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The ocular surface microbiome is altered in certain disease states. The aim of this study was to characterize the bovine bacterial ocular surface microbiome (BBOSM) in the context of ocular squamous cell carcinoma (OSCC). The conjunctiva of normal (n = 28) and OSCC (n = 10) eyes of cows aged 2 to 13 years from two farms in Louisiana and Wyoming were sampled using individual sterile swabs. DNA extraction followed by 16S ribosomal ribonucleic acid (rRNA) gene sequencing and real-time polymerase chain reaction (RT-PCR) were performed to, respectively, assess the relative and absolute BBOSM. Discriminant analysis (DA) was performed using RT-PCR data, and relative abundance analysis was performed using 16S rRNA gene sequencing data. The 11 most abundant phyla in both normal and OSCC-affected cows were identified using 16S rRNA gene sequencing analysis. The relative abundance of Euryarchaeota was found to be significantly lower (p = 0.0372) in OSCC eyes compared to normal eyes. Relative abundance differences within and between geographic locations were also identified. Quadratic DA categorized samples as OSCC or normal with 100% sensitivity and 83.3–100% specificity. Relative abundance analysis identified relative BBOSM phylum alterations in OSCC. Quadratic DA can be used to accurately categorize BBOSM from normal and OSCC ocular surface samples.

Tropical deforestation can have a significant effect on climate, but research attention has been directed mostly towards Amazonian deforestation. The southern part of West Africa (a region dependent on rain-fed agriculture and vulnerable to droughts and flooding) has seen significant deforestation since the 1950s. Many previous tropical deforestation studies have used idealized and exaggerated deforestation scenarios and parameterized convection models. In this study we estimate for the first time realistic historical deforestation from the Land-Use Harmonization dataset in West Africa and simulate the impacts in a 5 d ensemble forecast in June using a convection-permitting regional climate model. We find that sensible heat flux increases at the expense of latent heat flux in most deforested regions, and rainfall increases by an average of 8.4 % over deforested pixels from 18:00–06:00 UTC, whereas changes are much less pronounced during the day. Over large areas of deforestation approx. 300 km inland (e.g. west Guinea) the roughness-length and thermally enhanced convergence during the afternoon and evening occurs over the deforested areas resulting in increases in rainfall with little impact from reduced daytime humidity. In areas of coastal deforestation (e.g. Côte d'Ivoire), increased winds drive the sea breeze convection inland, resulting in evening rainfall reductions over the deforested area but increases further inland, in line with observations. We suggest our results would not be replicated in parameterized convection models, which are known to struggle with capturing peak convective activity in the late afternoon and long-lived nocturnal rainfall and with reproducing observed surface–rainfall feedbacks.

We studied the effect of feeding a single probiotic Limosilactobacillus reuteri DSM 17938 (LR 17938) on the luminal and plasma levels of amino acids and their derivatives in the suckling newborn mouse, using gas chromatography and high-performance liquid chromatography. We found that LR 17938 increased the relative abundance of many amino acids and their derivatives in stool, while it simultaneously significantly reduced the plasma levels of three amino acids (serine, citrulline, and taurine). Many peptides and dipeptides were increased in stool and plasma, notably gamma-glutamyl derivatives of amino acids, following ingestion of the LR 17938. Gamma-glutamyl transformation of amino acids facilitates their absorption. LR 17938 significantly upregulated N-acetylated amino acids, the levels of which could be useful biomarkers in plasma and warrant further investigation. Specific fecal microbiota were associated with higher levels of fecal amino acids and their derivatives. Changes in luminal and circulating levels of amino acid derivatives, polyamines, and tryptophan metabolites may be mechanistically related to probiotic efficacy.

Projections of future West African monsoon (WAM) precipitation change in response to increasing greenhouse gases are uncertain, and an improved understanding of the drivers of WAM precipitation change is needed to help aid model development and better inform adaptation policies in the region. This paper addresses one of those drivers, the direct radiative effect of increased CO2 (i.e., the impact of increased CO2 in the absence of SST warming and changes in plant physiology). An atmosphere-only model is used to examine both the equilibrium response and the evolution of the change over the days following the instantaneous CO2 increase. In response to the direct radiative effect, WAM precipitation increases due to a weakening of the shallow meridional circulation over North Africa, advecting less dry air into the convective column associated with the monsoon. Changes in the shallow circulation are associated with atmospheric and surface warming patterns over North Africa. A large-scale atmospheric warming pattern, whereby North Africa warms more than the monsoon region, leads to a northward shift in the Saharan heat low. In response to increased precipitation in the Sahel, local soil moisture feedbacks play a key role in determining the low-level circulation change and the location of the intertropical discontinuity. The large-scale warming patterns over North Africa result from differing levels of constraint applied by convective quasi-equilibrium. While this constraint acts strongly in the equatorial WAM region, preventing the region from warming in response to the direct radiative effect, North Africa is not strongly constrained and is therefore able to warm.

