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The SARS-CoV-2 virus is responsible for the novel coronavirus disease 2019 (COVID-19), which continues to spread to populations throughout the continental United States. Most state and local governments have adopted some level of “social distancing” policy, but infections have continued to spread despite these efforts. Absent a vaccine, authorities have few other tools by which to mitigate further spread of the virus. This begs the question of how effective social policy really is at reducing new infections that, left alone, would likely overwhelm the existing hospitalization capacity of many states. We developed a mathematical model that captures correlations between state-level “social distancing” policies and infection kinetics for all U.S. states, and use it to illustrate the link between social policy decisions, disease dynamics, and an effective reproduction number that changes over time, for case studies of Massachusetts, New Jersey, and Washington states. In general, our findings indicate that the potential for second waves of infection, which result after reopening states without an increase to immunity, can be mitigated by a return of social distancing policies as soon as possible after the waves are detected.

Diverse many-body systems, from soap bubbles to suspensions to polymers, learn and remember patterns in the drives that push them far from equilibrium. This learning may be leveraged for computation, memory, and engineering. Until now, many-body learning has been detected with thermodynamic properties, such as work absorption and strain. We progress beyond these macroscopic properties first defined for equilibrium contexts: We quantify statistical mechanical learning using representation learning, a machine-learning model in which information squeezes through a bottleneck. By calculating properties of the bottleneck, we measure four facets of many-body systems’ learning: classification ability, memory capacity, discrimination ability, and novelty detection. Numerical simulations of a classical spin glass illustrate our technique. This toolkit exposes self-organization that eludes detection by thermodynamic measures: Our toolkit more reliably and more precisely detects and quantifies learning by matter while providing a unifying framework for many-body learning.

An important sustainable development goal for any country is to ensure food security by producing a sufficient and safe food supply. This is the case for bovine milk where addition of non-dairy milks such as vegetables (e.g., soya or coconut) has become a common source of adulteration and fraud. Conventionally, gas chromatography techniques are used to detect key lipids (e.g., triacylglycerols) has an effective read-out of assessing milks origins and to detect foreign milks in bovine milks. However, such approach requires several sample preparation steps and a dedicated laboratory environment, precluding a high throughput process. To cope with this need, here, we aimed to develop a novel and simple method without organic solvent extractions for the detection of bovine and non-dairy milks based on lipids fingerprint by routine MALDI-TOF mass spectrometry (MS). The optimized method relies on the simple dilution of milks in water followed by MALDI-TOF MS analyses in the positive linear ion mode and using a matrix consisting of a 9:1 mixture of 2,5-dihydroxybenzoic acid and 2-hydroxy-5-methoxybenzoic acid (super-DHB) solubilized at 10 mg/mL in 70% ethanol. This sensitive, inexpensive, and rapid method has potential for use in food authenticity applications.

The sudden spread of COVID-19 infections in a region can catch its healthcare system by surprise. Can one anticipate such a spread and allow healthcare administrators to prepare for a surge a priori? We posit that the answer lies in distinguishing between two types of waves in epidemic dynamics. The first kind resembles a spatio-temporal diffusion pattern. Its gradual spread allows administrators to marshal resources to combat the epidemic. The second kind is caused by super-spreader events, which provide shocks to the disease propagation dynamics. Such shocks simultaneously affect a large geographical region and leave little time for the healthcare system to respond. We use time-series analysis and epidemiological model estimation to detect and react to such simultaneous waves using COVID-19 data from the time when the B.1.617.2 (Delta) variant of the SARS-CoV-2 virus dominated the spread. We first analyze India’s second wave from April to May 2021 that overwhelmed the Indian healthcare system. Then, we analyze data of COVID-19 infections in the United States (US) and countries with a high and low Indian diaspora. We identify the Kumbh Mela festival as the likely super-spreader event, the exogenous shock, behind India’s second wave. We show that a multi-area compartmental epidemiological model does not fit such shock-induced disease dynamics well, in contrast to its performance with diffusion-type spread. The insufficient fit to infection data can be detected in the early stages of a shock-wave propagation and can be used as an early warning sign, providing valuable time for a planned healthcare response. Our analysis of COVID-19 infections in the US reveals that simultaneous waves due to super-spreader events in one country (India) can lead to simultaneous waves in other places. The US wave in the summer of 2021 does not fit a diffusion pattern either. We postulate that international travels from India may have caused this wave. To support that hypothesis, we demonstrate that countries with a high Indian diaspora exhibit infection growth soon after India’s second wave, compared to countries with a low Indian diaspora. Based on our data analysis, we provide concrete policy recommendations at various stages of a simultaneous wave, including how to avoid it, how to detect it quickly after a potential super-spreader event occurs, and how to proactively contain its spread.

