Long-term weather data is absent in many places, complicating rain predictions for crops. Researchers found that the El Niño climate cycle can be a reliable substitute for weather data
Credit: Cocoa Care and T. Oberthu?r
When seasonal rains arrive late in Indonesia, farmers often take it as a sign that it is not worth investing in fertilizer for their crops. Sometimes they opt out of planting annual crops altogether. Generally, they’re making the right decision, as a late start to the rainy season is usually associated with the state of El Niño Southern Oscillation (ENSO) and low rainfall in the coming months.
New research published in the Nature journal Scientific Reports shows that ENSO, the weather-shaping cycle of warming and cooling of the Pacific Ocean along the Equator, is a strong predictor of cacao harvests up to two years before a harvest.
This is potentially very good news for smallholder farmers, scientists, and the global chocolate industry. The ability to predict harvest sizes well in advance could shape on-farm investment decisions, improve tropical crop research programs, and reduce risk and uncertainty in the chocolate industry.
Researchers say that the same methods – which pair advanced machine learning with rigorous, short-term data collection on farmer practices and yields – can apply to other rain-dependent crops including coffee and olives.
“The key innovation in this research is that you can effectively substitute weather data with ENSO data,” said Thomas Oberthür, a co-author and business developer at the African Plant Nutrition Institute (APNI) in Morocco. “Any crop that shares a production relationship with ENSO can be explored using this method.”
About 80 percent of global cropland depends on direct rainfall (as opposed to irrigation), accounting for almost 60 percent of production. But rainfall data is sparse and highly variable in many of these regions, making it difficult for scientists, policymakers and farmers groups to adapt to the vagaries of the weather.
No weather data? No problem
For the study, researchers used a type of machine learning that did not require weather records for the Indonesian cacao farms that participated in the research.
Rather, they relied on data on fertilizer application, yields and farm type, which they plugged into a Bayesian Neural Network (BNN) and found that ENSO phases predicted 75 % of the variation in yields.
In other words, the sea-surface temperature of the Pacific accurately predicted cacao harvests in a large majority of cases for the farms in the study. In some cases, accurate predictions were possible 25 months before the harvest.
For the uninitiated, a model that can accurately predict 50% of yield variation is usually cause to celebrate. And such long-range predictive accuracy for crop yields crops is rare.
“What this allows us to do is superimpose different management practices – such as fertilization regimes – on farms and deduce, with a high level of confidence, those interventions that work,” said James Cock, a co-author and emeritus researcher at the Alliance of Bioversity International and CIAT. “This is a whole paradigm shift toward operational research.”
Cock, a plant physiologist, said that while randomized control trials (RCTs) are generally considered the gold standard in research, these are extremely costly and consequently often impossible to perform in developing tropical agricultural areas. The approach used here is much lower cost, requires no expensive collection of weather records and provides useful guidelines on how to better manage crops under variable weather.
Ross Chapman, a data analyst and the study’s lead author, explained some of the key benefits of machine learning methods over conventional data analysis approaches:
“The BNN modeling differs from standard regression modeling because the algorithm takes input variables, such as sea-surface temperature and farm type, and then automatically ‘learns’ to recognize responses in other variables, such as crop yield,” Chapman said. “The learning process uses the same fundamental process that the human mind learns to recognize objects and patterns from real-life experience. In contrast, standard models require manual supervision of different variables via human-generated equations.”
The value of shared data
While machine learning may promise better crop yield predictions in the absence of weather data, scientists – or farmers themselves – still need to accurately collect certain production information and have that data readily available if machine-learning models are going to work.
In the case of the Indonesian cacao farms in the study, farmers had been part of a major chocolate company’s training program on best practices. They kept track of inputs such as fertilizer application, freely shared that data for analysis, and an organization with a local presence, the International Plant Nutrition Institute (IPNI), kept tidy records for researchers to use.
In addition, scientists had previously divided their farms into ten similar groups, where topography and soil conditions were similar. The researchers used data on harvests, fertilizer applications and yields from 2013 to 2018 to build their model.
The knowledge gained by cacao growers gives them confidence on how and when to invest in fertilizers. The agronomic skills this vulnerable group acquired shields them against a loss in their investment, which typically occurs when weather is adverse.