Intraseasonal soil moisture variability has the potential to feed back onto the West Africa monsoon circulation through its influence on surface turbulent fluxes and planetary boundary-layer characteristics. Using satellite observations and an atmospheric reanalysis, we investigate intraseasonal soil moisture-atmosphere feedbacks triggered by large-scale dynamics within the West African monsoon. Surprisingly, even though the surface response across the Sahel to strong convection is short-lived (days) and precipitation accumulations are spatially and temporally heterogeneous, a coherent regional-scale surface response to intraseasonal variability is observed. This surface response then feeds back onto the West African monsoon circulation. For example, during a dry intraseasonal event, Sahelian surface soil moisture significantly decreases, which elevates surface temperatures by 1.5°C and shifts the monsoon circulation southward by approximately 1.5° latitude. During a wet event meanwhile, the surface moistens and cools which leads to a northward monsoon shift. Alongside a low-level wind response, the African Easterly Jet (AEJ) also responds to surface changes due to variations in the meridional temperature gradient. For example, an increased temperature gradient during a dry event intensifies and shifts the AEJ southward. The combined response of low-level monsoon westerlies and the AEJ impacts low-level shear and characteristics of strong convection. Elevated low-level shear during a dry event promotes an intensification of deep convection across southern West Africa. This study provides new insight into the sensitivity of the West African monsoon circulation to intraseasonal soil moisture feedbacks and encourages similar research in other regions. An improved understanding and model representation of soil moisture-atmosphere feedbacks has the potential to improve forecasts beyond daily timescales and enhance early warning systems.

Africa is poised for a revolution in the quality and relevance of weather predictions, with potential for great benefits in terms of human and economic security. This revolution will be driven by recent international progress in nowcasting, numerical weather prediction, theoretical tropical dynamics, and forecast communication, but will depend on suitable scientific investment being made. The commercial sector has recognized this opportunity and new forecast products are being made available to African stakeholders. At this time, it is vital that robust scientific methods are used to develop and evaluate the new generation of forecasts. The Global Challenges Research Fund (GCRF) African Science for Weather Information and Forecasting Techniques (SWIFT) project represents an international effort to advance scientific solutions across the fields of nowcasting, synoptic and short-range severe weather prediction, subseasonal-to-seasonal (S2S) prediction, user engagement, and forecast evaluation. This paper describes the opportunities facing African meteorology and the ways in which SWIFT is meeting those opportunities and identifying priority next steps. Delivery and maintenance of weather forecasting systems exploiting these new solutions requires a trained body of scientists with skills in research and training, modeling and operational prediction, and communications and leadership. By supporting partnerships between academia and operational agencies in four African partner countries, the SWIFT project is helping to build capacity and capability in African forecasting science. A highlight of SWIFT is the coordination of three weather forecasting “Testbeds”—the first of their kind in Africa—which have been used to bring new evaluation tools, research insights, user perspectives, and communications pathways into a semioperational forecasting environment.

International audience; Due to associated hydrological risks, there is an urgent need to provide plausible quantified changes in future extreme rainfall rates. Convection-permitting (CP) climate simulations represent a major advance in capturing extreme rainfall and its sensitivities to atmospheric changes under global warming. However, they are computationally costly, limiting uncertainty evaluation in ensembles and covered time periods. This is in contrast to the Climate Model Intercomparison Project (CMIP) 5 and 6 ensembles, which cannot capture relevant convective processes, but provide a range of plausible projections for atmospheric drivers of rainfall change. Here, we quantify the sensitivity of extreme rainfall within West African storms to changes in atmospheric rainfall drivers, using both observations and a CP projection representing a decade under the Representative Concentration Pathway 8.5 around 2100. We illustrate how these physical relationships can then be used to reconstruct better-informed extreme rainfall changes from CMIP, including for time periods not covered by the CP model. We find reconstructed hourly extreme rainfall over the Sahel increases across all CMIP models, with a plausible range of 37%–75% for 2070–2100 (mean 55%, and 18%–30% for 2030–2060). This is considerably higher than the +0–60% (mean +30%) we obtain from a traditional extreme rainfall metric based on raw daily CMIP rainfall, suggesting such analyses can underestimate extreme rainfall intensification. We conclude that process-based rainfall scaling is a useful approach for creating time-evolving rainfall projections in line with CP model behaviour, reconstructing important information for medium-term decision making. This approach also better enables the communication of uncertainties in extreme rainfall projections that reflect our current state of knowledge on its response to global warming, away from the limitations of coarse-scale climate models alone.

Previous studies have suggested that the recent increase in tropical extreme deep convection, in particular over Asia and Africa during the boreal summer, has occurred in association with cooling in the tropical lower stratosphere. The present study is focused on the Sahel region of West Africa, where an increased occurrence of extreme precipitation events has been reported over recent decades. The results indicate that the changes over West Africa since the 1980s involve a cooling trend in the tropical lower stratosphere and tropopause layer, combined with warming in the troposphere. This feature is similar to that which might result from increased greenhouse-gas levels but is distinct from the interannual variation of precipitation associated with the transport of water vapor from the Atlantic Ocean. It is suggested that the decrease in the vertical temperature gradient in the tropical tropopause region enhances extreme deep convection over the Sahel, where penetrating convection is frequent, whereas tropospheric warming suppresses the shallower convection over the Guinea Coast. Therefore, the essential feature of the recent changes over West Africa is the depth of convection rather than the total amount of surface precipitation.

