exercise intensities on FC has not yet been explored. Twenty-five male athletes underwent 30 min of “low”- (35% < lactate threshold (LT)) and “high”- (20% > LT) intensity exercise bouts on a treadmill. Resting-state fMRI was acquired at 3 Tesla before and after exercise, together with the Positive and Negative Affect Scale (PANAS). Data of 22 subjects (3 dropouts) were analyzed using the FSL feat pipeline and a seed-to-network-based analysis with the bilateral amygdala as the seed region for determining associated FC changes in the “emotional brain. ” Data were analyzed using a repeated measures ANOVA. Comparisons between pre- and post-exercise were analyzed using a one-sample t-test, and a paired t-test was used for the comparison between “low” and “high” exercise conditions (nonparametric randomization approach, results reported at p < 0.05). Both exercise interventions induced significant increases in the PANAS positive affect scale. There was a significant interaction effect of amygdalar FC to the right anterior insula, and this amygdalar-insular FC correlated significantly with the PANAS positive affect scale (r = 0.47, p = 0.048) in the “high”-intensity exercise condition. Our findings suggest that mood changes after exercise are associated with prolonged alterations in amygdalar-insular FC and occur in an exercise intensity-dependent manner.
Computational wrapping: A universal method to wrap 3D-curved surfaces with nonstretchable materials for conformal devices

Computational wrapping provides a universal method to wrap arbitrary curved 3D shapes with 2D-based brittle materials. This study starts from the counterintuitive question of how we can render conventional stiff, nonstretchable, and even brittle materials sufficiently conformable to fully wrap curved surfaces, such as spheres, without failure. Here, we extend the geometrical design method of computational origami to wrapping. Our computational wrapping approach provides a robust and reliable method for fabricating conformal devices for arbitrary curved surfaces with a computationally designed nonpolyhedral developable net. This computer-aided design transforms two-dimensional (2D)–based materials, such as Si wafers and steel sheets, into various targeted conformal structures that can fully wrap desired 3D structures without fracture or severe plastic deformation. We further demonstrate that our computational wrapping approach enables a design platform that can transform conventional nonstretchable 2D-based devices, such as electroluminescent lighting and flexible batteries, into conformal 3D curved devices.
Methicillin-resistant Staphylococcus aureus in Metabolic Syndrome Patients at the Mbouda Hospitals, West Region of Cameroon

Background Studies have revealed an increased risk of contracting Staphylococcus aureus infections in patients suffering from metabolic diseases. Methicillin-resistant Staphylococcus aureus (MRSA) in metabolic syndrome subjects is less reported in the medical literature. This study aimed at isolating and establishing the distribution of antibiotic-resistant Staphylococcus aureus from faecal samples in metabolic syndrome subjects from Mbouda Hospitals, West Region of Cameroon. Methods A cross-sectional study was conducted from May 2016 to May 2018 in 114 participants in whom Staphylococcus aureus was detected. Thirty (30) participants were suffering from metabolic syndrome and 84 did not suffer from this pathology. Staphylococcus aureus isolation was based on culture and confirmed by polymerase chain reaction (PCR) of the nuc gene. The Kirby-Bauer disk diffusion method was used for drug susceptibility assay. Molecular detection of the mecA gene by PCR was performed to screen MRSA. Results From the 114 Staphylococcus aureus isolates, the prevalence of the mecA gene confirming MRSA was 79.82%, higher than that of methicillin-sensitive Staphylococcus aureus (MSSA) (20.17%). The frequency of MRSA was higher in participants with metabolic syndrome (80.00%) compared to non-metabolic syndrome (79.76%) participants without significant difference (p=0.977). The antimicrobial susceptibility test revealed that the amikacin susceptibility profile was significantly different in metabolic and non-metabolic syndrome participants (p=0.037, chi-square=6.59). Regarding metabolic syndrome status, 72.62% of isolates were multidrug-resistant in non-metabolic syndrome participants versus 63.33% in metabolic syndrome participants. Conclusion This study suggests that metabolic syndrome patients harbour MRSA strains in their intestines even as the difference was not statistically significant with non-metabolic syndrome participants. The need for appropriate antimicrobial use to halt or at least limit the spread of resistance is suggested in the care of metabolic syndrome patients and the entire population.
A Five-Genes-Based Prognostic Signature for Cervical Cancer Overall Survival Prediction

