Miracle-dz/UniFAR-FTUs huggingface dataset:
HNF1α maintains pancreatic α and β cell functions in primary human islets

HNF1A haploinsufficiency underlies the most common form of human monogenic diabetes (HNF1A–maturity onset diabetes of the young [HNF1A-MODY]), and hypomorphic HNF1A variants confer type 2 diabetes risk. But a lack of experimental systems for interrogating mature human islets has limited our understanding of how the transcription factor HNF1α regulates adult islet function. Here, we combined conditional genetic targeting in human islet cells, RNA-Seq, chromatin mapping with cleavage under targets and release using nuclease (CUT&RUN), and transplantation-based assays to determine HNF1α-regulated mechanisms in adult human pancreatic α and β cells. Short hairpin RNA–mediated (shRNA-mediated) suppression of HNF1A in primary human pseudoislets led to blunted insulin output and dysregulated glucagon secretion after transplantation in mice, recapitulating phenotypes observed in patients with diabetes. These deficits corresponded with altered expression of genes encoding factors critical for hormone secretion, including calcium channel subunits, ATPase transporters, and extracellular matrix constituents. Additionally, HNF1A loss led to upregulation of transcriptional repressors, providing evidence for a mechanism of transcriptional derepression through HNF1α. CUT&RUN mapping of HNF1α DNA binding sites in primary human islets imputed a subset of HNF1α-regulated genes as direct targets. These data elucidate mechanistic links between HNF1A loss and diabetic phenotypes in mature human α and β cells.
Introduction to neogeography

Neogeography combines the complex techniques of cartography and GIS and places them within reach of users and developers.This Short Cut introduces you to the growing number of tools, frameworks, and resources available that make it easy to create maps and share the locations of your interests and history.Learn what existing and emerging standards such as GeoRSS, KML, and Microformats mean; how to add dynamic maps and locations to your web site; how to pinpoint the locations of your online visitors; how to create genealogical maps and Google Earth animations of your family's ancestry; or how to geotag and share your travel photographs.
Vaping industry participation standards in health organizations: an exploratory policy content analysis

Abstract The vaping industry has been found to employ similar tactics to tobacco industry actors to seek credibility and distort the scientific evidence base around the health harms of nicotine vaping products. As vaping industry interests undermine vaping control efforts, safeguards are necessary to protect against this influence. We aimed to examine health organizations’ policies on vaping industry participation in their activities in Australia. A descriptive approach integrating policy analysis and key informant surveys was used to obtain vaping industry participation information from health research stakeholders. Descriptive statistics on organization type, policy document type, policy document industry focus (tobacco or vaping) and respondent role and responsibility were collected. We used framework analysis to identify themes describing organizational allowances, constraints, and rationale for vaping industry research participation. Relevant health organizations were identified within Australia for policy searching (n = 156), which identified 47 unique policy documents. After contacting 267 key stakeholders from eligible organizations, 31 survey responses were analysed. Research organizations and universities were highly represented in both the policy and survey data. Most health research stakeholders recognized that vaping industry interests counteract public health priorities and opposed vaping industry participation. However, many organizations lacked clear, vaping industry-specific participation policies. To protect the integrity of the emerging evidence base around vaping harms which inform vaping policy, health organizations require strong, comprehensive policies to resist vaping industry participation in research.
Prediction of Complications and Prognostication in Perioperative Medicine: A Systematic Review and PROBAST Assessment of Machine Learning Tools

Background: The utilization of artificial intelligence and machine learning as diagnostic and predictive tools in perioperative medicine holds great promise. Indeed, many studies have been performed in recent years to explore the potential. The purpose of this systematic review is to assess the current state of machine learning in perioperative medicine, its utility in prediction of complications and prognostication, and limitations related to bias and validation. Methods: A multidisciplinary team of clinicians and engineers conducted a systematic review using the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) protocol. Multiple databases were searched, including Scopus, Cumulative Index to Nursing and Allied Health Literature (CINAHL), the Cochrane Library, PubMed, Medline, Embase, and Web of Science. The systematic review focused on study design, type of machine learning model used, validation techniques applied, and reported model performance on prediction of complications and prognostication. This review further classified outcomes and machine learning applications using an ad hoc classification system. The Prediction model Risk Of Bias Assessment Tool (PROBAST) was used to assess risk of bias and applicability of the studies. Results: A total of 103 studies were identified. The models reported in the literature were primarily based on single-center validations (75%), with only 13% being externally validated across multiple centers. Most of the mortality models demonstrated a limited ability to discriminate and classify effectively. The PROBAST assessment indicated a high risk of systematic errors in predicted outcomes and artificial intelligence or machine learning applications. Conclusions: The findings indicate that the development of this field is still in its early stages. This systematic review indicates that application of machine learning in perioperative medicine is still at an early stage. While many studies suggest potential utility, several key challenges must be first overcome before their introduction into clinical practice. This systematic review and meta-analysis identified 103 studies that employed artificial intelligence or machine learning to predict perioperative outcomes, but the overall quality was only modest with only 13% being externally validated. The authors conclude that the artificial intelligence and machine learning may hold great promise but are not ready for prime time.
UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL FACULDADE DE AGRONOMIA PROGRAMA DE PÓS-GRADUAÇÃO EM CIÊNCIA DO SOLO ATRIBUTOS FÍSICOS DO SOLO E PRODUTIVIDADE DA SOJA EM FUNÇÃO DE DOSES DE RESÍDUOS VEGETAIS E TRÁFEGO DE MÁQUINAS EM SEMEADURA DIRETA

