Miracle-dz/UniFAR-FTUs huggingface dataset:
Fourier-Transform InfraRed Spectroscopy Can Quickly Type Gram-Negative Bacilli Responsible for Hospital Outbreaks

The typing of epidemic bacterial pathogens in hospitals relies on DNA-based, expensive, and time-consuming techniques, that are often limited to retrospective studies. However, the quick identification of epidemic pathogens in the routine of the microbiology laboratories would expedite infection control procedures that limit the contamination of new patients. IR Biotyper (Bruker Daltonics GmbH) is a new typing machine based on Fourier-transform infrared (FTIR) spectroscopy which generates spectra, aiming at typing the micro-organisms within 3 h. This technique discriminates the isolates by exploring the differences of the surface cell polysaccharides. In this work, we evaluated the ability of the FTIR spectroscopy to recognize Gram-negative bacilli clones responsible for hospital outbreaks. Isolates of Pseudomonas aeruginosa (n = 100), Klebsiella pneumoniae (n = 16), Enterobacter cloacae (n = 23), and Acinetobacter baumannii (n = 20) were typed by the reference methods Multi-Locus Sequence Typing (defining sequence types – STs) along with or without pulsed field gel electrophoresis (PFGE) (defining pulsotypes), and by FTIR spectroscopy. The congruence of FTIR spectroscopy clustering was compared to those of MLST and PFGE by Adjusted Rand index and Adjusted Wallace coefficient. We found that FTIR spectroscopy accurately clustered P. aeruginosa, K. pneumoniae, and E. cloacae isolates belonging to the same ST. The performance of the FTIR spectroscopy was slightly lower for A. baumannii. Furthermore, FTIR spectroscopy also correctly clustered P. aeruginosa isolates having a similar pulsotype. Overall, the IR Biotyper can quickly (in less than 3 h) detect the spread of clones of P. aeruginosa, K. pneumoniae, E. cloacae, and A. baumannii. The use of this technique by clinical microbiology laboratories may help to tackle the spread of epidemic clones by the quick implementation of infection control measures.
Factors Associated With Psychosocial Functioning and Outcome of Individuals With Recent-Onset Schizophrenia and at Ultra-High Risk for Psychosis

Background: Patients with schizophrenia have impairments in social functioning and are readmitted to healthcare institutions frequently. Individuals at ultra-high risk (UHR) for psychosis already present poor social functioning; among those individuals, the conversion rate from the putative prodromal phase to overt psychosis is 20%–30% within 1–2 years. Here, we analyzed the factor structure of self-related variables and neuro- and socio-cognitive function, and investigated whether these factors were associated with psychosocial function and prognostic outcome in individuals with recent-onset schizophrenia (ROSPR) or at UHR for psychosis. Methods: We evaluated 60 individuals at UHR for psychosis, 47 individuals with ROSPR, and 71 healthy controls using a comprehensive neurocognitive test battery and self-reported attribution scales, self-esteem, resilience, aberrant subjective experiences of schizotypy (physical anhedonia, social anhedonia, magical ideation, and perceptual aberration), and basic symptoms. We assessed psychosocial function with the Quality of Life Scale (QLS). Results: Factor analysis of all subjects revealed a four-factor structure comprising social-cognitive bias, reflective self, neurocognition, and pre-reflective self factors. Multiple regression analysis at baseline revealed that the factor structure predicted QLS. In the UHR group, social-cognitive bias, reflective self, neurocognition, and negative symptoms were significant determinants, explaining 38.0% of total QLS score variance. In the ROSPR group, reflective self and negative symptoms were significant determinants, explaining 54.4% of total QLS score variance. During follow-up, 13 individuals at UHR for psychosis developed psychosis (cumulative prevalence: 31.2% ± 7.6% at 6 years), with neurocognition score at baseline remaining a significant predictor of conversion [χ2(1) = 4.009, p = 0.045; hazard ratio 0.56, 95% confidence interval 0.31–0.99, p = 0.048]. Five patients with schizophrenia were (re)admitted during follow-up (cumulative prevalence: 16.1% ± 7.1% at 6 years); no factor was found to predict (re)admission. Conclusion: Factor analysis revealed an intrinsic four-factor structure of social-cognitive bias, reflective self, neurocognition, and pre-reflective self. The four factors were associated with social functioning at baseline and prodrome-to-psychosis conversion during follow-up, indicating the clinical significance of the four-factor structure. These findings provide a framework for understanding schizophrenia.
Risk Attitudes Affect Livestock Biosecurity Decisions With Ramifications for Disease Control in a Simulated Production System