Aims. This study is aimed at identifying a prognostic signature for cervical cancer. Main Methods. The gene expression data and clinical information of cervical cancer and normal cervical tissues were acquired from The Cancer Genome Atlas and from three datasets of the Gene Expression Omnibus database. DESeq2 and Limma were employed to screen differentially expressed genes (DEGs). The overlapping DEGs among all datasets were considered the final DEGs. Then, the functional enrichment analysis was performed. Moreover, the Cox proportional hazards regression was performed to establish a prognostic signature of the DEGs. The Kaplan-Meier analysis was applied to test the model. Relationships between gene expression and clinicopathological parameters in cervical cancer, including age, HPV status, histology, stage, and lymph node metastasis, were analysed by the chi-square test. The somatic mutations of these prognostic genes were assessed through cBioPortal. The robustness of the model was verified in another two independent validation cohorts. Key Findings. In total, 169 overlapping upregulated genes and 29 overlapping downregulated genes were identified in cervical cancer compared with normal cervical tissues. Functional enrichment analysis indicated that the DEGs were mainly enriched in DNA replication, the cell cycle, and the p53 signalling pathway. Finally, a 5-gene- (ITM2A, DSG2, SPP1, EFNA1, and MMP1) based prognostic signature was built. According to this model, each patient was given a prognostic-related risk value. The Kaplan-Meier analysis showed that a higher risk was related to worse overall survival in cervical cancer, with an area under the receiver operating characteristic curve of 0.811 for 15 years. The validity of this model in the prediction of cervical cancer outcome was verified in another two independent datasets. In addition, our study also found that the low expression of ITM2A was associated with cervical adenocarcinoma. Interestingly, DSG2 was associated with the HPV status of cervical cancer. Significance. Our study constructed a prognostic model in cervical cancer and discovered two novel genes, ITM2A and DSG2, associated with cervical carcinogenesis and survival.
A sensitive and robust thin-film x-ray detector using 2D layered perovskite diodes

Solution-processed 2D perovskite diodes with fully depleted junction enable highly sensitive and robust thin-film x-ray detectors. Solid-state radiation detectors, using crystalline semiconductors to convert radiation photons to electrical charges, outperform other technologies with high detectivity and sensitivity. Here, we demonstrate a thin-film x-ray detector comprised with highly crystalline two-dimensional Ruddlesden-Popper phase layered perovskites fabricated in a fully depleted p-i-n architecture. It shows high diode resistivity of 1012 ohm·cm in reverse-bias regime leading to a high x-ray detecting sensitivity up to 0.276 C Gyair−1 cm−3. Such high signal is collected by the built-in potential underpinning operation of primary photocurrent device with robust operation. The detectors generate substantial x-ray photon–induced open-circuit voltages that offer an alternative detecting mechanism. Our findings suggest a new generation of x-ray detectors based on low-cost layered perovskite thin films for future x-ray imaging technologies.
Distinct Patterns of Brain Activity Characterise Lexical Activation and Competition in Spoken Word Production

According to a prominent theory of language production, concepts activate multiple associated words in memory, which enter into competition for selection. However, only a few electrophysiological studies have identified brain responses reflecting competition. Here, we report a magnetoencephalography study in which the activation of competing words was manipulated by presenting pictures (e.g., dog) with distractor words. The distractor and picture name were semantically related (cat), unrelated (pin), or identical (dog). Related distractors are stronger competitors to the picture name because they receive additional activation from the picture relative to other distractors. Picture naming times were longer with related than unrelated and identical distractors. Phase-locked and non-phase-locked activity were distinct but temporally related. Phase-locked activity in left temporal cortex, peaking at 400 ms, was larger on unrelated than related and identical trials, suggesting differential activation of alternative words by the picture-word stimuli. Non-phase-locked activity between roughly 350–650 ms (4–10 Hz) in left superior frontal gyrus was larger on related than unrelated and identical trials, suggesting differential resolution of the competition among the alternatives, as reflected in the naming times. These findings characterise distinct patterns of activity associated with lexical activation and competition, supporting the theory that words are selected by competition.
Two Randomized Trials Provide No Consistent Evidence for Nonmusical Cognitive Benefits of Brief Preschool Music Enrichment

