Miracle-dz/UniFAR-FTUs huggingface dataset:
Highly active rubiscos discovered by systematic interrogation of natural sequence diversity

CO2 is converted into biomass almost solely by the enzyme rubisco. The poor carboxylation properties of plant rubiscos have led to efforts that made it the most kinetically characterized enzyme, yet these studies focused on < 5% of its natural diversity. Here, we searched for fast‐carboxylating variants by systematically mining genomic and metagenomic data. Approximately 33,000 unique rubisco sequences were identified and clustered into ≈ 1,000 similarity groups. We then synthesized, purified, and biochemically tested the carboxylation rates of 143 representatives, spanning all clusters of form‐II and form‐II/III rubiscos. Most variants (> 100) were active in vitro, with the fastest having a turnover number of 22 ± 1 s−1—sixfold faster than the median plant rubisco and nearly twofold faster than the fastest measured rubisco to date. Unlike rubiscos from plants and cyanobacteria, the fastest variants discovered here are homodimers and exhibit a much simpler folding and activation kinetics. Our pipeline can be utilized to explore the kinetic space of other enzymes of interest, allowing us to get a better view of the biosynthetic potential of the biosphere.
THE INFLUENCE OF MEDIA CONDITIONS ON THE UTILISATION OF MONOSACCHARIDES BY A STRAIN OF SACCHAROMYCES UVARUM (CARLSBERGENSIS)

The utilisation of glucose and fructose by the brewing yeast species Saccharomyces uvarum (carlsbergensis) was investigated. When sucrose was used as the substrate, one of the hydrolysis products, glucose was taken up preferentially over the other hydrolysis product fructose. However, when glucose and fructose were added separately to the media, the uptake profile for each sugar was very similar. Growth promoting media enhanced the differential uptake, whereas non-growth promoting media reduced it. Increase in osmotic pressure of the medium eliminated the preferential uptake of glucose over fructose. The results suggest the presence of a complex uptake system and could be explained by a combination of (1) molecular configuration of the sugars in aqueous solutions, (2) differential phosphorylation effect of glucose and fructose and (3) intracellular accumulation of ethanol in yeast.
Differential TGFB1-Signalling in Endometrium from Women with Endometriosis: Importance of Appropriate Housekeeping Genes

Purpose Endometriosis is characterised by inflammation, fibrosis and scarring, all processes known to involve transforming growth factor-β1 (TGFB1). We examined the expression of genes involved in TGFB1 signalling in epithelium and stroma from eutopic versus ectopic endometrium in women with endometriosis. Methods Eutopic and ectopic endometrium was collected during laparoscopy from women with endometriosis (n = 4 proliferative, n = 7 secretory). Laser capture microdissection was used to collect glandular epithelium and CD10-positive stroma from ectopic lesions and eutopic endometrium. Quantitative real-time RT-PCR was used to examine TGFB1, SMAD family member-2 (SMAD2), SMAD3 and SMAD4 mRNA. Expression of mRNA was relative to an RNA-spike. B2M and RPL13A mRNA, and 18S rRNA were also examined; however, expression varied between eutopic and ectopic sites making them unsuitable housekeeping genes in this model. Results TGFB1, SMAD3 and SMAD4 mRNA expression was significantly higher in eutopic versus ectopic glandular epithelium; SMAD3 expression was significantly higher in secretory versus proliferative phase eutopic epithelium. TGFB1 expression was significantly higher in eutopic versus ectopic stroma. Conclusions Variations in TGFB1, SMAD3 and SMAD4 mRNA expression in eutopic relative to ectopic tissues are consistent with a specific function in eutopic endometrium not replicated in lesions. We suggest that TGFB1-mediated activity is altered in ectopic lesions relative to eutopic endometrium in women with endometriosis, which may affect lesion maintenance. Further research examining the functional consequences of TGFB1 signalling variations is required, including extension of these studies to women without the disorder. Further studies must also carefully consider their housekeeping method and its impact on data and conclusions.
Draft Genome Sequence of Actinomyces neuii UMB1295, Isolated from the Female Urinary Tract

Actinomyces neuii is an opportunistic pathogen. Within the urogenital tract, it has been associated with bacterial vaginosis and overactive bladder symptoms. Here, we investigate a draft genome sequence of A. neuii UMB1295, which was isolated from a catheterized urine sample from a woman with a urinary tract infection. ABSTRACT Actinomyces neuii is an opportunistic pathogen. Within the urogenital tract, it has been associated with bacterial vaginosis and overactive bladder symptoms. Here, we investigate a draft genome sequence of A. neuii UMB1295, which was isolated from a catheterized urine sample from a woman with a urinary tract infection.
RNomenclature