Thanks to their collaboration with the researchers, now their knowledge can be, in a way, shared with growers of other crops in other regions of the world.
“This research could not have happened without dedicated farmers, IPNI and a strong farmers’ support organization, Community Solutions International, to pull everyone together,” Cock said, emphasizing the importance of multidisciplinary collaboration and balancing stakeholder’s different needs.
“What scientists want is to know why something happens,” he said. “Farmers want to know what works.”
APNI’s Oberthür said strong predictive modeling could benefit both farmers and researchers, and fuel further collaboration.
“You need to have tangible results if you’re a farmer who is also collecting data, which is a lot of work,” Oberthür said. “This modeling, which can provide farmers with beneficial information, may help incentivize data collection since farmers will see that they are contributing to something that provides benefits to them on their farms.”
About the Alliance
The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) delivers research-based solutions that harness agricultural biodiversity and sustainably transform food systems to improve people’s lives. Alliance solutions address the global crises of malnutrition, climate change, biodiversity loss, and environmental degradation.
The Alliance is part of CGIAR, a global research partnership for a food-secure future.
No lasting benefit to tubes over antibiotics for childhood ear infections
PITTSBURGH, May 12, 2021 – There is no long-term benefit to surgically placing tympanostomy tubes in a young child’s ears to reduce the rate of recurrent ear infections during the ensuing two years compared with giving oral antibiotics to treat ear infections, a randomized trial led by UPMC Children’s Hospital of Pittsburgh and University of Pittsburgh pediatrician-scientists determined.
The trial results, published today in the New England Journal of Medicine, are among the first since the pneumococcal vaccine was added to pediatric vaccination schedules, providing updated evidence that may help shape pediatric guidelines on treating recurrent ear infections. Importantly, despite their greater use of antibiotics, the trial found no evidence of increased bacterial resistance among children in the medical-management group.
“Subjecting a young child to the risks of anesthesia and surgery, the possible development of structural changes of the tympanic membrane, blockage of the tube or persistent drainage through the tube for recurrent ear infections, which ordinarily occur less frequently as the child ages, is not something I would recommend in most instances,” said lead author Alejandro Hoberman, M.D., director of the Division of General Academic Pediatrics at UPMC Children’s Hospital and the Jack L. Paradise Endowed Professor of Pediatric Research at Pitt’s School of Medicine.
“We used to often recommend tubes to reduce the rate of ear infections, but in our study, episodic antibiotic treatment worked just as well for most children,” he said. “Another theoretical reason to resort to tubes is to use topical ear drops rather than systemic oral antibiotics in subsequent infections in the hope of preventing the development of bacterial resistance, but in this trial, we did not find increased resistance with oral antibiotic use. So, for most children with recurrent ear infections, why undergo the risks, cost and nuisance of surgery?”
Next to the common cold, ear infections are the most frequently diagnosed illness in U.S. children. Ear infections can be painful, force lost time at work and school, and may cause hearing loss. Tympanostomy tube placement, which is a surgical procedure to insert tiny tubes into a child’s eardrums to prevent the accumulation of fluid, is the most common operation performed on children after the newborn period.
Hoberman and his team enrolled 250 children ages 6 to 35 months of age at UPMC Children’s Hospital, Children’s National Medical Center in Washington, D.C., and Kentucky Pediatric and Adult Research in Bardstown, Ky. All of the children had had medically verified recurrent ear infections and had received the pneumococcal conjugate vaccine. They were randomly assigned to receive “medical management,” which involved receiving oral antibiotics at the time of ear infections, or the surgical insertion of tubes and antibiotic ear drops. The children were followed for two years.
Overall, there were no differences between children in the two groups when it came to the rate or severity of ear infections. And, though the children in the medical management group received more antibiotics, there also was no evidence of increased antimicrobial resistance in samples taken from the children. The trial also didn’t find any difference between the two groups in the children’s quality of life or in the effect of the children’s illness on parents’ quality of life.
One short-term benefit of placing tympanostomy tubes was that, on average, it took about two months longer for a child to develop a first ear infection after tubes were placed, compared with children whose ear infections were managed with antibiotics.