Pan-Africa convection-permitting regional climate model simulations have been performed to study the impact of high resolution and the explicit representation of atmospheric moist convection on the present and future climate of Africa. These unique simulations have allowed European and African climate scientists to understand the critical role that the representation of convection plays in the ability of a contemporary climate model to capture climate and climate change, including many impact-relevant aspects such as rainfall variability and extremes. There are significant improvements in not only the small-scale characteristics of rainfall such as its intensity and diurnal cycle, but also in the large-scale circulation. Similarly, effects of explicit convection affect not only projected changes in rainfall extremes, dry spells, and high winds, but also continental-scale circulation and regional rainfall accumulations. The physics underlying such differences are in many cases expected to be relevant to all models that use parameterized convection. In some cases physical understanding of small-scale change means that we can provide regional decision-makers with new scales of information across a range of sectors. We demonstrate the potential value of these simulations both as scientific tools to increase climate process understanding and, when used with other models, for direct user applications. We describe how these ground-breaking simulations have been achieved under the U.K. Government’s Future Climate for Africa Programme. We anticipate a growing number of such simulations, which we advocate should become a routine component of climate projection, and encourage international coordination of such computationally and human-resource expensive simulations as effectively as possible.

A coherent synoptic sequence, mostly over North Africa, is identified whereby an upper-level midlatitude trough (in November–March) excites several days of quasi-stationary near-surface warming across the Sahara, leading to rainfall events over northern Congo (NC), and perturbed weather more widely. Ahead of NC rainfall events, composite sequences first identify troughs for several days near Iberia, followed by relatively quick transfer to the Central Mediterranean (CMed). Iberia and CMed daily trough-strength indices reveal that both lead to warming and NC rainfall. Iberia trough linkages develop through West Africa and take longer to reach NC, while CMed linkages reach NC faster (2–3 days), with impact extent focused mostly south and east of CMed. Building up to the rainfall events, initial warming over the central Sahara migrates southeastward close to NC, ultimately with typical magnitude of about 1–2°C at 10–15°N. Such anomalies are statistically predictive for NC daily rainfall and associated nearby atmospheric features: anomalous low-level southerly wind and increased moisture; anomalous low-level westerly wind and vertical easterly shear to 600 hPa; increased mid-level moisture (600 hPa), which along with low-level moisture, connects northward into midlatitudes. A secondary route identified by which Iberia troughs can impact NC rainfall is through direct atmospheric teleconnection with precipitation to the west of NC, and subsequent migration of that convection eastward into NC. The eastern side of NC generally shows a small lag on western parts, and links more strongly to CMed troughs. Taken together, the lagged synoptic expression of Iberia and CMed troughs is widespread over several days, including much of North Africa (to equatorial latitudes), southwestern Asia, eastern Africa and the western Indian Ocean. Overall, these results can contribute to situational awareness for weather forecasters across the zones influenced by the troughs, while also providing a framework for climate timescale analyses.

Treg deficiency causes a lethal, CD4(+) T cell-driven autoimmune disease called IPEX syndrome (immunodysregulation, polyendocrinopathy, and enteropathy, with X-linked inheritance) in humans and in the scurfy (SF) mouse, a mouse model of the disease. Feeding Limosilactobacillus reuteri DSM 17938 (LR 17938, LR) to SF mice reprograms the gut microbiota, reduces disease progression, and prolongs lifespan. However, the efficacy and mechanism of LR, compared with other probiotics, in producing these effects is unknown. We compared LR with Lacticaseibacillus rhamnosus GG (LGG), an extensively investigated probiotic. LR was more effective than LGG in prolonging survival. Both probiotics restored the fecal microbial alpha diversity, but they produced distinct fecal bacterial clusters and differentially modulated microbial relative abundance (RA). LR increased the RA of phylum_Firmicutes, genus_Oscillospira whereas LR reduced phylum_Bacteroidetes, genus_Bacteroides and genus_Parabacteroides, reversing changes attributed to the SF phenotype. LGG primarily reduced the RA of genus_Bacteroides. Both LR and LGG reduced the potentially pathogenic taxon class_γ-proteobacteria. Plasma metabolomics revealed substantial differences among 696 metabolites. We observed similar changes of many clusters of metabolites in SF mice associated with treatment with either LR or LGG. However, a unique effect of LR was to increase the abundance of plasma adenosine metabolites such as inosine, which we previously showed had immune modulatory effects. In conclusion: 1) different probiotics produce distinct signatures in the fecal microbial community in mice with Treg deficiency; and 2) when comparing different probiotics, there are strain-specific microbial products with different anti-inflammatory properties, reinforcing the concept that “one size does not fit all” in the treatment of autoimmune disease. NEW & NOTEWORTHY In the treatment of Treg-deficiency-induced autoimmunity, Limosilactobacillus reuteri DSM 17938 (LR) showed greater efficacy than Lacticaseibacillus rhamnosus GG (LGG). The study demonstrated that two different probiotics produce distinct signatures in the fecal microbial community in mice with Treg deficiency, but with many similarities in global plasma metabolites in general. However, there are strain-specific microbial products with different anti-inflammatory properties, reinforcing the concept that “one size does not fit all” in the treatment of autoimmune disease.