RNAs that do not encode proteins, increasing evidence shows, are the rule rather than the exception. How do we call these RNAs? The term non-coding RNA should be rejected, we argue, since it constitutes a contradiction in terms: most if not all RNAs carry a code, even though that code may not specify an amino acid sequence. In naming these RNAs, we suggest to follow a natural distinction between two broad classes of RNAs. Class I RNAs are those that are transcribed but not translated, i.e., do not contain a translatable Open Reading Frame (ORF). Class II RNAs are transcribed and subsequently translated into amino acid sequences by the ribosomal translational apparatus. Class II RNAs comprise the familiar mRNAs, including peptide-coding RNAs. Class I RNAs, we suggest, are most fittingly called utRNAs (untranslated RNAs). The term npcRNAs (non-peptide/protein coding) can be used synonymously
A preliminary assessment of the impact of disturbance and handling on Weddell seals of McMurdo Sound, Antarctica

Abstract There has been growing concern over the impact of increased human disturbance and research effects on Antarctic species. The Weddell seal of McMurdo Sound in particular has been used as a model species for over four decades of research, with some individuals handled multiple times over a single season. Using opportunistic data, we performed an assessment of blood indicators in adult males (n = 26) and adult females (n = 24) based on high versus low disturbance areas, with results showing no variation in overall seal health. In addition, we performed a preliminary analysis of blood and faecal indicators of inflammation and stress collected from adult, non-lactating females (n = 13) handled twice in less than two weeks for research purposes. There was no indication of a change in white blood cells, platelets, globulins or haptoglobins, or faecal corticosteroids (all P > 0.05). While based on a small, opportunistic sample size with limited power in some cases, preliminary results indicate there is no acute impact of repeated handling or difference in overall traffic level on adult Weddell seals.
Taxonomic value of pore pattern in the integument of calanoid copepods (Crustacea)

Integumental sensilla and gland openings occur in the integuments of calanoid copepods in what are, essentially, bilaterally symmetrical patterns. Their presence is most easily determined by digestion of the integument in hot alkali to destroy the soft tissues. The sites of the sensilla and gland openings are then seen in the integument, stained with chlorazol black, as spots of light under the light microscope. These pores, or holes, in the integument result from the digestion of the neural innervation of the sensilla or from the digestion of the ducts of the glands which traverse the integument from the epidermis to the outside. The patterns of distribution of these pores are examined in 249 species representing 89 genera ascribed to 28 families of the calanoid copepods. The investigation is confined to the patterns in the five metasomal segments of the species. The metasomal pattern is peculiar to most species and represents a species signature. The pore signature of an individual species consists of several constituent elements. The pores group into several complexes within which individual pores may or may not be developed in that species. The primary elements of these complexes are subscribed to by the signature of the superfamily to which the species belongs. The superfamilial signature with the addition of secondary elements forms the familial signature which is further diversified to form the generic signature. The generic signature is usually further complicated to produce the species signature. In some genera, however, the generic metasomal signature is not complicated to any degree in the constituent species and the distinctive elements of the species pore signature are found more or less restricted to the urosomal segments. These patterns of pores that can be traced from the species and genus through to the corresponding superfamily form one suite of pores. A second suite of pores is developed within some genera and families that probably represents specialization within these taxa. There is a gradual modification of the pore signatures that corresponds with current concepts of the phylogeny of the Copepoda.
Network Self-configuration for Edge Elements using Self-Organizing Networks Architecture (SONAr)

: 5G networks deployment is already a commercial reality, while the speciﬁcation groups move towards 5G standalone standardization. With the need for network slicing and edge computing capabilities – and there-fore, inherent SDN and NFV adoption in a cloud environment –, these networks’ complexity will require some degree of automation. The concept of Self-Organizing Networks (SON) is a trend for next-generation systems, as it is already used in the mobile radio access network (RAN) context. In this work, we will present a self-conﬁguration (one of the four basic self-* properties of SON) system basic design proposal, within the context of Self-Organizing Networks Architecture (SONAr) framework. We will discuss the generic system architecture and present one practical application example, using the self-conﬁguration platform to automatically conﬁgure the network to receive an eNodeB (4G base station) edge component. All the system design is being conceived to work on a carrier-grade production environment, with application versatility, reliability, and scalability.
Efeito da temperatura na avaliação da qualidade fisiológica de sementes do maracujá-doce (Passiflora alata Dryander)