Hog producers' operational decisions can be informed by an awareness of risks associated with emergent and endemic diseases. Outbreaks of porcine epidemic diarrhea virus (PEDv) have been re-occurring every year since the first onset in 2013 with substantial losses across the hog production supply chain. Interestingly, a decreasing trend in PEDv incidence is visible. We assert that changes in human behaviors may underlie this trend. Disease prevention using biosecurity practices is used to minimize risk of infection but its efficacy is conditional on human behavior and risk attitude. Standard epidemiological models bring important insights into disease dynamics but have limited predictive ability. Since research shows that human behavior plays a driving role in the disease spread process, the explicit inclusion of human behavior into models adds an important dimension to understanding disease spread. Here we analyze PEDv incidence emerging from an agent-based model (ABM) that uses both epidemiological dynamics and algorithms that incorporate heterogeneous human decisions. We investigate the effects of shifting fractions of hog producers between risk tolerant and risk averse positions. These shifts affect the dynamics describing willingness to increase biosecurity as a response to disease threats and, indirectly, change infection probabilities and the resultant intensity and impact of the disease outbreak. Our ABM generates empirically verifiable patterns of PEDv transmission. Scenario results show that relatively small shifts (10% of the producer agents) toward a risk averse position can lead to a significant decrease in total incidence. For significantly steeper decreases in disease incidence, the model's hog producer population needed at least 37.5% of risk averse. Our study provides insight into the link between risk attitude, decisions related to biosecurity, and consequent spread of disease within a livestock production system. We suggest that it is possible to create positive, lasting changes in animal health by nudging the population of livestock producers toward more risk averse behaviors. We make a case for integrating social and epidemiological aspects in disease spread models to test intervention strategies intended to improve biosecurity and animal health at the system scale.
Sex Differences in Brain Injury and Repair in Newborn Infants: Clinical Evidence and Biological Mechanisms

Differences in the development of the male and female brain are an evolving area of investigation. We are beginning to understand the underpinnings of male and female advantages due to differences in brain development as well as the consequences following hypoxic-ischemic brain injury in the newborn. The two main factors that appear to affect outcomes are gestation age at the time of injury and sex of the subject. This review starts with a summary of differences in the anatomy and physiology of the developing male and female brain. This is followed by a review of the major factors responsible for the observed differences in the face of normal development and hypoxic injury. The last section reviews the response of male and female subjects to various neuroprotective strategies that are currently being used and where there is a need for additional information for more precise therapy based on the sex of the infant.
The Fluctuations of Leukocytes and Circulating Cytokines in Septic Humanized Mice Vary With Outcome