Another finding of the trial was that the rate of ear infections among children in both groups fell with increasing age. The rate of infections was 2.6 times higher in children younger than 1 year, compared with the oldest children in the trial, those between 2 and 3 years, regardless of whether they received medical management or tube insertion.
“Most children outgrow ear infections as the Eustachian tube, which connects the middle-ear with the back of the throat, works better,” Hoberman said. “Previous studies of tubes were conducted before children were universally immunized with pneumococcal conjugate vaccine, which also has reduced the likelihood of recurrent ear infections. It’s important to recognize that most children outgrow ear infections as they grow older. However, we must appreciate that for the relatively few children who continue to meet criteria for recurrent ear infections–three in six months or four in one year–after having met those criteria initially, placement of tympanostomy tubes may well be beneficial.”
Additional study authors are Diego Preciado, M.D., Ph.D., and Daniel E. Felton, M.D., both of Children’s National Medical Center; Jack L. Paradise, M.D., David H. Chi, M.D., MaryAnn Haralam, M.S.N., C.R.N.P., Diana H. Kearney, R.N., C.C.R.C., Sonika Bhatnagar, M.D., M.P.H., Gysella B. Muñiz Pujalt, M.D., Timothy R. Shope, M.D., M.P.H., Judith M. Martin, M.D., Marcia Kurs-Lasky, M.S., Hui Liu, M.S., Kristin Yahner, M.S., Jong-Hyeon Jeong, Ph.D., Jennifer P. Nagg, R.N., Joseph E. Dohar, M.D., and Nader Shaikh, M.D., M.P.H., all of Pitt; Norman L. Cohen, M.D., and Brian Czervionke, M.D., both of UPMC Children’s Community Pediatrics; and Stan L. Block, M.D., of Kentucky Pediatric and Adult Research.
This research was funded by National Institute on Deafness and Other Communication Disorders grant NCT02567825.
To read this release online or share it, visit http://www.
About the University of Pittsburgh School of Medicine
As one of the nation’s leading academic centers for biomedical research, the University of Pittsburgh School of Medicine integrates advanced technology with basic science across a broad range of disciplines in a continuous quest to harness the power of new knowledge and improve the human condition. Driven mainly by the School of Medicine and its affiliates, Pitt has ranked among the top 10 recipients of funding from the National Institutes of Health since 1998. In rankings recently released by the National Science Foundation, Pitt ranked fifth among all American universities in total federal science and engineering research and development support.
Likewise, the School of Medicine is equally committed to advancing the quality and strength of its medical and graduate education programs, for which it is recognized as an innovative leader, and to training highly skilled, compassionate clinicians and creative scientists well-equipped to engage in world-class research. The School of Medicine is the academic partner of UPMC, which has collaborated with the University to raise the standard of medical excellence in Pittsburgh and to position health care as a driving force behind the region’s economy. For more information about the School of Medicine, see http://www.
About UPMC Children’s Hospital of Pittsburgh
Regionally, nationally, and globally, UPMC Children’s Hospital of Pittsburgh is a leader in the treatment of childhood conditions and diseases, a pioneer in the development of new and improved therapies, and a top educator of the next generation of pediatricians and pediatric subspecialists. With generous community support, UPMC Children’s Hospital has fulfilled this mission since its founding in 1890. UPMC Children’s is recognized consistently for its clinical, research, educational, and advocacy-related accomplishments, including ranking in the top 10 on the 2020-2021 U.S. News & World Report Honor Roll of America’s Best Children’s Hospitals. UPMC Children’s also ranks 15th among children’s hospitals and schools of medicine in funding for pediatric research provided by the National Institutes of Health (FY2019).
Contact: Allison Hydzik
E-mail: [email protected]
Contact: Andrea Kunicky
E-mail: [email protected]
Research reveals ancient people had more diverse gut microorganisms
MISSOULA – Only an anthropologist would treasure millennia-old human feces found in dry caves.
Just ask Dr. Meradeth Snow, a University of Montana researcher and co-chair of UM’s Department of Anthropology. She is part of an international team, led by the Harvard Medical School-affiliated Joslin Diabetes Center, that used human “paleofeces” to discover that ancient people had far different microorganisms living in their guts than we do in modern times.
