Miracle-dz/UniFAR-FTUs huggingface dataset:
Antibiotic Resistance of Campylobacter Species in a Pediatric Cohort Study

The objective of this study was to determine the phenotypic patterns of antibiotic resistance and the epidemiology of drug-resistant Campylobacter spp. from a low-resource setting. ABSTRACT The objective of this study was to determine the phenotypic patterns of antibiotic resistance and the epidemiology of drug-resistant Campylobacter spp. from a low-resource setting. A birth cohort of 303 patients was followed until 5 years of age. Stool samples from asymptomatic children (n = 10,008) and those with diarrhea (n = 3,175) were cultured for Campylobacter. Disk diffusion for ciprofloxacin (CIP), nalidixic acid (NAL), erythromycin (ERY), azithromycin (AZM), tetracycline (TE), gentamicin (GM), ampicillin (AMP), amoxicillin and clavulanic acid (AMC), ceftriaxone (CRO), chloramphenicol (C), and trimethoprim-sulfamethoxazole (TMS) was determined. Antibiotic resistances in Campylobacter jejuni and non-C. jejuni isolates from surveillance and diarrhea samples were compared, and the association between personal macrolide exposure and subsequent occurrence of a macrolide-resistant Campylobacter spp. was assessed. Of 917 Campylobacter isolates, 77.4% of C. jejuni isolates and 79.8% of non-C. jejuni isolates were resistant to ciprofloxacin, while 4.9% of C. jejuni isolates and 24.8% of non-C. jejuni isolates were not susceptible to azithromycin. Of the 303 children, 33.1% had been diagnosed with a Campylobacter strain nonsusceptible to both azithromycin and ciprofloxacin. Personal macrolide exposure did not affect the risk of macrolide-resistant Campylobacter. Amoxicillin and clavulanic acid (94.0%) was one of the antibiotics with the highest rates of susceptibility. There is a high incidence of quinolone- and macrolide-resistant Campylobacter infections in infants under 24 months of age. Given the lack of association between personal exposure to macrolides and a subsequent Campylobacter infection resistant to macrolides, there is a need to evaluate the source of multidrug-resistant (MDR) Campylobacter. This study provides compelling evidence to propose amoxicillin/clavulanic acid as a treatment for campylobacteriosis.
Deep Object-Centric Policies for Autonomous Driving

While learning visuomotor skills in an end-to-end manner is appealing, deep neural networks are often uninterpretable and fail in surprising ways. For robotics tasks, such as autonomous driving, models that explicitly represent objects may be more robust to new scenes and provide intuitive visualizations. We describe a taxonomy of “object-centric” models which leverage both object instances and end-to-end learning. In the Grand Theft Auto V simulator, we show that object-centric models outperform object-agnostic methods in scenes with other vehicles and pedestrians, even with an imperfect detector. We also demonstrate that our architectures perform well on real-world environments by evaluating on the Berkeley DeepDrive Video dataset, where an object-centric model outperforms object-agnostic models in the low-data regimes.
Testing the Empathizing–Systemizing theory of sex differences and the Extreme Male Brain theory of autism in half a million people

Significance In the largest study to date of autistic traits, we test 10 predictions from the Empathizing–Systemizing (E-S) theory of sex differences and the Extreme Male Brain (EMB) theory of autism. We confirmed that typical females on average are more empathic, typical males on average are more systems-oriented, and autistic people on average show a “masculinized” profile. The strengths of the study are the inclusion of a replication sample and the use of big data. These two theories can be considered to have strong support. We demonstrate that D-scores (difference between E and S) account for 19 times the variance in autistic traits than do other demographic variables, including sex, underscoring the importance of brain types in autism. The Empathizing–Systemizing (E-S) theory of typical sex differences suggests that individuals may be classified based on empathy and systemizing. An extension of the E-S theory, the Extreme Male Brain (EMB) theory suggests that autistic people on average have a shift towards a more masculinized brain along the E-S dimensions. Both theories have been investigated in small sample sizes, limiting their generalizability. Here we leverage two large datasets (discovery n = 671,606, including 36,648 autistic individuals primarily; and validation n = 14,354, including 226 autistic individuals) to investigate 10 predictions of the E-S and the EMB theories. In the discovery dataset, typical females on average showed higher scores on short forms of the Empathy Quotient (EQ) and Sensory Perception Quotient (SPQ), and typical males on average showed higher scores on short forms of the Autism Spectrum Quotient (AQ) and Systemizing Quotient (SQ). Typical sex differences in these measures were attenuated in autistic individuals. Analysis of “brain types” revealed that typical females on average were more likely to be Type E (EQ > SQ) or Extreme Type E and that typical males on average were more likely to be Type S (SQ > EQ) or Extreme Type S. In both datasets, autistic individuals, regardless of their reported sex, on average were “masculinized. ” Finally, we demonstrate that D-scores (difference between EQ and SQ) account for 19 times more of the variance in autistic traits (43%) than do other demographic variables including sex. Our results provide robust evidence in support of both the E-S and EMB theories.
In vivo storage of oocytes leads to lower survival, increased abnormalities and may affect the ploidy status in the yellowtail tetra Astyanax altiparanae