Convection over the Tibetan Plateau (TP) has been linked to heavy rain and flooding in downstream parts of China. Understanding processes which influence the development of convection on the TP could contribute to better forecasting of these extreme events. TP scale (~1000 km) soil moisture gradients have been shown to influence formation of convective systems over the eastern TP. The importance of smaller-scale (~10 km) variability has been identified in other regions (including the Sahel and Mongolia) but has yet to be investigated for the TP. In addition, compared to studies over flat terrain, much less is known about soil moisture–convection feedbacks above complex topography. In this study we use satellite observations of cold cloud, land surface temperature, and soil moisture to analyze the effect of mesoscale soil moisture heterogeneity on the initiation of strong convection in the complex TP environment. We find that strong convection is favored over negative (positive) land surface temperature (soil moisture) gradients. The signal is strongest for less vegetation and low topographic complexity, though still significant up to a local standard deviation of 300 m in elevation, accounting for 65% of cases. In addition, the signal is dependent on background wind. Strong convective initiation is only sensitive to local (tens of kilometers) soil moisture heterogeneity for light wind speeds, though large-scale (hundreds of kilometers) gradients may still be important for strong wind speeds. Our results demonstrate that, even in the presence of complex topography, local soil moisture variability plays an important role in storm development.

Mesoscale convective systems (MCSs) are the major source of extreme rainfall over land in the tropics and are expected to intensify with global warming. In the Sahel, changes in surface temperature gradients and associated changes in wind shear have been found to be important for MCS intensification in recent decades. Here we extend that analysis to southern West Africa (SWA) by combining 34 years of cloud-top temperatures with rainfall and reanalysis data. We identify clear trends in intense MCSs since 1983 and their associated atmospheric drivers. We also find a marked annual cycle in the drivers, linked to changes in the convective regime during the progression of the West African monsoon. Before the peak of the first rainy season, we identify a shear regime where increased temperature gradients play a crucial role for MCS intensity trends. From June onward, SWA moves into a less unstable, moist regime during which MCS trends are mainly linked to frequency increase and may be more influenced by total column water vapor. However, during both seasons we find that MCSs with the most intense convection occur in an environment with stronger wind shear, increased low-level humidity, and drier midlevels. Comparing the sensitivity of MCS intensity and peak rainfall to low-level moisture and wind shear conditions preceding events, we find a dominant role for wind shear. We conclude that MCS trends are directly linked to a strengthening of two distinct convective regimes that cause the seasonal change of SWA MCS characteristics. However, the convective environment that ultimately produces the most intense MCSs remains the same.

Motivation We compiled a global database of long-term riverine fish surveys from 46 regional and national monitoring programmes and from individual academic research efforts, with which numerous basic and applied questions in ecology and global change research can be explored. Such spatially and temporally extensive datasets have been lacking for freshwater systems in comparison to terrestrial ones. Main types of variables contained The database includes 11,386 time-series of riverine fish community catch data, including 646,270 species-specific abundance records, together with metadata related to the geographical location and sampling methodology of each time-series. Spatial location and grain The database contains 11,072 unique sampling locations (stream reach), spanning 19 countries, five biogeographical realms and 402 hydrographical basins world-wide. Time period and grain The database encompasses the period 1951-2019. Each time-series is composed of a minimum of two yearly surveys (mean = 8 years) and represents a minimum time span of 10 years (mean = 19 years). Major taxa and level of measurement The database includes 944 species of ray-finned fishes (Class Actinopterygii). Software format csv. Main conclusion Our collective effort provides the most comprehensive long-term community database of riverine fishes to date. This unique database should interest ecologists who seek to understand the impacts of human activities on riverine fish biodiversity and to model and predict how fish communities will respond to future environmental change. Together, we hope it will promote advances in macroecological research in the freshwater realm.

Some of the highest summer monsoon rainfall in South Asia falls on the windward slopes of the Western Ghats mountains on India’s west coast and offshore over the eastern Arabian Sea. Understanding of the processes determining the spatial distribution and temporal variability of this region remains incomplete. In this paper, new Interaction of Convective Organization and Monsoon Precipitation, Atmosphere, Surface and Sea (INCOMPASS) aircraft and ground-based measurements of the summer monsoon over the Western Ghats and upstream of them are presented and placed within the context of remote sensing observations and reanalysis. The transition from widespread rainfall over the eastern Arabian Sea to rainfall over the Western Ghats is documented in high spatial and temporal resolution. Heavy rainfall offshore during the campaign was associated primarily with mid-tropospheric humidity, secondarily with sea surface temperature, and only weakly with orographic blocking. A mid-tropospheric dry intrusion suppressed deep convection offshore in the latter half of the campaign, allowing the build-up of low-level humidity in the onshore flow and enhancing rainfall over the mountains. Rainfall on the lee side of the Western Ghats occurred during the latter half of the campaign in association with enhanced mesoscale easterly upslope flow. Diurnal cycles in rainfall offshore (maximum in the morning) and on the mountains (maximum in the afternoon) were observed. Considerable zonal and temporal variability was seen in the offshore boundary layer, suggesting the presence of convective downdrafts and cold pools. Persistent drying of the subcloud mixed layer several hundred kilometres off the coast was observed, suggesting strong mixing between the boundary layer and the free troposphere. These observations provide quantitative targets to test models and suggest hypotheses on the physical mechanisms determining the distribution and variability in rainfall in the Western Ghats region.