Snow said studying the gut microbes found in the ancient fecal material may offer clues to combat diseases like diabetes that afflict people living in today’s industrialized societies.
“We need to have some specific microorganisms in the right ratios for our bodies to operate effectively,” Snow said. “It’s a symbiotic relationship. But when we study people today – anywhere on the planet – we know that their gut microbiomes have been influenced by our modern world, either through diet, chemicals, antibiotics or a host of other things. So understanding what the gut microbiome looked like before industrialization happened helps us understand what’s different in today’s guts.”
This new research was published May 12 in the prestigious journal Nature. The article is titled “Reconstruction of ancient microbial genomes from the human gut.” Snow and UM graduate student Tre Blohm are among the 28 authors of the piece, who hail from institutions around the globe.
Snow said the feces they studied came from dry caves in Utah and northern Mexico. So what does the 1,000-year-old human excrement look like?
“The caves these paleofeces came from are known for their amazing preservation,” she said. “Things that would normally degrade over time look almost brand new. So the paleofeces looked like, well, feces that are very dried out.”
Snow and Blohm worked hands-on with the precious specimens, suiting up in a clean-room laboratory at UM to avoid contamination from the environment or any other microorganisms – not an easy task when the tiny creatures are literally in and on everything. They would carefully collect a small portion that allowed them to separate out the DNA from the rest of the material. Blohm then used the sequenced DNA to confirm the paleofeces came from ancient people.
The senior author of the Nature paper is Aleksandar Kostic of the Joslin Diabetes Center. In previous studies of children living in Finland and Russia, he and his partners revealed that kids living in industrialized areas – who are much more likely to develop Type 1 diabetes than those in non-industrialized areas – have very different gut microbiomes.
“We were able to identify specific microbes and microbial products that we believe hampered a proper immune education in early life,” Kostic said. “And this leads later on to higher incidents of not just Type 1 diabetes, but other autoimmune and allergic diseases.”
Kostic wanted to find a healthy human microbiome without the effects of modern industrialization, but he became convinced that couldn’t happen with any modern living people, pointing out that even tribes in the remote Amazon are contracting COVID-19.
So that’s when the researchers turned to samples collected from arid environments in the North American Southwest. The DNA from eight well-preserved ancient gut samples were compared with the DNA of 789 modern samples. Half the modern samples came from people eating diets where most food comes from grocery stores, and the remainder came from people consuming non-industrialized foods mostly grown in their own communities.
The differences between microbiome populations were striking. For instance, a bacterium known as Treponema succinifaciens wasn’t in a single “industrialized” population’s microbiome the team analyzed, but it was in every single one of the eight ancient microbiomes. But researchers found the ancient microbiomes did match up more closely with modern non-industrialized population’s microbiomes.
The scientists found that almost 40% of the ancient microbial species had never been seen before. Kostic speculated on what caused the high genetic variability:
“In ancient cultures, the foods you’re eating are very diverse and can support a more eclectic collection of microbes,” Kostic said. “But as you move toward industrialization and more of a grocery-store diet, you lose a lot of nutrients that help to support a more diverse microbiome.”
Moreover, the ancient microbial populations incorporated fewer genes related to antibiotic resistance. The ancient samples also featured lower numbers of genes that produce proteins that degrade the intestinal mucus layer, which then can produce inflammation that is linked with various diseases.
Snow and several coauthors and museum collection managers also led a project to ensure the inclusion of Indigenous perspectives in the research.
“This was a really vital part of the work that had to accompany this kind of research,” she said. “Initially, we sent out multiple letters and emails and called the tribal historic preservation officers of the all the recognized tribes in the Southwest region. Then we met with anyone who was interested, doing short presentations and answering questions and following up with interested parties.
“The feedback we received was noteworthy, in that we needed to keep in mind that these paleofeces have to ties their ancestors, and we needed to be – and hopefully have been – as respectful as possible about them,” she said.
“There is a long history of misuse of genetic data from Indigenous communities, and we strove to be mindful of this by meeting and speaking with as many people as possible to obtain their insights and perspectives. We hope that this will set a precedent for us as scientists and others working with genetic material from Indigenous communities past and present.”