Summary In this study we analyzed whether the in vivo storage of oocytes (time after ovulation until fertilization) affects the survival and the ploidy status of the yellowtail tetra Astyanax altiparanae. Fish were induced to spawn and, after ovulation, a small aliquot was stripped and immediately fertilized (positive control group). Subsequently, aliquots (~150 oocytes) were stripped and fertilized at various time points of 60, 120, 180 or 240 min. Developmental stages, abnormalities, survival and the ploidy status of the hatched larvae were examined. As expected, in the control group, 100% of the larvae were diploid. Conversely, triploid individuals were observed just at the 60 min treatment time point (0.6%). In vivo storage of oocytes also influenced the survival rates (P < 0.05); the 180 and 240 min samples, respectively, presented lower survival rates at gastrula (50.10±6.26% and 40.92±5.32%), and somite (17.80±5.14% and 4.41±2.76%) stages and lower hatching rates (12.01±4.04% and 4.41±2.76%). A higher percentage (99.27±0.40%) of normal larvae and only a few abnormal larvae (0.73±0.40%) were observed in the control group (P = 0.0000). This observation did not differ from that observed at the 60 min treatment point (P = 0.9976). A significant increase in the percentage of abnormalities was observed in the other treatments, and, after 240 min, the highest percentage of abnormal larvae was seen (P=0.0024; 83.33±16.67%). In conclusion, we showed that oocyte ageing had a significant effect on survival and may affect the ploidy status in A. atiparanae.
A regularity index for dendrites - local statistics of a neuron's input space

Neurons collect their inputs from other neurons by sending out arborized dendritic structures. However, the relationship between the shape of dendrites and the precise organization of synaptic inputs in the neural tissue remains unclear. Inputs could be distributed in tight clusters, entirely randomly or else in a regular grid-like manner. Here, we analyze dendritic branching structures using a regularity index R, based on average nearest neighbor distances between branch and termination points, characterizing their spatial distribution. We find that the distributions of these points depend strongly on cell types, indicating possible fundamental differences in synaptic input organization. Moreover, R is independent of cell size and we find that it is only weakly correlated with other branching statistics, suggesting that it might reflect features of dendritic morphology that are not captured by commonly studied branching statistics. We then use morphological models based on optimal wiring principles to study the relation between input distributions and dendritic branching structures. Using our models, we find that branch point distributions correlate more closely with the input distributions while termination points in dendrites are generally spread out more randomly with a close to uniform distribution. We validate these model predictions with connectome data. Finally, we find that in spatial input distributions with increasing regularity, characteristic scaling relationships between branching features are altered significantly. In summary, we conclude that local statistics of input distributions and dendrite morphology depend on each other leading to potentially cell type specific branching features.
Migration and transformation of dissolved carbon during accumulated cyanobacteria decomposition in shallow eutrophic lakes: a simulated microcosm study