Despite the widespread use of oxytocin for induction of labor, mechanistic insights into fetal/neonatal wellbeing are lacking because of the absence of an animal model that recapitulates modern obstetric practice. Here, we create and validate a hi-fidelity pregnant rat model that mirrors labor induction with oxytocin in laboring women. The model consists of an implantable preprogrammed microprocessor-controlled infusion pump that delivers a gradually escalating dose of intravenous oxytocin to induce birth at term gestation. We validated the model with molecular biological experiments on the uterine myometrium and telemetry-supported assessment of changes in intrauterine pressure. Finally, we applied this model to test the hypothesis that labor induction with oxytocin would be associated with oxidative stress in the newborn brain. Analysis of biomarkers of oxidative stress and changes in the expression of associated genes were no different between oxytocin-exposed and saline-treated pups, suggesting that oxytocin-induced labor was not associated with oxidative stress in the developing brain. Collectively, we provide a viable and realistic animal model for labor induction and augmentation with oxytocin that would enable new lines of investigation related to the impact of perinatal oxytocin exposure on the mother-infant dyad.

International audience; The hair bundle of cochlear hair cells is the site of auditory mechanoelectrical transduction. It is formed by three rows of stiff microvilli-like protrusions of graduated heights, the short, middle-sized, and tall stereocilia. In developing and mature sensory hair cells, stereocilia are connected to each other by various types of fibrous links. Two unconventional cadherins, protocadherin-15 (PCDH15) and cadherin-23 (CDH23), form the tip-links, whose tension gates the hair cell mechanoelectrical transduction channels. These proteins also form transient lateral links connecting neighboring stereocilia during hair bundle morphogenesis. The proteins involved in anchoring these diverse links to the stereocilia dense actin cytoskeleton remain largely unknown. We show that the long isoform of whirlin (L-whirlin), a PDZ domain-containing submembrane scaffold protein, is present at the tips of the tall stereocilia in mature hair cells, together with PCDH15 isoforms CD1 and CD2; L-whirlin localization to the ankle-link region in developing hair bundles moreover depends on the presence of PCDH15-CD1 also localizing there. We further demonstrate that L-whirlin binds to PCDH15 and CDH23 with moderate-to-high affinities in vitro. From these results, we suggest that L-whirlin is part of the molecular complexes bridging PCDH15-, and possibly CDH23-containing lateral links to the cytoskeleton in immature and mature stereocilia. The sensory cells of the cochlea (inner and outer hair cells) convert acoustic waves into receptor potentials by the process of mechanoelectrical transduction (MET) 1,2. This process takes place in the hair bundle, a mechanosensi-tive antenna formed by thick and stiff microvilli-like protrusions called stereocilia, organized in three rows of graduated height (i.e., short, middle-sized, and tall stereocilia) at the apical surface of the hair cells. Stereocilia are connected, within and between rows, by various types of fibrous links, expressed both in the developing and the mature cochlea. According to the current view of the MET process, cationic transducer channels located at the tips of short and middle-sized stereocilia 3 are gated by the sound-evoked periodic tension of the tip link, an open

Canine atopic dermatitis (cAD) is a common hereditary clinical syndrome in domestic dogs with no definitive diagnostic tests, which causes marked morbidity and has a high economic impact internationally. We created a novel questionnaire for Labrador (LR) and Golden retriever (GR) owners to evaluate canine skin health with respect to clinical signs of cAD. 4,111 dogs had fully completed questionnaires (2,803 LR; 1,308 GR). ‘Cases’ (793) had a reported veterinary diagnosis of cAD, and ‘controls’ (1652) had no current or past clinical signs of cAD and were aged >3 years. Remaining dogs (1666) were initially categorised as ‘Other’. Simulated annealing was used comparing ‘Cases’ and ‘Others’ to select a novel set of features able to classify a known case. Two feature sets are proposed, one for use on first evaluation and one for dogs with a history of skin problems. A sum for each list when applied to the whole population (including controls) was able to classify ‘Cases’ with a sensitivity of 89% to 94% and specificity of 71% to 69%, respectively, and identify potentially undiagnosed cases. Our findings demonstrate for the first time that owner questionnaire data can be reliably used to aid in the diagnostic process of cAD.