The press for aim minimum tillage plowing and maintenance of soil cover with straw in order to reduce its loss and degradation. However, the lack of mobilization over the total area associated with the accumulation of agricultural machinery traffic in inappropriate time can cause physical damage to soil structure that may harm the development of cultivated plants. Thus, the objective was to evaluate the detrimental effects of traffic on wheeled agricultural machinery (tractor and combine) the physical attributes of soil and yield of soybeans, and how management with the addition of different amounts of waste in coverage can assist in maintenance and / or improve the physical quality. The experiment was conducted at the Experimental Station-UFRGS, in Eldorado do Sul, in a Red / Yellow Hapludox. Doses of mulch cover on which the main treatments were 0, 2, 4, 6 and 8 Mg ha dry weight of Avena strigosa. These were divided according to the local driving wheels of the tractor, harvester and no traffic. The design was a randomized block in split plot design with three replications. In areas trafficked by the treads of agricultural machinery density, microporosity and mechanical resistance to penetration were higher, and total porosity and macroporosity smaller, in relation to sites with no traffic. The tensile force on shank of fertilizer was higher in treatment with application of 8 Mg ha over the place without the application of mulch in winter, for tractor traffic and no traffic sites. The average values of transveral sectional area, maximum depth and volume of soil in the row did not differ depending on the residue dose and sites with no traffic and machinery. The contents of particulate organic matter and soil organic matter increased with increasing doses of residue in coverage, but were only significant when the lowest doses (0 and 2 Mg ha) were compared to the higher dose (8 Mg ha). Both number of plants ha, and soybean yield were not significantly influenced by treatments with different residue doses and by machinery traffic and no traffic treatments. 2 M. Sc. Dissertation in Soil Science. Programa de Pós-Graduação em Ciência do Solo, Faculdade de Agronomia, UFRGS. Porto Alegre. (80p.)March, 2011. Financial support by CNPq.
COVID-19: A complex disease with a unique metabolic signature

Plasma of COVID-19 patients contains a strong metabolomic/lipoproteomic signature, revealed by the NMR analysis of a cohort of >500 patients sampled during various waves of COVID-19 infection, corresponding to the spread of different variants, and having different vaccination status. This composite signature highlights common traits of the SARS-CoV-2 infection. The most dysregulated molecules display concentration trends that scale with disease severity and might serve as prognostic markers for fatal events. Metabolomics evidence is then used as input data for a sex-specific multi-organ metabolic model. This reconstruction provides a comprehensive view of the impact of COVID-19 on the entire human metabolism. The human (male and female) metabolic network is strongly impacted by the disease to an extent dictated by its severity. A marked metabolic reprogramming at the level of many organs indicates an increase in the generic energetic demand of the organism following infection. Sex-specific modulation of immune response is also suggested.
Implementation of Precision Oncology in the National Healthcare System: A Statement Proposal Endorsed by Italian Scientific Societies

PURPOSE Precision oncology (PO) promises positive results for patients. To date, in Italy, the effort to implement PO has been made autonomously by regional health institutions in a top-down fashion. This approach is not very efficient and jeopardizes patients' equal access to PO. Similar outcomes have been recorded in other Western countries. We tested a method of collaboration among professionals, scientific societies, and government institutions to facilitate the delivery of PO innovation to patients' bedsides. METHOD We designed an organizational research project on the basis of a bottom-up approach. We started by observing PO-related activities in five health care authorities (HCAs) in one Italian region. We then compared the issues that emerged with those of three additional HCAs in other Italian regions. Using the results of the initial observation and adopting validated multiple-step consensus methods, we finally derived 14 statements that were approved by the four main scientific societies of oncology and pathology at the national level. RESULTS The 14 statements addressed the main issues linked to the implementation of PO in clinical practice. The strong professional consensus advocated for prompt adoption within the national healthcare system. CONCLUSIONS The consensus on the statements that were obtained shows the importance of a synergistic effort among professionals, scientific societies, and health care institutions in defining homogeneous solutions for innovation implementation within the health care system.
The Stroop effect and mental imagery