The decomposition processes of accumulated cyanobacteria can release large amounts of organic carbon and affect the carbon cycling in shallow eutrophic lakes. However, the migration and transformation mechanisms of dissolved carbon (DC) require further study and discussion. In this study, a 73-day laboratory microcosm experiment using suction samplers (Rhizon and syringe) was conducted to understand the migration and transformation of DC during the cyanobacteria decomposition. The decomposition of cyanobacteria biomass caused anoxic and reduction conditions, and changed the acid-base environment in the water column. During the early incubation (days 0–18), a large amount of cyanobacteria-derived particulate organic matter (POM) was decomposed into dissolved organic carbon (DOC) in the overlying water, reaching the highest peak value of 1.82 g L−1 in the treatment added the high cyanobacteria biomass (470 g). After 18 days of incubation, the mineralization of increased DOC to dissolved inorganic carbon (DIC) maintained a high DIC level of overlying water in treatments added cyanobacteria biomass. The treatment added the medium cyanobacteria biomass (235 g) presented the lower DOC/total dissolved carbon ratio than the high cyanobacteria biomass associated with the lower mineralization from DOC to DIC. Due to the concentration differences of DIC at water-sediment interface, the main migration of DIC from pore water to overlying water occurred in the treatment without added cyanobacteria biomass. However, the treatments added the cyanobacteria biomass presented the obvious diffusion of DOC and the low migration of DIC at the water-sediment interface. The diffusive fluxes of DOC at the water-sediment interface increased with the cyanobacteria biomass added, reaching the maximum value of 411.01 mg/(m2·d) in the treatment added the high cyanobacteria biomass. In the overlying water, the group added the sediment and medium cyanobacteria biomass presented a faster degradation of cyanobacteria-derived POM to DOC and a higher mineralization level of DOC to DIC than added the medium cyanobacteria biomass without sediment. Therefore, during accumulated cyanobacteria decomposition, the biomass of accumulated cyanobacteria and sediment property can influence the migration and transformation of DC, playing an important role in carbon cycling in shallow eutrophic lakes.
Right ventricular function in infants with bronchopulmonary dysplasia and pulmonary hypertension: a pilot study

Premature birth and bronchopulmonary dysplasia (BPD) are risk factors for the development of echocardiographic signs of pulmonary hypertension (PH) and are associated with changes in cardiac structure and function. It is unclear whether this association persists beyond early infancy. The aims of this study are to prospectively investigate the prevalence of PH in children with severe BPD and to investigate the effect of BPD and PH on myocardial structure and function at six months corrected age. Preterm infants (gestational age ≤ 32 weeks) with severe BPD were included. Echocardiography was used to define PH and to measure speckle tracking derived longitudinal and circumferential strain of the left ventricle (LV) and right ventricle (RV). Sixty-nine infants with a median (interquartile range [IQR]) gestational age of 25.6 (24.9–26.4) weeks and a median birthweight of 770 (645–945) gram were included. Eight (12%) infants had signs of PH at six months corrected age. RV fractional area change was lower in infants with severe BPD and PH at six months compared to infants without PH (35% ± 9% vs. 43% ± 9%, P = 0.03). RV mean longitudinal systolic strain was lower in infants with severe BPD and PH compared to infants without PH (17.6% [−19.5%/−16.1%] vs. −20.9% [−25.9%/−17.9%], P = 0.04). RV size and LV longitudinal and circumferential strain in children with BPD with or without PH were similar. Signs of PH were found in 12% of infants with severe BPD at six months corrected age and the presence of PH is associated with reduced RV systolic function.
Sunflower resistance to multiple downy mildew pathotypes revealed by recognition of conserved effectors of the oomycete Plasmopara halstedii