Significance Soil moisture plays a key role in the climate system by affecting rainfall and drought over land. Through its impact on temperature, humidity, and wind in the lower atmosphere, it can influence where thunderstorms initiate. However, in many regions of the world, traveling storm clusters known as mesoscale convective systems (MCSs) are the dominant source of rainfall, and very little is known about their response to surface conditions once triggered. We use satellite observations to demonstrate that dry soils at scales ≥200 km frequently create atmospheric conditions that intensify mature MCSs in the Sahel, long after their initiation. This surface-driven predictability of hazardous weather has potentially important applications, particularly in Africa, where the population is increasingly exposed to flood risk., Soil moisture can feed back on rainfall through the impact of surface fluxes on the environment in which convection develops. The vast majority of previous research has focused on the initiation of convection, but in many regions of the world, the majority of rain comes from remotely triggered mesoscale convective systems (MCSs). Here we conduct a systematic observational analysis of soil moisture feedbacks on propagating MCSs anywhere in the world and show a strong positive impact of drier soils on convection within mature MCSs. From thousands of storms captured in satellite imagery over the Sahel, we find that convective cores within MCSs are favored on the downstream side of dry patches ≥200 km across. The effect is particularly strong during the afternoon–evening transition when convection reaches its diurnal peak in intensity and frequency, with dry soils accounting for an additional one in five convective cores. Dry soil patterns intensify MCSs through a combination of convergence, increased instability, and wind shear, all factors that strengthen organized convection. These favorable conditions tend to occur in the vicinity of a surface-induced anomalous displacement of the Sahelian dry line/intertropical discontinuity, suggesting a strong link between dry line dynamics and soil moisture state. Our results have important implications for nowcasting of severe weather in the Sahel and potentially in other MCS hotspot regions of the world.

Background Inflammation persists among persons with human immunodeficiency virus (PWH) despite effective antiretroviral therapy and may contribute to T-cell dysfunction. Alcohol use is prevalent among PWH and promotes intestinal leak, dysbiosis, and a proinflammatory milieu. Whether alcohol use is associated with T-cell late differentiation remains to be investigated. Methods Data and samples from PWH (N = 359 of 365) enrolled in the New Orleans Alcohol Use in HIV Study were used. Alcohol use was assessed by self-report (Alcohol Use Disorders Identification Test; lifetime alcohol exposure; 30-day Alcohol Timeline Followback) and phosphatidylethanol (PEth) quantitation. In a subset of participants, fecal bacterial content was assessed by ribosomal 16S marker gene deep sequencing and quantitative polymerase chain reaction. Intestinal leak was assessed by fecal-to-plasma α-1-antitrypsin (A1AT) enzyme-linked immunosorbent assay ratio. Peripheral T-cell populations were quantified by flow cytometry. Results Alcohol Use Disorder Identification Test scores were positively associated with activated-senescent, exhausted, and terminal effector memory CD45RA+CD8+ but not CD4+ T cells (cells/μL) after confounder adjustment (P Conclusions Alcohol use among PWH is associated with CD8+ T-cell late differentiation, intestinal leak, and dysbiosis. Alcohol-associated dysbiosis is implicated in CD8+ T-cell senescence.

This article presents a land–atmosphere case-study for a single day during monsoon onset, incorporating data from a research aircraft, satellite products and model outputs. The unique aircraft observations reveal temperature and humidity contrasts of up to 5 K and 4 g/kg in the planetary boundary layer induced by spatial variations in soil moisture. Both antecedent rain and irrigation were found to be drivers of this atmospheric variability. There is also evidence of soil moisture-induced mesoscale circulations above some surfaces. This is the first time such responses have been observed in situ over India. Soil moisture-driven temperature anomalies are larger than those found in previous observational studies in the African Sahel. Moreover, irrigation in the region is extensive, unlike in the Sahel, and has a similar atmospheric effect to antecedent rainfall. This implies that historical changes in irrigation practices are likely to have had an important influence on mesoscale processes within the Indian monsoon. We also examine evidence linking soil moisture and cloud formation. Above wetter soils we observed a suppression of shallow cloud, whilst the initiation of deep convection occurred mostly in areas affected by wet–dry soil moisture boundaries. To investigate the impact of soil moisture heterogeneity on large-scale wind flow, three model depictions of the day are assessed: the European Centre for Medium-Range Weather Forecasts ERA-Interim and ERA5 reanalyses, and a high-resolution (1.5 km) simulation generated using the Indian National Centre for Medium Range Weather Forecasting regional convection-permitting Unified Model. We find evidence indicating surface flux uncertainties in the models lead to ∼3.5 hPa anomalies in the monsoon trough. This does affect the simulation of monsoon circulation and rainfall. Better representation of mesoscale land–atmosphere coupling is likely to improve the depiction of convection within weather and climate models over India.