A temporal decline in human and dog sperm quality is thought to reflect a common environmental aetiology. This may reflect direct effects of seminal chemicals on sperm function and quality. Here we report the effects of diethylhexyl phthalate (DEHP) and polychlorinated biphenyl 153 (PCB153) on DNA fragmentation and motility in human and dog sperm. Human and dog semen was collected from registered donors (n = 9) and from stud dogs (n = 11) and incubated with PCB153 and DEHP, independently and combined, at 0x, 2x, 10x and 100x dog testis concentrations. A total of 16 treatments reflected a 4 × 4 factorial experimental design. Although exposure to DEHP and/or PCB153 alone increased DNA fragmentation and decreased motility, the scale of dose-related effects varied with the presence and relative concentrations of each chemical (DEHP.PCB interaction for: DNA fragmentation; human p

Our objectives were to assess the prevalence of cardiometabolic complications in children, adolescents, and young adult survivors of childhood acute lymphoblastic leukemia (cALL), to identify their predictors and the risk compared to the Canadian population. We performed a cardiometabolic assessment of cALL survivors from the PETALE cohort (n = 247, median age at visit of 21.7 years). In our group, overweight and obesity affected over 70% of women. Pre-hypertension and hypertension were mostly common in men, both adults (20%) and children (19%). Prediabetes was mainly present in women (6.1% of female adult survivors) and 41.3% had dyslipidemia. Cranial radiation therapy was a predictor of dyslipidemia (RR: 1.60, 95% CI: 1.07–2.41) and high LDL-cholesterol (RR: 4.78, 95% CI: 1.72–13.28). Male gender was a predictor for pre-hypertension and hypertension (RR: 5.12, 95% CI: 1.81–14.46). Obesity at the end of treatment was a predictor of obesity at interview (RR: 2.07, 95% CI: 1.37–3.14) and of metabolic syndrome (RR: 3.04, 95% CI: 1.14–8.09). Compared to the general population, cALL survivors were at higher risk of having the metabolic syndrome, dyslipidemia, pre-hypertension/hypertension and high LDL-cholesterol, while the risk for obesity was not different. Our results support the need for early screening and lifestyle intervention in this population.

TNFα is a homotrimeric pro-inflammatory cytokine, whose direct targeting by protein biotherapies has been an undeniable success for the treatment of chronic inflammatory diseases. Despite many efforts, no orally active drug targeting TNFα has been identified so far. In the present work, we identified through combined in silico/in vitro/in vivo approaches a TNFα direct inhibitor, compound 1, displaying nanomolar and micromolar range bindings to TNFα. Compound 1 inhibits the binding of TNFα with both its receptors TNFRI and TNFRII. Compound 1 inhibits the TNFα induced apoptosis on L929 cells and the TNFα induced NF-κB activation in HEK cells. In vivo, oral administration of compound 1 displays a significant protection in a murine TNFα-dependent hepatic shock model. This work illustrates the ability of low-cost combined in silico/in vitro/in vivo screening approaches to identify orally available small-molecules targeting challenging protein-protein interactions such as homotrimeric TNFα.

Scientific Reports 7: Article number: 41662; published online: 06 February 2017; updated: 28 April 2017 This Article contains typographical errors. In the results section under subheading ‘The C-terminal domain adopts an immunoglobulin fold in solution’, “A search for structurally similar proteins possessing using the Dali server identified many proteins containing an Ig-like fold, including immunoglobulin receptors, fibroblast growth factor receptors and the T-cell surface glycoprotein CD4.

Adverse temporal trends in human semen quality and cryptorchidism in infants have been associated with exposure to environmental chemicals (ECs) during development. Here we report that a population of breeding dogs exhibit a 26 year (1988-2014) decline in sperm quality and a concurrent increased incidence of cryptorchidism in male offspring (1995-2014). A decline in the number of males born relative to the number of females was also observed. ECs, including diethylhexyl phthalate (DEHP) and polychlorinated biphenyl 153 (PCB153), were detected in adult dog testes and commercial dog foods at concentrations reported to perturb reproductive function in other species. Testicular concentrations of DEHP and PCB153 perturbed sperm viability, motility and DNA integrity in vitro but did not affect LH stimulated testosterone secretion from adult testis explants. The direct effects of chemicals on sperm may therefore contribute to the decline in canine semen quality that parallels that reported in the human.

Adverse temporal trends in human semen quality and cryptorchidism in infants have been associated with exposure to environmental chemicals (ECs) during development. Here we report that a population of breeding dogs exhibit a 26 year (1988–2014) decline in sperm quality and a concurrent increased incidence of cryptorchidism in male offspring (1995–2014). A decline in the number of males born relative to the number of females was also observed. ECs, including diethylhexyl phthalate (DEHP) and polychlorinated biphenyl 153 (PCB153), were detected in adult dog testes and commercial dog foods at concentrations reported to perturb reproductive function in other species. Testicular concentrations of DEHP and PCB153 perturbed sperm viability, motility and DNA integrity in vitro but did not affect LH stimulated testosterone secretion from adult testis explants. The direct effects of chemicals on sperm may therefore contribute to the decline in canine semen quality that parallels that reported in the human.