Sepsis remains a major challenge in translational research given its heterogeneous pathophysiology and the lack of specific therapeutics. The use of humanized mouse chimeras with transplanted human hematopoietic cells may improve the clinical relevance of pre-clinical studies. However, knowledge of the human immuno-inflammatory response during sepsis in humanized mice is scarce; it is unclear how similar or divergent mouse and human-origin immuno-inflammatory responses in sepsis are. In this study, we evaluated the early outcome-dependent immuno-inflammatory response in humanized mice generated in the NSG strain after cecal ligation and puncture (CLP) sepsis. Mice were observed for 32 h post-CLP and were assigned to either predicted-to-die (P-DIE) or predicted-to-survive (P-SUR) groups for retrospective comparisons. Blood samples were collected at baseline, 6 and 24 h, whereas the bone marrow and spleen were collected between 24 and 32 h post-CLP. In comparison to P-SUR, P-DIE humanized mice had a 3-fold higher frequency of human splenic monocytes and their CD80 expression was reduced by 1.3-fold; there was no difference in the HLA-DR expression. Similarly, the expression of CD80 on the bone marrow monocytes from P-DIE mice was decreased by 32% (p < 0.05). Sepsis induced a generalized up-regulation of both human and murine plasma cytokines (TNFα, IL-6, IL-10, IL-8/KC, MCP-1); it was additionally aggravated in P-DIE vs. P-SUR. Human cytokines were strongly overridden by the murine ones (approx. ratio 1:9) but human TNFα was 7-fold higher than mouse TNFα. Interestingly, transplantation of human cells did not influence murine cytokine response in NSG mice, but humanized NSG mice were more susceptible to sepsis in comparison with NSG mice (79 vs. 33% mortality; p < 0.05). In conclusion, our results show that humanized mice reflect selected aspects of human immune responses in sepsis and therefore may be a feasible alternative in preclinical immunotherapy modeling.
Subjective Beliefs About Trust and Reciprocity Activate an Expected Reward Signal in the Ventral Striatum

There is overwhelming evidence that the evaluation of both reward decisions and their associated outcomes are closely linked with bilateral activation of the ventral striatum, with these insights stemming from tasks such as the monetary incentive delay task for lotteries and multiround Trust Games for social settings. The essential element in these tasks is an externally provided cue associated with specific gains/trustworthy partners and losses/non-trustworthy partners. However, in reality people typically use their own beliefs to guide their decision-making and assess the likelihood of positive or and negative outcomes. As when participants assess the relationship between cues and rewards, individuals should anticipate rewards in correspondence to their beliefs, i.e., the higher the belief of obtaining a reward in the future, the higher the anticipation of reward. In this study, we use decision-makers’ own, naturally occurring, beliefs about both social and non-social contexts to examine the subsequent outcome of their choices. We hypothesize that mechanisms of belief-mediated reward processing are mediated by neural activation in the ventral striatum. An essential feature of our design is the elicitation of individuals’ beliefs prior to the decision-making task itself. Furthermore, our incentivized, non-deceptive, decision-making task distinguishes between social – implemented by a Trust Game – and non-social sources, as well as risk and ambiguity as underlying types of uncertainty. Our main result shows that individual beliefs regarding reciprocity likelihoods in both the Trust Game and the lottery influence the amount invested. Subsequently, only the investment amount in the Trust Game parametrically modulates anticipatory reward and outcome evaluation in the ventral striatum. This study demonstrates a first approach at using participants’ subjective sets of beliefs to examine reward processing. We discuss its potential promise, outline some limitations, and propose follow-up studies to extend the current approach.
Association of Anesthetic Exposure Time With Clinical Outcomes After Endovascular Therapy for Acute Ischemic Stroke

Background: The optimal sedative regimen with general anesthesia (GA) or conscious sedation for patients undergoing endovascular therapy (EVT) remains controversial. Apart from sedative regimen, the duration of anesthetic exposure may affect clinical outcomes. We aimed to determine whether there is an association between anesthetic exposure time and clinical outcomes in mechanically ventilated stroke patients undergoing EVT for large vessel occlusion. Methods: This was an observational study of consecutive ischemic stroke patients who underwent EVT for anterior circulation large vessel occlusion under GA from January 2016 to March 2018. To minimize confounding by indication, we restricted our analysis to patients whose anesthetic exposure lasted <72 h. Multivariable logistic regression modeling adjusted for covariates was employed to evaluate whether 90-days independent functional outcome (defined as modified Rankin Scale scores 0–2) and 90-days survival could be predicted by anesthetic exposure time. Results: During the study period, 138 patients with ischemic stroke who underwent EVT received GA and fulfilled our study criteria: median age was 77 years (interquartile range, 65–82); 46.4% were men; median NIHSS score was 18 (15–21), median ASPECT score was 7 (6–8). Median duration of GA was 5.4 (2.5–19.7) h. Logistic regression modeling revealed an independent association between duration of anesthetic exposure and both 90-days independent functional outcome (p = 0.034) and 90-days survival (p = 0.011). Each additional 15-min of anesthetic exposure decreased the likelihood of achieving an independent functional outcome at 90 days by 1.5% and of being alive at 90 days by 1.0%. Conclusion: Our data promotes the notion that ischemic stroke patients who require peri-interventional GA for EVT should be extubated as soon as possible after the procedure.
N-acetylcysteine Amide Ameliorates Blast-Induced Changes in Blood-Brain Barrier Integrity in Rats