Extreme rainfall is expected to increase under climate change, carrying potential socioeconomic risks. However, the magnitude of increase is uncertain. Over recent decades, extreme storms over the West African Sahel have increased in frequency, with increased vertical wind shear shown to be a cause. Drier midlevels, stronger cold pools, and increased storm organization have also been observed. Global models do not capture the potential effects of lower- to midtropospheric wind shear or cold pools on storm organization since they parameterize convection. Here we use the first convection-permitting simulations of African climate change to understand how changes in thermodynamics and storm dynamics affect future extreme Sahelian rainfall. The model, which simulates warming associated with representative concentration pathway 8.5 (RCP8.5) until the end of the twenty-first century, projects a 28% increase of the extreme rain rate of MCSs. The Sahel moisture change on average follows Clausius–Clapeyron scaling, but has regional heterogeneity. Rain rates scale with the product of time-of-storm total column water (TCW) and in-storm vertical velocity. Additionally, prestorm wind shear and convective available potential energy both modulate in-storm vertical velocity. Although wind shear affects cloud-top temperatures within our model, it has no direct correlation with precipitation rates. In our model, projected future increase in TCW is the primary explanation for increased rain rates. Finally, although colder cold pools are modeled in the future climate, we see no significant change in near-surface winds, highlighting avenues for future research on convection-permitting modeling of storm dynamics.

We have previously demonstrated promotion of diethylnitrosamine (DEN) initiated liver tumorigenesis after feeding diets high in fat or ethanol (EtOH) to male mice. This was accompanied by hepatic induction of the proto-oncogene PIKE (Agap2). Switch of dietary protein from casein to soy protein isolate (SPI) significantly reduced tumor formation in these models. We have linked EtOH consumption in mice to microbial dysbiosis. Adoptive transfer studies demonstrate that microbiota from mice fed ethanol can induce hepatic steatosis in the absence of ethanol suggesting that microbiota or the microbial metabolome play key roles in development of fatty liver disease. Feeding SPI significantly changed gut bacteria in mice increasing alpha diversity (P < 0.05) and levels of Clostidiales spp. Feeding soy formula to piglets also resulted in significant changes in microbiota, the pattern of bile acid metabolites and in inhibition of the intestinal-hepatic FXR/FGF19-SHP pathway which has been linked to both steatosis and hepatocyte proliferation. Moreover, feeding SPI also resulted in induction of hepatic PPARα signaling and inhibition of PIKE mRNA expression coincident with inhibition of steatosis and cancer prevention. Feeding studies in the DEN model with differing dietary fats demonstrated tumor promotion specific to the saturated fat, cocoa butter relative to diets containing olive oil or corn oil associated with microbial dysbiosis including dramatic increases in Lachnospiraceae particularly from the genus Coprococcus. Immunohistochemical analysis demonstrated that tumors from EtOH-fed mice and patients with alcohol-associated HCC also expressed high levels of a novel cytochrome P450 enzyme CYP2W1. Additional adoptive transfer experiments and studies in knockout mice are required to determine the exact relationship between soy effects on the microbiota, expression of PIKE, CYP2W1, PPARα activation and prevention of tumorigenesis.

Early administration of Lactobacillus reuteri DSM 17938 (LR) prevents necrotizing enterocolitis and inhibits regulatory T-cell (Treg)-deficiency-associated autoimmunity in mice. In humans, LR reduces crying time in breastfed infants with colic, modifies severity in infants with acute diarrheal illnesses, and improves pain in children with functional bowel disorders. In healthy breastfed newborns with evolving microbial colonization, it is unclear if early administration of LR can modulate gut microbiota and their metabolites in such a way as to promote homeostasis. We gavaged LR (107colony-forming units/day, daily) to C57BL/6J mice at age of day 8 for 2 wk. Both male and female mice were investigated in these experiments. We found that feeding LR did not affect clinical phenotype or inflammatory biomarkers in plasma and stool, but LR increased the proportion of Foxp3+regulatory T cells (Tregs) in the intestine. LR also increased bacterial diversity and the relative abundance of p_Firmicutes, f_Lachnospiraceae, f_Ruminococcaceae, and genera Clostridium and Candidatus arthromitus, while decreasing the relative abundance of p_Bacteriodetes, f_Bacteroidaceae, f_Verrucomicrobiaceae, and genera Bacteroides, Ruminococcus, Akkermansia, and Sutterella. Finally, LR exerted a major impact on the plasma metabolome, upregulating amino acid metabolites formed via the urea, tricarboxylic acid, and methionine cycles and increasing tryptophan metabolism. In conclusion, early oral administration of LR to healthy breastfed mice led to microbial and metabolic changes which could be beneficial to general health.NEW & NOTEWORTHY Oral administration of Lactobacillus reuteri DSM 17938 (LR) to healthy breastfed mice promotes intestinal immune tolerance and is linked to proliferation of beneficial gut microbiota. LR upregulates plasma metabolites that are involved in the urea cycle, the TCA cycle, methionine methylation, and the polyamine pathway. Herein, we show that LR given to newborn mice specifically increases levels of tryptophan metabolites and the purine nucleoside adenosine that are known to enhance tolerance to inflammatory stimuli.