The classic Stroop task is very simple: you have to name the color of words printed on a page. If these words are color words (like “red” or “blue”), where the color named and the color it is printed in are different (say, “red” printed in blue), the reaction time increases significantly. My aim is to argue that the existing psychological explanations of the Stroop effect need to be supplemented. The Stroop effect is not exclusively about access to motor control. It is also, to a large extent, about interferences in perceptual processing. To put it briefly, reading the color word triggers—laterally and automatically—visual imagery of the color and this interferes with the processing of the perceived color of the word. In other words, the Stroop effect is to a large extent a sensory phenomenon, and it has less to do with attention, conflict monitoring, or other higher-level phenomena.
Exploratory comparison of flower visiting behavior and pollination ability of mason bees, bumble bees, and honey bees

This study explored the flower visiting behaviors and pollination abilities of mason bees (Osmia excavata Alfken (Hymenoptera: Megachilidae)), bumble bees (Bombus terrestris (Linnaeus, 1758) (Hymenoptera: Apidae)), and Italian honey bees (Apis mellifera ligustica Spinola (Hymenoptera: Apidae)) in apple orchards in early spring in Jinan (located in the central region of Shandong) and Yantai (located in the Peninsula of Shandong). We compared the pollen collection patterns, flower visiting behavior, flying speed, and effects on apple pollination of the 3 types of bees. The frequencies of flower visits were significantly higher for mason bees (12.89/min in Jinan and 10.63/min in Yantai) than bumble bees and Italian honey bees in the 2 regions. The single flower residence times were significantly higher for Italian honey bees (8.22 s in Jinan and 9.43 s in Yantai), but Italian honey bees were most affected by the climate. The 3 bees differed significantly in terms of the amount of apple pollen collected and their effects on the fruit setting rate in apples (mason bees > bumble bees > Italian honey bees). The results showed that the mason bee was the most suitable pollinating species for spring apple orchards; Bumble bees were more suitable as alternative pollinators during cloudy and low temperatures; Italian honey bees were able to take advantage of their large number of worker bees in sunny and warm weather. Compared to individual bee species, a combination of 2 or 3 species of bees might be more advantageous in dealing with complex and variable weather conditions.
Trace fossil nomenclature and the Planolites-Palaeophycus dilemma

Because of fundamental differences between trace fossils and body fossils, ichnologic nomenclature is beset with difficulties. Foremost is inconsistent treatment by the International Commission on Zoological Nomenclature (lack of sanction for post-1930 names, confusion over the "rule of priority") and inadequate curation of type specimens. However, ichnologists have contributed their own problems via inadequate diagnoses and descriptions, misconceptions of ichnologic and taxonomic principles, proliferation of names and failure to engage in true monographic revisions. All these difficulties are illustrated in a thorough reevaluation of the ichnogenera Planolites Nicholson and Palaeophycus Hall. Contrary to a popular but ill-founded scheme in which these ichnogenera are differentiated simply on the presence or absence of branches, Planolites is an unlined burrow infilled with sediments having textural and fabricational characters unlike those of the host rock, whereas Palaeophycus is a lined burrow filled with sediments typically identical to those of the surrounding matrix. Planolites represents active backfilling of sediment in an ephemeral burrow constructed by a mobile deposit feeder and Palaeophycus represents passive sedimentation within an open dwelling burrow constructed by a predaceous or suspension-feeding animal. In addition to ichnological nomenclature and ethology, the ramifications are important in paleoecology, sedimentology and diagenetic studies. Currently recognized ichnospecies of Planolites include P. montanus Richter, P. beverleyensis (Billings) and P. annularis Walcott. Those of Palaeophycus include P. heberti (Saporta), P. tubularis Hall, P. striatus Hall, P. sulcatus (Miller and Dyer) and P. alternatus n. ichnosp.
Diversity in clinical trial inclusion for peripheral artery disease lower extremity endovascular interventions: a systematic review protocol

Aim: This review provides a study protocol for a systematic review of peripheral artery disease (PAD) clinical trials to examine the eligibility criteria, demographic representation, and enrollment strategies among PAD patients undergoing lower extremity (LE) endovascular interventions. Methods: This systematic review will be conducted according to the Cochrane Collaboration methodology for systematic reviews and following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocols (PRISMA-P). Eligible studies will include randomized controlled trials (RCTs) between January 2012 and December 2022. The primary outcome will be a description and summary of the frequency of the reporting of demographic characteristics. The feasibility of a meta-analysis or meta-regression will be explored, but if determined to be infeasible, the Synthesis Without Meta-analysis (SWiM) reporting guideline will be followed for the reporting of findings. Discussion: The findings may help to quantify existing inequities in clinical trial participation that may be addressed through optimizing enrollment strategies for future PAD trials. Systematic review registration: PROSPERO (CRD42022378304)
Tackling seizures in patients with Alzheimer’s disease