The domestic dog is one of our most popular companions and longest relationships, occupying different roles, from pet to working guide dog for the blind. As dogs age different behavioural issues occur and in some cases dogs may be relinquished or removed from their working service. Here we analyse a dataset on working guide dogs that were removed from their service between 1994 and 2013. We use the withdrawal reasons as a proxy for the manifestation of undesirable behaviour. More than 7,500 dogs were in the dataset used, 83% of which were retired (due to old age) and 17% were withdrawn for behavioural issues. We found that the main reasons for behaviour withdrawal were environmental anxiety, training and fear/aggression. Breed and sex had an effect on the odds of dogs being withdrawn under the different reasons. The age at withdrawal for the different withdrawal reasons suggested that dogs were more likely to develop fear/aggression related issues early on, whilst issues related to training could develop at almost any age. We found no evidence for heterosis effecting behaviour. We believe that this work is relevant to the pet dog population and had implications for understanding ageing and genetic influences on behaviour.

Recent paleoclimate reconstructions have challenged the traditional view that Northern Hemisphere insolation and associated feedbacks drove synchronous global climate and ice-sheet volume during the last glacial cycle. Here we focus on the response of the Patagonian Ice Sheet, and demonstrate that its maximum expansion culminated at 28,400 ± 500 years before present (28.4 ± 0.5 ka), more than 5,000 years before the minima in 65°N summer insolation and the formally-defined Last Glacial Maximum (LGM) at 21,000 ± 2,000 years before present. To investigate the potential drivers of this early LGM (eLGM), we simulate the effects of orbital changes using a suite of climate models incorporating prescribed and evolving sea-ice anomalies. Our analyses suggest that Antarctic seaice expansion at 28.5 ka altered the location and intensity of the Southern Hemisphere storm track, triggering regional cooling over Patagonia of 5°C that extends across the wider mid-southern latitudes. In contrast, at the LGM, continued sea-ice expansion reduced regional temperature and precipitation further, effectively starving the ice sheet and resulting in reduced glacial expansion. Our findings highlight the dominant role that orbital changes can play in driving Southern Hemisphere glacial climate via the sensitivity of mid-latitude regions to changes in Antarctic sea-ice extent. The Last Glacial Maximum (LGM) – traditionally defined from sea level records as having taken place between 23,000 and 19,000 calendar years ago – was apparently driven by insolation changes at 65°N 1,2 , and reflects the period when the world’s ice sheets reached their maximum extents, locking up the greatest volume of ocean water 1 . However, as sea level is an integrated signal, it cannot be used to distinguish globally synchronous ice-sheet maxima from the variable regional ice sheet maxima that may provide critical insights into the mechanisms of regional and hemispheric climate change.

International audience; The lysine and glutamic acid rich protein KERP1 is a unique surface adhesion factor associated with virulence in the human pathogen Entamoeba histolytica. Both the function and structure of this protein remain unknown to this date. Here, we used circular dichroism, analytical ultracentrifugation and bioinformatics modeling to characterize the structure of KERP1. Our findings revealed that it is an α-helical rich protein organized as a trimer, endowed with a very high thermal stability (Tm = 89.6°C). Bioinformatics sequence analyses and 3D-structural modeling indicates that KERP1 central segments could account for protein trimerization. Relevantly, expressing the central region of KERP1 in living parasites, impair their capacity to adhere to human cells. Our observations suggest a link between the inhibitory effect of the isolated central region and the structural features of KERP1.

In the late twentieth century, the sub-thermocline waters of the southern tropical and subtropical Indian Ocean experienced a sharp cooling. This cooling has been previously attributed to an anthropogenic aerosol-induced strengthening of the global ocean conveyor, which transfers heat from the subtropical gyre latitudes toward the North Atlantic. From the mid-1990s the sub-thermocline southern Indian Ocean experienced a rapid temperature trend reversal. Here we show, using climate models from phase 5 of the Coupled Model Intercomparison Project, that the late twentieth century sub-thermocline cooling of the southern Indian Ocean was primarily driven by increasing anthropogenic aerosols and greenhouse gases. The models simulate a slow-down in the sub-thermocline cooling followed by a rapid warming towards the mid twenty-first century. The simulated evolution of the Indian Ocean temperature trend is linked with the peak in aerosols and their subsequent decline in the twenty-first century, reinforcing the hypothesis that aerosols influence ocean circulation trends. O cean warming is a key signature of climate change, with the oceans accounting for more than 90% of the Earth’s warming since the 1950s 1 . Warming in the upper 700 m over 1960–1999 ranges from 0.04–