Convection‐permitting models perform better at representing the diurnal cycle and the intermittency of convective rainfall over land than parameterized‐convection models. However, most of the previous model assessments have been from an Eulerian point of view, while key impacts of the rainfall depend on a storm‐relative perspective of the system lifecycle. Here a storm‐tracking algorithm is used to generate storm‐centered Lagrangian lifecycle statistics of precipitation over West Africa from regional climate model simulations and observations. Two versions of the Met Office Unified Model with and without convection parameterization at 4‐, 12‐, and 25‐km resolution were analyzed. In both of the parameterized‐convection simulations, storm lifetimes are too short compared to observations, and storms have no preferred propagation direction; the diurnal cycle of initiations and dissipations and the spatial distribution of storms are also inaccurate. The storms in the convection‐permitting simulations have more realistic diurnal cycles and lifetimes but are not as large as the largest observed storms. The convection‐permitting model storms propagate in the correct direction, although not as fast as observed storms, and they have a much improved spatial distribution. The rainfall rate of convection‐permitting storms is likely too intense compared to observations. The improved representation of the statistics of organized convective lifecycles shows that convection‐permitting models provide better simulation of a number of aspects of high‐impact weather, which are critical to climate impacts in this important geographic region, providing the high rainfall rates can be taken into account.

The INCOMPASS field campaign combines airborne and ground measurements of the 2016 Indian monsoon, towards the ultimate goal of better predicting monsoon rainfall. The monsoon supplies the majority of water in South Asia, but forecasting from days to the season ahead is limited by large, rapidly developing errors in model parametrizations. The lack of detailed observations prevents thorough understanding of the monsoon circulation and its interaction with the land surface: a process governed by boundary- layer and convective-cloud dynamics. INCOMPASS used the UK Facility for Airborne Atmospheric Measurements (FAAM) BAe-146 aircraft for the first project of this scale in India, to accrue almost 100 h of observations in June and July 2016. Flights from Lucknow in the northern plains sampled the dramatic contrast in surface and boundary-layer structures between dry desert air in the west and the humid environment over the northern Bay of Bengal. These flights were repeated in pre-monsoon and monsoon conditions. Flights from a second base at Bengaluru in southern India measured atmospheric contrasts from the Arabian Sea, over the Western Ghats mountains, to the rain shadow of southeast India and the south Bay of Bengal. Flight planning was aided by forecasts from bespoke 4 km convection-permitting limited-area models at the Met Office and India's NCMRWF. On the ground, INCOMPASS installed eddy- covariance flux towers on a range of surface types, to provide detailed measurements of surface fluxes and their modulation by diurnal and seasonal cycles. These data will be used to better quantify the impacts of the atmosphere on the land surface, and vice versa. INCOMPASS also installed ground instrumentation supersites at Kanpur and Bhubaneswar. Here we motivate and describe the INCOMPASS field campaign. We use examples from two flights to illustrate contrasts in atmospheric structure, in particular the retreating mid-level dry intrusion during the monsoon onset.

// Jacob M. Loupe 1,4,* , Patrick J. Miller 1,5,* , Benjamin P. Bonner 1,* , Elaine C. Maggi 1 , Jyothi Vijayaraghavan 1 , Jovanny Zabaleta 2 , Christopher M. Taylor 3 , Fern Tsien 1 , Judy S. Crabtree 1 and Andrew D. Hollenbach 1 1 Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, USA 2 Department of Pediatrics and Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA 3 Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA 4 Center for Human Genetic Research, Massachusetts General Hospital, Richard B. Simches Research Center, Boston, MA, USA 5 Tulane University, New Orleans, LA, USA * These authors have contributed equally to this work Correspondence to: Andrew D. Hollenbach, email: // Keywords : aneuploidy, Pax3-FOXO1, myogenesis, phosphorylation, alveolar rhabdomyosarcoma Received : April 07, 2016 Accepted : August 10, 2016 Published : August 30, 2016 Abstract While many solid tumors are defined by the presence of a particular oncogene, the role that this oncogene plays in driving transformation through the acquisition of aneuploidy and overcoming growth arrest are often not known. Further, although aneuploidy is present in many solid tumors, it is not clear whether it is the cause or effect of malignant transformation. The childhood sarcoma, Alveolar Rhabdomyosarcoma (ARMS), is primarily defined by the t(2;13)(q35;q14) translocation, creating the PAX3-FOXO1 fusion protein. It is unclear what role PAX3-FOXO1 plays in the initial stages of tumor development through the acquisition and persistence of aneuploidy. In this study we demonstrate that PAX3-FOXO1 serves as a driver mutation to initiate a cascade of mRNA and miRNA changes that ultimately reprogram proliferating myoblasts to induce the formation of ARMS. We present evidence that cells containing PAX3-FOXO1 have changes in the expression of mRNA and miRNA essential for maintaining proper chromosome number and structure thereby promoting aneuploidy. Further, we demonstrate that the presence of PAX3-FOXO1 alters the expression of growth factor related mRNA and miRNA, thereby overriding aneuploid-dependent growth arrest. Finally, we present evidence that phosphorylation of PAX3-FOXO1 contributes to these changes. This is one of the first studies describing how an oncogene and post-translational modifications drive the development of a tumor through the acquisition and persistence of aneuploidy. This mechanism has implications for other solid tumors where large-scale genomics studies may elucidate how global alterations contribute to tumor phenotypes allowing the development of much needed multi-faceted tumor-specific therapeutic regimens.