ABSTRACT Introduction In past years, a possible bidirectional link between epilepsy and Alzheimer’s disease (AD) has been proposed: if AD patients are more likely to develop epilepsy, people with late-onset epilepsy evidence an increased risk of dementia. Furthermore, current research suggested that subclinical epileptiform discharges may be more frequent in patients with AD and network hyperexcitability may hasten cognitive impairment. Areas covered In this narrative review, the authors discuss the recent evidence linking AD and epilepsy as well as seizures semeiology and epileptiform activity observed in patients with AD. Finally, anti-seizure medications (ASMs) and therapeutic trials to tackle seizures and network hyperexcitability in this clinical scenario have been summarized. Expert opinion There is growing experimental evidence demonstrating a strong connection between seizures, neuronal hyperexcitability, and AD. Epilepsy in AD has shown a good response to ASMs both at the late and prodromal stages. The new generation ASMs with fewer cognitive adverse effects seem to be a preferable option. Data on the possible effects of network hyperexcitability and ASMs on AD progression are still inconclusive. Further clinical trials are mandatory to identify clear guidelines about treatment of subclinical epileptiform discharges in patients with AD without seizures.
Adaptive Online Decomposition of Surface EMG Using Progressive FastICA Peel-Off

This study presents a method for adaptive online decomposition of high-density surface electromyogram (SEMG) signals to overcome the performance degradation during long-term recordings. The proposed method utilized the progressive FastICA peel-off (PFP) method and integrated a practical double-thread-parallel algorithm into the conventional two-stage calculation approach. During the offline initialization stage, a set of separation vectors was computed. In the subsequent online decomposition stage, a backend thread was implemented to periodically update the separation vectors using the constrained FastICA algorithm and the automatic PFP method. Concurrently, the frontend thread employed the newly updated separation vectors to accurately extract motor unit (MU) spike trains in real time. To assess the effectiveness of the proposed method, simulated and experimental SEMG signals from abductor pollicis brevis muscles of ten subjects were used for evaluation. The results demonstrated that the proposed method outperformed the conventional method, which relies on fixed separation vectors. Specifically, the proposed method showed an improved matching rate by 3.63% in simulated data and 1.98% in experimental data, along with an increased motor unit number by 2.39 in simulated data and 1.30 in experimental data. These findings illustrated the feasibility of the proposed method to enhance the performance of online SEMG decomposition. As a result, this work holds promise for various applications that require accurate MU firing activities in decoding neural commands and building neural-machine interfaces.
Effects of the CDM on Poverty Eradication and Global Climate Protection

In an impure public good model we analyze the effects of CDM transfers on poverty as well as on the global climate protection level. We construct an analytical model of a developing and an industrialized region, both of which independently seek to maximize their utility – a function of private consumption, domestic air quality, and global climate protection. They do so by distributing their finite expenditures across (1) the aggregate consumption good, (2) end-of-pipe pollution control technologies, and (3) greenhouse gas abatement. Based on our analytical findings, we develop two sets of simulations for China in which we vary the rate of the CDM transfer. The simulations differ by the assumption of China’s domestic air quality policy – the first assumes a technology-standards policy which fixes a level of end-of-pipe SO2 control, whereas the second assumes a technology-neutral policy which simply fixes the level of total SO2 emissions.
Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation

SUMMARY Transcript stability is an important determinant of its abundance and, consequently, translational output. Transcript destabilisation can be rapid and is well suited for modulating the cellular response. However, it is unclear the extent to which RNA stability is altered under changing environmental conditions in plants. We previously hypothesised that recovery‐induced transcript destabilisation facilitated a phenomenon of rapid recovery gene downregulation (RRGD) in Arabidopsis thaliana (Arabidopsis) following light stress, based on mathematical calculations to account for ongoing transcription. Here, we test this hypothesis and investigate processes regulating transcript abundance and fate by quantifying changes in transcription, stability and translation before, during and after light stress. We adapt syringe infiltration to apply a transcriptional inhibitor to soil‐grown plants in combination with stress treatments. Compared with measurements in juvenile plants and cell culture, we find reduced stability across a range of transcripts encoding proteins involved in RNA binding and processing. We also observe light‐induced destabilisation of transcripts, followed by their stabilisation during recovery. We propose that this destabilisation facilitates RRGD, possibly in combination with transcriptional shut‐off that was confirmed for HSP101, ROF1 and GOLS1. We also show that translation remains highly dynamic over the course of light stress and recovery, with a bias towards transcript‐specific increases in ribosome association, independent of changes in total transcript abundance, after 30 min of light stress. Taken together, we provide evidence for the combinatorial regulation of transcription and stability that occurs to coordinate translation during light stress and recovery in Arabidopsis.