Summary Over the last 40 years, new sunflower downy mildew isolates (Plasmopara halstedii) have overcome major gene resistances in sunflower, requiring the identification of additional and possibly more durable broad‐spectrum resistances. Here, 354 RXLR effectors defined in silico from our new genomic data were classified in a network of 40 connected components sharing conserved protein domains. Among 205 RXLR effector genes encoding conserved proteins in 17 P. halstedii pathotypes of varying virulence, we selected 30 effectors that were expressed during plant infection as potentially essential genes to target broad‐spectrum resistance in sunflower. The transient expression of the 30 core effectors in sunflower and in Nicotiana benthamiana leaves revealed a wide diversity of targeted subcellular compartments, including organelles not so far shown to be targeted by oomycete effectors such as chloroplasts and processing bodies. More than half of the 30 core effectors were able to suppress pattern‐triggered immunity in N. benthamiana, and five of these induced hypersensitive responses (HR) in sunflower broad‐spectrum resistant lines. HR triggered by PhRXLRC01 co‐segregated with Pl22 resistance in F3 populations and both traits localized in 1.7 Mb on chromosome 13 of the sunflower genome. Pl22 resistance was physically mapped on the sunflower genome recently sequenced, unlike all the other downy mildew resistances published so far. PhRXLRC01 and Pl22 are proposed as an avirulence/resistance gene couple not previously described in sunflower. Core effector recognition is a successful strategy to accelerate broad‐spectrum resistance gene identification in complex crop genomes such as sunflower.
When User Experience Designers Partner with Data Scientists

The increasing capacity to capture and feed behavioral data for systems to learn is transforming the design of user experiences. In this paper, we discuss two effects of this emerging toolkit. On the one hand, creating experiences with learning algorithms is pushing designers to consider how users begin, evolve, and end their interactions, which themselves produce and consume data. On the other hand, the design of experiences powered by machine learning is now occurring in new, multidisciplinary teams, which presents a variety of frictions and opportunities for misunderstandings which must be overcome. We discuss the similarities and differences in the methods that designers and data scientists use in their work, and conclude with a series of touch points and principles that partnerships between designers and data scientists can consider for productive relationships.
European Lone Actor Terrorists Versus “Common” Homicide Offenders: An Empirical Analysis

The term “Lone Actor” has been applied to a variety of violent individuals who are thought to act out of ideological motivations using terrorist tactics. So far, much of the research is U.S.-based. There is an empirical vacuum of Lone Actor violence in Europe and a conceptual gap in how these acts may be understood as a variation of homicidal behavior. We examine and compare characteristics of European Lone Actors to European “common” homicide offenders. Lone Actor terrorists constitute a heterogeneous group that is similar to homicide offenders but differs in terms of substance use, weapon use, and target. These findings may be understood in the context of instrumental versus expressive aims.
Extinction of Fear Memory Attenuates Conditioned Cardiovascular Fear Reactivity

Post-traumatic stress disorder (PTSD) is characterized by a heightened emotional and physiological state and an impaired ability to suppress or extinguish traumatic fear memories. Exaggerated physiological responses may contribute to increased cardiovascular disease (CVD) risk in this population, but whether treatment for PTSD can offset CVD risk remains unknown. To further evaluate physiological correlates of fear learning, we used a novel pre-clinical conditioned cardiovascular testing paradigm and examined the effects of Pavlovian fear conditioning and extinction training on mean arterial pressure (MAP) and heart rate (HR) responses. We hypothesized that a fear conditioned cardiovascular response could be detected in a novel context and attenuated by extinction training. In a novel context, fear conditioned mice exhibited marginal increases in MAP (∼3 mmHg) and decreases in HR (∼20 bpm) during CS presentation. In a home cage context, the CS elicited significant increases in both HR (100 bpm) and MAP (20 mmHg). Following extinction training, the MAP response was suppressed while CS-dependent HR responses were variable. These pre-clinical data suggest that extinction learning attenuates the acute MAP responses to conditioned stimuli over time, and that MAP and HR responses may extinguish at different rates. These results suggest that in mouse models of fear learning, conditioned cardiovascular responses are modified by extinction training. Understanding these processes in pre-clinical disease models and in humans with PTSD may be important for identifying interventions that facilitate fear extinction and attenuate hyper-physiological responses, potentially leading to improvements in the efficacy of exposure therapy and PTSD–CVD comorbidity outcomes.
Association of Long-term Ambient Black Carbon Exposure and Oxidative Stress Allelic Variants With Intraocular Pressure in Older Men