OBJECTIVE: To dissect potential confounding effects of breast milk and formula feeding on crying + fussing, fecal calprotectin, and gut microbiota in babies with colic. We hypothesized that infant colic is associated with gut inflammation linked to intestinal dysbiosis. STUDY DESIGN: A nested case-control design of 3 of our studies was used to analyze clinical and laboratory data at presentation, comparing babies with colic with controls. All investigators other than the biostatistician were blinded during data analysis. Subjects were recruited based on their age and crying + fussy time. We screened 65 infants, 37 with colic, as defined by Barr diary (crying + fussing time >3 hours daily), who were compared with 28 noncolicky infants. RESULTS: Fecal calprotectin was elevated in babies with colic. For each mode of infant feeding (breast milk, formula, or breast + formula), infants’ fecal calprotectin was higher in babies with colic. Infants with colic had similar levels of fecal alpha diversity (richness) when compared with controls, and alpha diversity was lower in breast-fed babies. Beta diversity at the phylum level revealed significant differences in microbial population. A phylum difference resulted from reduced Actinobacteria (95% of which are Bifidobacilli) in babies with colic. Species significantly associated with colic were Acinetobacter and Lactobacillus iners. CONCLUSIONS: Colic is linked with gut inflammation (as determined by fecal calprotectin) and dysbiosis, independent of mode of feeding, with fewer Bifidobacilli. (J Pediatr 2018;203:55–61). TRIAL REGISTRATION: Clinicaltrials.gov: https://register.clinicaltrials.gov/ and https://register.clinicaltrials.gov/.

Background Identification of bacteria in human vaginal specimens is commonly performed using 16S ribosomal RNA (rRNA) gene sequences. However, studies utilize different 16S primer sets, sequence databases, and parameters for sample and database clustering. Our goal was to assess the ability of these methods to detect common species of vaginal bacteria. Methods We performed an in silico analysis of 16S rRNA gene primer sets, targeting different hypervariable regions. Using vaginal samples from women with bacterial vaginosis, we sequenced 16S genes using the V1-V3, V3-V4, and V4 primer sets. For analysis, we used an extended Greengenes database including 16S gene sequences from vaginal bacteria not already present. We compared results with those obtained using the SILVA 16S database. Using multiple database and sample clustering parameters, each primer set's ability to detect common vaginal bacteria at the species level was determined. We also compared these methods to the use of DADA2 for denoising and clustering of sequence reads. Results V4 sequence reads clustered at 99% identity and using the 99% clustered, extended Greengenes database provided optimal species-level identification of vaginal bacteria. Conclusions This study is a first step toward standardizing methods for 16S rRNA gene sequencing and bioinformatics analysis of vaginal microbiome data.

Background The sequence of events preceding incident bacterial vaginosis (iBV) is unclear. Methods African American women who have sex with women, who had no Amsel criteria and Nugent scores of 0-3, were followed for 90 days to detect iBV (defined as a Nugent score of 7-10 on at least 2-3 consecutive days), using self-collected vaginal swab specimens. For women with iBV (cases) and women maintaining normal vaginal flora (healthy women), 16S ribosomal RNA gene sequencing targeting V4 was performed. Longitudinal vaginal microbiome data were analyzed. Results Of 204 women screened, 42 enrolled; of these, 45% developed iBV. Sequencing was performed on 448 specimens from 14 cases and 8 healthy women. Among healthy women, Lactobacillus crispatus dominated the vaginal microbiota in 75%. In contrast, prior to iBV, the vaginal microbiota in 79% of cases was dominated by Lactobacillus iners and/or Lactobacillus jensenii/Lactobacillus gasseri. The mean relative abundance of Prevotella bivia, Gardnerella vaginalis, Atopobium vaginae, and Megasphaera type I became significantly higher in cases 4 days before (P. bivia), 3 days before (G. vaginalis), and on the day of (A. vaginae and Megasphaera type I) iBV onset. The mean relative abundance of Sneathia sanguinegens, Finegoldia magna, BV-associated bacteria 1-3, and L. iners was not significantly different between groups before onset of iBV. Conclusion G. vaginalis, P. bivia, A. vaginae, and Megasphaera type I may play significant roles in iBV.