Snow said the research overall revealed some fascinating things.
“The biggest finding is that the gut microbiome in the past was far more diverse than today – and this loss of diversity is something we are seeing in humans around the world,” she said. “It’s really important that we learn more about these little microorganisms and what they do for us in our symbiotic relationships.
“In the end, it could make us all healthier.”
C-Path announces accelerated data sharing collaboration with Tufts Medical Center
FDA grant supports use of real-world data to generate real-world evidence in neonates
TUCSON, Ariz., May 12, 2021 — Critical Path Institute (C-Path) and Tufts Medical Center have announced a joint venture to integrate the first patient-level clinical trial data to generate actionable real-world evidence (RWE) for neonatal drug development, from real-world neonate data (RWD). This activity, funded by a grant from the U.S. Food and Drug Administration (FDA), is being executed through a neonatal pilot project within C-Path’s International Neonatal Consortium (INC). The data sharing collaboration and transfer also marks the fastest on record for C-Path — starting with the Data Contribution Agreement negotiations and receipt of the data in three months’ time this March.
“I’m extremely proud of both team’s efforts to move swiftly to integrate data, increase our understanding of neonates and improve drug development for this underserved population,” said INC Executive Director Kanwaljit Singh, M.D., M.P.H. “Dr. Jonathan Davis was key in this collaboration and we thank him for all he’s done to move this project forward quickly.”
This effort allows a unique set of clinical trial data to be integrated and managed by C-Path’s Data Collaboration Center (DCC) to support analyses run by its Quantitative Medicine Program. “This will significantly add to the goal of defining actionable reference ranges of commonly used laboratory values in neonates and the development of a natural history model of bronchopulmonary dysplasia,” indicated C-Path’s Chief Science Officer and project Co-Principal Investigator Klaus Romero, M.D., M.S., F.C.P.
The clinical trial data sets shared by Tufts MC will be integrated with other patient-level RWD from electronic health records and data from national registries and networks. Each year in the U.S., 10 percent of neonates are born preterm, creating an urgent need to improve survival and outcome. However, there is minimal new drug development and most existing drugs have insufficient evidence to support safety, efficacy and dosage in this high-risk population.
“I am privileged to work with this exceptional team of clinical and data scientists at C-Path that will make real advances in neonatology,” said Jonathan Davis, M.D., Chief of Newborn Medicine, Associate Director of the Tufts Clinical and Translational Science Institute at Tufts Children’s Hospital, and Co-Principal Investigator. “This collaboration is a perfect marriage. A balance between clinical care, clinical trials, and data science that has never been done before in the neonatology space.”
For more than 15 years, C-Path has engaged in numerous successful partnerships with the FDA and industry to act as a catalyst for drug development. The public-private partnership with FDA, industry, the academic community and families of preterm neonates is unprecedented. The overall goal is to collect, aggregate, standardize and analyze RWD and generate RWE to accelerate drug development efforts. “This style of partnership holds great promise to benefit the unmet needs of the neonatal population and will likely be generalizable to other populations and therapeutic areas as well,” said Singh.
C-Path’s DCC will develop the Real-World Data and Analytics Platform (RW-DAP) as an integrated database and analytics hub designed to be used in generating actionable RWE that can be leveraged to inform drug development in areas where RWD can play a relevant role. It will promote the sharing of relevant RWD and facilitate the optimization of future RWD collection. By integrating relevant RWD in a format suitable for analytics, the RW-DAP will accelerate the understanding of disease progression (including causes for variance in disease progression), clinical outcome measures and biomarkers, and facilitate the development of mathematical models of disease and innovative clinical trial designs. RW-DAP will be positioned to generate solutions to drug development, which can be made publicly available to qualified researchers in industry, government, regulatory agencies and academia.
“C-Path’s INC is well-equipped to lead this project. Real-world data and real-world evidence are crucial to understanding how medical product is performing, and more importantly, how we can make adjustments and explore its potential benefits for other therapeutic areas,” Romero said. “The development of the RW-DAP fits right within DCC’s impressive body of work.”