Importance Elevated intraocular pressure is a major risk factor for glaucoma, a leading cause of irreversible blindness worldwide. Environmental air pollution has been suggested as a potential contributor to elevated intraocular pressure; however, no studies have demonstrated such an association to date. Objective To investigate the association of long-term ambient black carbon exposure with intraocular pressure in community-dwelling older adults. Design, Setting, and Participants This population-based analysis, conducted from October 18, 2017, through March 22, 2018, used data from the all-male, New England–based Normative Aging Study of the US Department of Veterans Affairs. The analysis included 419 older men with a total of 911 follow-up study visits between January 1, 2000, and December 30, 2011. Intraocular pressure was measured by Goldmann applanation tonometry during the study visits. Validated spatiotemporal models were used to generate 1-year black carbon exposure levels at the addresses of the participants. Main Outcomes and Measures An independently developed genetic score approach was used to calculate allelic risk scores for 3 pathways associated with black carbon toxicity: endothelial function, oxidative stress, and metal processing. The associations among black carbon exposure, allelic risk scores, and intraocular pressure were explored using linear mixed-effects models. Results All 419 participants were men with a mean (SD) age of 75.3 (6.9) years. The mean (SD) 1-year black carbon exposure was 0.51 (0.18) &mgr;g/m3, and the mean (SD) intraocular pressure for the left eye was 14.1 (2.8) mm Hg and for the right eye was 14.1 (3.0) mm Hg. Of the 911 visits, 520 (57.1%) had a high endothelial function allelic risk score, 644 (70.7%) had a high metal-processing allelic risk score, and 623 (68.4%) had a high oxidative stress allelic risk score. In fully adjusted linear mixed-effects models, the association of black carbon with intraocular pressure was greater in individuals with a high oxidative stress allelic score (&bgr; = 0.36; 95% CI, 0.003-0.73) compared with individuals with a low score (&bgr; = −0.35; 95% CI, −0.86 to 0.15). Conclusions and Relevance Ambient black carbon exposure may be a risk factor for increased intraocular pressure in individuals susceptible to other biological oxidative stressors. If additional studies confirm these results, monitoring ambient black carbon exposure and physiological oxidative stress may prevent the development and progression of intraocular pressure–related disease.
In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using short‐lifetime near‐infrared dyes and time‐gated imaging

We introduce a simple new approach for time‐resolved multiplexed analysis of complex systems using near‐infrared (NIR) dyes, applicable to in vitro and in vivo studies. We show that fast and precise in vitro quantification of NIR fluorophores' short (subnanosecond) lifetime and stoichiometry can be done using phasor analysis, a computationally efficient and user‐friendly representation of complex fluorescence intensity decays obtained with pulsed laser excitation and time‐gated camera imaging. We apply this approach to the study of binding equilibria by Förster resonant energy transfer using two different model systems: primary/secondary antibody binding in vitro and ligand/receptor binding in cell cultures. We then extend it to dynamic imaging of the pharmacokinetics of transferrin engagement with the transferrin receptor in live mice, elucidating the kinetics of differential transferrin accumulation in specific organs, straightforwardly differentiating specific from nonspecific binding. Our method, implemented in a freely‐available software, has the advantage of time‐resolved NIR imaging, including better tissue penetration and background‐free imaging, but simplifies and considerably speeds up data processing and interpretation, while remaining quantitative. These advances make this method attractive and of broad applicability for in vitro and in vivo molecular imaging and could be extended to applications as diverse as image‐guided surgery or optical tomography.
An Online Attention-based Model for Speech Recognition

Attention-based end-to-end models such as Listen, Attend and Spell (LAS), simplify the whole pipeline of traditional automatic speech recognition (ASR) systems and become popular in the field of speech recognition. In previous work, researchers have shown that such architectures can acquire comparable results to state-of-the-art ASR systems, especially when using a bidirectional encoder and global soft attention (GSA) mechanism. However, bidirectional encoder and GSA are two obstacles for real-time speech recognition. In this work, we aim to stream LAS baseline by removing the above two obstacles. On the encoder side, we use a latency-controlled (LC) bidirectional structure to reduce the delay of forward computation. Meanwhile, an adaptive monotonic chunk-wise attention (AMoChA) mechanism is proposed to replace GSA for the calculation of attention weight distribution. Furthermore, we propose two methods to alleviate the huge performance degradation when combining LC and AMoChA. Finally, we successfully acquire an online LAS model, LC-AMoChA, which has only 3.5% relative performance reduction to LAS baseline on our internal Mandarin corpus.