Traumatic brain injury resulting from exposure to blast overpressure (BOP) is associated with neuropathology including impairment of the blood-brain barrier (BBB). This study examined the effects of repeated exposure to primary BOP and post-blast treatment with an antioxidant, N-acetylcysteine amide (NACA) on the integrity of BBB. Anesthetized rats were exposed to three 110 kPa BOPs separated by 0.5 h. BBB integrity was examined in vivo via a cranial window allowing imaging of pial microcirculation by intravital microscopy. Tetramethylrhodamine isothiocyanate Dextran (TRITC-Dextran, mw = 40 kDa or 150 kDa) was injected intravenously 2.5 h after the first BOP exposure and the leakage of TRITC-Dextran from pial microvessels into the brain parenchyma was assessed. The animals were randomized into 6 groups (n = 5/group): four groups received 40 kDa TRITC-Dextran (BOP-40, sham-40, BOP-40 NACA, and sham-40 NACA), and two groups received 150 kDa TRITC-Dextran (BOP-150 and sham-150). NACA treated groups were administered NACA 2 h after the first BOP exposure. The rate of TRITC-Dextran leakage was significantly higher in BOP-40 than in sham-40 group. NACA treatment significantly reduced TRITC-Dextran leakage in BOP-40 NACA group and sham-40 NACA group presented the least amount of leakage. The rate of leakage in BOP-150 and sham-150 groups was comparable to sham-40 NACA and thus these groups were not assessed for the effects of NACA. Collectively, these data suggest that BBB integrity is compromised following BOP exposure and that NACA treatment at a single dose may significantly protect against blast-induced BBB breakdown.
Young Children Selectively Imitate Models Conforming to Social Norms

This study investigated whether toddlers would selectively imitate a demonstrator who exhibits familiarity with cultural practices in their tool-using habits over a demonstrator who consistently uses tools in an unconventional way. Three-year-old children (n = 45) watched videos depicting two models, one of whom performed tool-using actions in a conventional way, while the other model deviated from social conventions. Then, both models introduced a technique to build a tower (differing in one element). Moreover, the context of the demonstration was also manipulated: in one condition, the models expressed their teaching intentions, while in the other they performed the actions without communicative signals. Children were more willing to copy the actions of the conventionally behaving model, irrespective of the context of the demonstration.
Goethite Hinders Azo Dye Bioreduction by Blocking Terminal Reductive Sites on the Outer Membrane of Shewanella decolorationis S12

Iron (hydr)oxides are the most ubiquitous Fe(III)-containing minerals in the near-surface environments and can regulate organic pollutant biotransformation by participating in bacterial extracellular electron transfer under anaerobic conditions. Mechanisms described so far are based on their redox properties in bacterial extracellular respiration. Here, we find that goethite, a typical iron (hydr)oxide, inhibits the bioreduction of different polar azo dyes by Shewanella decolorationis S12 not through electron competition, but by the contact of its surface Fe(III) with the bacterial outer surface. Through the combined results of attenuated total reflectance (ATR) Fourier transform infrared spectroscopy, two-dimensional correlation spectroscopy, and confocal laser scanning microscope, we found that the outer membrane proteins MtrC and OmcA of strain S12 are key binding sites for goethite surface. Meanwhile, they were identified as the important reductive terminals for azo dyes. These results suggest that goethite may block the terminal reductive sites of azo dyes on the bacterial outer membrane to inhibit their bioreduction. This discovered role of goethite in bioreduction provides new insight into the microbial transformation processes of organic pollutants in iron (hydr)oxide-containing environments.
The Embodied Brain of SOVEREIGN2: From Space-Variant Conscious Percepts During Visual Search and Navigation to Learning Invariant Object Categories and Cognitive-Emotional Plans for Acquiring Valued Goals