With the purpose to study favorable conditions of temperature for seeds germination of sweet passion-fruit (Passiflora alata Dryander), it was used, as treatment, five plants for seeds and two germination temperatures, with no light: 25oC constant and alternate 20-30oC. Mucilage of seeds, proceeding from mature fruits, completely yellow, were extracted using a mixer at low rotation. The characteristic of the evaluated seeds were: weigh, dried matter contend, water content, germination percentage (of normal seedlings) , of abnormal seedlings, of dormant and died seeds. It was concluded that alternated temperature at 20-30oC actuated significantly to obtain higher percentage of germination and low percentage of dormant seeds. These last ones, for seeds of all plants, was elevated under temperature of 25oC, showing great influence of temperature fact, on dormancy surpassing.
Simulated climate change in subarctic soils: responses in nematode species composition and dominance structure

The nematode fauna at two contrasting subarctic sites was studied at Abisko, Swedish Lapland. One site was a dwarf shrub dominated, tree-line heath (450 m a.s.l.) and the other a high altitude fellfield (1150 m a.s.l.). Responses in the composition of the nematode fauna to eight growing seasons with simulated climate change were monitored. The environmental manipulations consisted of temperature increase by using passive greenhouses, NPK fertilization, and a combination of both. A total of 98 species was found at the sites, with twice as many species at the heath compared to the climatically harsh fellfield. Species similarity was low, most likely due to differences in soil type and vegetation cover. The environmental perturbations caused distinct changes in dominance and trophic structure. Taxa common at both sites responded similarly with increases in Aphelenchoides, Filenchus and Plectus , and decreases in Eudorylaimus, Monhystrella and Teratocephalus . Generally, the manipulations changed the trophic composition in favour of fungal and plant feeding species, indicating a shift in the decomposition pathway. Modification provoquee du climat dans des sols subarctiques: reaction de la composition specifique des nematodes et de la structure de la dominance - La faune des nematodes a ete etudiee a Abisko (Laponie suedoise) en deux sites subarctiques contrastes. L'un consistait une vegetation de bruyere dominee par des buissons nains (a 450 m d'altitude) et l'autre etait situe sur un coteau a haute altitude (1150 m). La reaction de la faune nematologique aux modifications provoquees du climat a ete observee. Ces modifications comprenaient une augmentation de la temperature par utilisation de serres passives, une fertilisation NPK et une combinaison des deux. Un total de 98 especes ont ete trouvees dans les deux sites. La similitude des especes etait peu elevee, ce tres probablement du aux differences dans les types de sols et la couverture vegetale. Le nombre d'especes etait deux fois plus eleve sous bruyeres, que pour le coteau au climat rude. Apres huit saisons de croissance ayant comporte des perturbations de l'environnement, de nets changements sont apparus dans la dominance et la structure trophique. Les nematodes communs aux deux sites ont montre une reaction similaire, positive pour les Aphelenchoides, Filenchus et Plectus et negative pour les Eudorylaimus, Monhystrella et Teratocephalus. En general, les modifications ont change la composition trophique en faveur des especes fungivores et herbivores, indiquant par la des changements dans le mode de decomposition des vegetaux.
The Use of De-identification Methods for Secure and Privacy-enhancing Big Data Analytics in Cloud Environments

: Big data analytics are interlinked with distributed processing frameworks and distributed database systems, which often make use of cloud computing services providing the necessary infrastructure. However, storing sensitive data in public clouds leads to security and privacy issues, since the cloud service presents a central point of attack for external adversaries as well as for administrators and other parties which could obtain necessary privileges from the cloud service provider. To enable data security and privacy in such a setting, we argue that solutions using de-identiﬁcation methods are most suitable. Thus, this position paper presents the starting point for our future work aiming at the development of a privacy-preserving tool based on de-identiﬁcation methods to meet security and privacy requirements while simultaneously enabling data processing.
Blood acid–base, haematological and haemostatic effects of hydroxyethyl starch (130/0.4) compared to succinylated gelatin colloid infusions in normovolaemic dogs