Young children regularly engage in musical activities, but the effects of early music education on children's cognitive development are unknown. While some studies have found associations between musical training in childhood and later nonmusical cognitive outcomes, few randomized controlled trials (RCTs) have been employed to assess causal effects of music lessons on child cognition and no clear pattern of results has emerged. We conducted two RCTs with preschool children investigating the cognitive effects of a brief series of music classes, as compared to a similar but non-musical form of arts instruction (visual arts classes, Experiment 1) or to a no-treatment control (Experiment 2). Consistent with typical preschool arts enrichment programs, parents attended classes with their children, participating in a variety of developmentally appropriate arts activities. After six weeks of class, we assessed children's skills in four distinct cognitive areas in which older arts-trained students have been reported to excel: spatial-navigational reasoning, visual form analysis, numerical discrimination, and receptive vocabulary. We initially found that children from the music class showed greater spatial-navigational ability than did children from the visual arts class, while children from the visual arts class showed greater visual form analysis ability than children from the music class (Experiment 1). However, a partial replication attempt comparing music training to a no-treatment control failed to confirm these findings (Experiment 2), and the combined results of the two experiments were negative: overall, children provided with music classes performed no better than those with visual arts or no classes on any assessment. Our findings underscore the need for replication in RCTs, and suggest caution in interpreting the positive findings from past studies of cognitive effects of music instruction.
Resistance to Syngeneic RadLV Tumor Cells Mimics H-2 D Control of RadLV-Induced Neoplasm

Resistance to radiation-leukemia virus-induced leukemia is mediated by gene(s) in the H-2D region of the major murine histocompatibifity complex (1). The mechanisms by which gene(s) in this region affect leukemogenesis are hitherto unknown. However, previous observations (2) suggest a role in disease resistance for changes in H-2 expression occurring immediately after virus inoculation. For example, gene products (antigens) of the H-2D region show the most marked and prolonged changes in expression after virus inoculation. In addition, elevated H-2D antigen expression after virus inoculation occurs for thymocytes of resistant but not susceptible mice. Furthermore, there is an inverse relation between expression of H-2D and viral antigens. Viral antigen expression is greater in susceptible animals, whereas H-2D antigen expression is maximal for virus-infected resistant mice. Finally, H-2 antigens usually disappear from the surface of radiation-induced leukemia virus (RadLV) l transformed cultures when overt leukemia develops. Thus, resistance to the disease is associated with increased H-2 antigenic expression, and the onset of leukemia is associated with disappearance of these antigens. Several mechanisms by which changes in H-2 antigen expression may overtlv influence the course of the disease have been previously suggested (2). Although the effect of increased H-2 expression on the other steps required for oncogenesis remains to be evaluated, the observations reported herein suggest that elevated H-2 antigen expression enhances the effectiveness of the host's immune responses to virus-int? cted cells and may function in resistance to leukemogenesis.
JCB: REPORT

D. Mérino, M. Giam, and P.D. Hughes contributed equally to this paper. Correspondence to Philippe Bouillet: bouillet@wehi.edu. au O.M. Siggs’ present address is Dept. of Genetics, The Scripps Research Institute, La Jolla, CA 92037. Abbreviations used in this paper: MOMP, mitochondrial outer membrane permeabilization; PKD, polycystic kidney disease; tBid, truncated Bid; WBC, white blood cell; WT, wild type. Introduction
Human Ether-à-go-go –related Gene K (cid:49) Channel Gating Probed with Extracellular Ca 2 (cid:49) Evidence for Two Distinct Voltage Sensors

Human ether-à-go-go –related gene ( HERG ) encoded K (cid:49) channels were expressed in Chinese hamster ovary (CHO-K1) cells and studied by whole-cell voltage clamp in the presence of varied extracellular Ca 2 (cid:49) concentrations and physiological external K (cid:49) . Elevation of external Ca 2 (cid:49) from 1.8 to 10 mM resulted in a reduction of whole-cell K (cid:49) current amplitude, slowed activation kinetics, and an increased rate of deactivation. The midpoint of the voltage dependence of activation was also shifted (cid:49) 22.3 (cid:54) 2.5 mV to more depolarized potentials. In con-trast, the kinetics and voltage dependence of channel inactivation were hardly affected by increased extracellular Ca 2 (cid:49) . Neither Ca 2 (cid:49) screening of diffuse membrane surface charges nor open channel block could explain these changes. However, selective changes in the voltage-dependent activation, but not inactivation gating, account for the effects of Ca 2 (cid:49) on Human ether-à-go-go –related gene current amplitude and kinetics. The differential effects of extracellular Ca 2 (cid:49) on the activation and inactivation gating indicate that these processes have distinct voltage-sens-ing mechanisms. Thus, Ca 2 (cid:49) appears to directly interact with externally accessible channel residues to alter the membrane potential detected by the activation voltage sensor, yet Ca 2 (cid:49) binding to this site is ineffective in modify-ing the inactivation