This article develops a model of how reactive and planned behaviors interact in real time. Controllers for both animals and animats need reactive mechanisms for exploration, and learned plans to efficiently reach goal objects once an environment becomes familiar. The SOVEREIGN model embodied these capabilities, and was tested in a 3D virtual reality environment. Neural models have characterized important adaptive and intelligent processes that were not included in SOVEREIGN. A major research program is summarized herein by which to consistently incorporate them into an enhanced model called SOVEREIGN2. Key new perceptual, cognitive, cognitive-emotional, and navigational processes require feedback networks which regulate resonant brain states that support conscious experiences of seeing, feeling, and knowing. Also included are computationally complementary processes of the mammalian neocortical What and Where processing streams, and homologous mechanisms for spatial navigation and arm movement control. These include: Unpredictably moving targets are tracked using coordinated smooth pursuit and saccadic movements. Estimates of target and present position are computed in the Where stream, and can activate approach movements. Motion cues can elicit orienting movements to bring new targets into view. Cumulative movement estimates are derived from visual and vestibular cues. Arbitrary navigational routes are incrementally learned as a labeled graph of angles turned and distances traveled between turns. Noisy and incomplete visual sensor data are transformed into representations of visual form and motion. Invariant recognition categories are learned in the What stream. Sequences of invariant object categories are stored in a cognitive working memory, whereas sequences of movement positions and directions are stored in a spatial working memory. Stored sequences trigger learning of cognitive and spatial/motor sequence categories or plans, also called list chunks, which control planned decisions and movements toward valued goal objects. Predictively successful list chunk combinations are selectively enhanced or suppressed via reinforcement learning and incentive motivational learning. Expected vs. unexpected event disconfirmations regulate these enhancement and suppressive processes. Adaptively timed learning enables attention and action to match task constraints. Social cognitive joint attention enables imitation learning of skills by learners who observe teachers from different spatial vantage points.
Low Nitrogen Priming Enhances Photosynthesis Adaptation to Water-Deficit Stress in Winter Wheat (Triticum aestivum L.) Seedlings

Drought is among the main environmental stressors that reduces wheat production. Nitrogen (N) availability affects plant adaptation to abiotic stress, but the effect of low N (LN) on drought tolerance is unclear. To identify the effect of LN priming on water-deficit stress tolerance in wheat seedlings, we primed cultivar Yangmai158 with 0.25 mM N for 7 days, and then added 20% polyethylene glycol 6000 as a water-deficit treatment for 5 days. The net photosynthetic rate (Pn), plant biomass, and plant growth rate (GR) were significantly reduced under water-deficit conditions; such decreases were less severe in LN-primed (LND) plants than non-primed (CKD) plants. The leaf relative water content (LRWC) decreased under water-deficit conditions, which in turn led to a reduced transpiration rate, stomatal conductance, and intercellular CO2 concentration (Ci), causing a stomatal limitation on photosynthesis. LN priming also enhanced root growth, resulting in a higher LRWC and less stomatal limitation in LND plants than CKD plants. PSII quantum efficiency, photochemical quenching, and maximum PSII quantum efficiency were reduced under water-deficit conditions, indicating photoinhibition. However, LN priming increased the electron flux to photorespiration and the Mehler pathway, reducing photoinhibition. In conclusion, LN priming improved the leaf water status and increased alternative electron flux to attenuate photoinhibition, thus alleviating the inhibition of photosynthesis, and growth due to water deficiency.