C-Path’s INC will continue to meet and work with collaborators and new data contributors to integrate additional patient-level datasets. For more information on collaborating with INC, and how to contribute data, please email Adriana Burns at [email protected]
Critical Path Institute is supported by the Food and Drug Administration (FDA) of the U.S. Department of Health and Human Services (HHS) and is 55% funded by FDA/HHS, totaling $14,575,306, and 45% funded by non-government source(s), totaling $11,916,747. The contents are those of the author(s) and do not necessarily represent the official views of, nor an endorsement by, FDA/HHS or the U.S. Government. For more information, please visit FDA.gov.
Critical Path Institute (C-Path) is an independent, nonprofit organization established in 2005 as a public and private partnership. C-Path’s mission is to catalyze the development of new approaches that advance medical innovation and regulatory science, accelerating the path to a healthier world. An international leader in forming collaborations, C-Path has established numerous global consortia that currently include more than 1,600 scientists from government and regulatory agencies, academia, patient organizations, disease foundations, and dozens of pharmaceutical and biotech companies. C-Path U.S. is headquartered in Tucson, Arizona and C-Path, Ltd. EU is headquartered in Dublin, Ireland, with additional staff in multiple other locations. For more information, visit c-path.org and c-path.eu.
Previously unknown letter reveals Einstein’s thinking on bees, birds and physics
A recently discovered letter written by Albert Einstein discusses a link between physics and biology, seven decades before evidence emerges.
Credit: Dyer et al. 2021, J Comp Physiol A / The Hebrew University of Jerusalem
The 1949 letter by the physicist and Nobel laureate discusses bees, birds and whether new physics principles could come from studying animal senses.
It’s a position still being realised within physics to this day, with a growing body of research and understanding of how animals such as birds and bees find their way around.
Now a study led by RMIT University in Melbourne, Australia, discusses how recent discoveries in migratory birds back up Einstein’s thinking 72 years ago.
The previously unpublished letter was shared with researchers by Judith Davys – Einstein had addressed it to her late husband, radar researcher Glyn Davys.
RMIT’s Associate Professor Adrian Dyer has published significant studies into bees and is the lead author of the new paper on Einstein’s letter, published in the Journal of Comparative Physiology A.
Dyer said the letter shows how Einstein envisaged new discoveries could come from studying animals.
“Seven decades after Einstein proposed new physics might come from animal sensory perception, we’re seeing discoveries that push our understanding about navigation and the fundamental principles of physics,” he said.
The letter also proves Einstein met with Nobel laurate Karl von Frisch, who was a leading bee and animal sensory researcher.
In April 1949, von Frisch presented his research on how honeybees navigate more effectively using the polarisation patterns of light scattered from the sky.
The day after Einstein attended von Frisch’s lecture, the two researchers shared a private meeting.
Although this meeting wasn’t formally documented, the recently discovered letter from Einstein provides insight into what they might have talked about.
“It is thinkable that the investigation of the behaviour of migratory birds and carrier pigeons may someday lead to the understanding of some physical process which is not yet known,” Einstein wrote.
Professor Andrew Greentree, a theoretical physicist at RMIT, said Einstein also suggested that for bees to extend our knowledge of physics, new types of behaviour would need to be observed.
“Remarkably, it is clear through his writing that Einstein envisaged new discoveries could come from studying animals’ behaviours,” Greentree said.
More than 70 years since Einstein sent his letter, research is revealing the secrets of how migratory birds navigate while flying thousands of kilometres to arrive at a precise destination.
In 2008, research on thrushes fitted with radio transmitters showed, for the first time, that these birds use a form of magnetic compass as their primary orientation guide during flight.
One theory for the origin of magnetic sense in birds is the use of quantum randomness and entanglement. Both of these physics concepts were first proposed by Einstein.
The letter to Glyn Davys shows the openness of Einstein’s mind to novel possibilities observed in nature and the evidence that he took an interest in von Frish and his bee research.
‘Einstein, von Frisch and the honeybee: a historical letter comes to light’, with Adrian Dyer, Andrew Greentree, Jair Garcia, Elinya Dyer, Scarlett Howard and Fredrich Barth, is published in the Journal of Comparative Physiology A (DOI: 10.1007/s00359-021-01490-6).
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