Synthetic colloids are commonly administered to dogs to treat absolute or relative hypovolaemia. Voluven® (tetrastarch 130/0.4) and Gelofusine® (succinylated gelatin) are available to veterinarians in South Africa. In humans, use of these products has caused acid–base derangements, changes in haematology and impaired haemostasis. We aimed to investigate these effects in healthy normovolaemic dogs. Eight healthy adult beagle dogs underwent a cross-over study, receiving Voluven® or Gelofusine® (10 mL/kg/h for 120 min) once each with a 14-day washout between treatments. Dogs were premedicated with dexmedetomidine (10 µg/kg intramuscularly). Anaesthesia was induced with propofol and the dogs were maintained with isoflurane-in-oxygen. The anaesthetised dogs were connected to a multi-parameter monitor to monitor physiological parameters throughout. Catheters placed in a jugular vein and dorsal metatarsal artery allowed sampling of venous and arterial blood. Blood was collected immediately prior to commencement of colloid infusion, after 60 min infusion and at the end of infusion (120 min) to allow for arterial blood gas analysis, haematology and coagulation testing (activated partial thromboplastin time [aPTT], prothrombin time [PT] and thromboelastography [TEG]). There was no effect, between treatments or over time, on blood pH. The haemoglobin concentration, erythrocyte count and haematocrit decreased significantly over time (all p < 0.01), with no differences between treatments, and remained within normal clinical ranges. There were no differences between treatments or over time for the TEG, aPTT and PT tests of haemostasis. At the dose studied, Voluven® and Gelofusine® had comparably negligible effects on blood acid–base balance and coagulation in normovolaemic dogs.
Urinary corticosterone metabolite responses to capture, and annual patterns of urinary corticosterone in wild and captive endangered Fijian ground frogs (Platymantis vitiana)

This study was based on the development of a non-invasive glucocorticoid enzyme-immunoassay for the assessment of stress in wild and captive endangered Fijian ground frogs (Platymantis vitiana). Enzyme-immunoassays were developed and validated for the first time to non-invasively measure both cortisol and corticosterone metabolites in frog urine. Frog urine showed parallel displacement with corticosterone but not cortisol standards, therefore corticosterone enzyme immunoassays were used to examine stress in wild and captive frogs. Urinary corticosterone metabolite concentrations increased in frog urine (n = 4) at 6 h, 1 day and 2 days after injection with adrenocorticotropic hormone (0.44 μg g–1 bodyweight), indicating that the corticosterone enzyme-immunoassay could detect changes in circulating corticosterone in frogs. Urinary concentrations of corticosterone were measured in wild frogs (n = 18) after capture in the field. The first measurement beyond the initial sample was at 2–3 h. Mean urinary corticosterone concentrations rose after the initial sample and were significantly elevated in samples collected 3–4 h after capture. This is the first demonstration of a urinary corticosterone response to capture in amphibians. Urinary corticosterone metabolite concentrations for all months combined were lower in captive males than in wild males, and differed between vitellogenic, non-vitellogenic and captive females. Concentrations did not differ between captive and wild females. In conclusion, urinary corticosterone enzyme immunoassays can be used in frogs for assessing stress responses to capture and natural stress profiles of both captive and wild populations.
Effect of high temperature stress on peroxidase activity and electrolyte leakage in maize in relation to sporulation of Bipolaris maydis race T.

Exposure of maize (Zea mays L.) leaves to high temperature stress, i.e., 42 C for 6 hr before inoculation with Bipolaris maydis race T followed by incubation in the dark at 28 C for 24 hr, resulted in a significant decrease in peroxidase activity in both resistant and susceptible isolines compared with the control. Exposure to high temperature stress resulted in a significant increase in electrolyte leakage as well as in sporulation in both isolines
Stroke Prevention

Supplemental Digital Content is available in the text. In 44 years of practicing stroke prevention, I have learned many lessons; in this article, I hope to impart some of them. Three areas of my research are discussed. Controlling resistant hypertension is markedly improved by physiologically individualized therapy based on renin/aldosterone phenotyping; this is particularly important in black patients. Measurement of carotid plaque burden strongly predicts cardiovascular risk and is useful for genetic research and for a process called treating arteries instead of risk factors. Doing so in high-risk patients with asymptomatic carotid stenosis was associated with a >80% reduction in the 2-year risk of stroke and myocardial infarction. It also permitted the identification of extremes of atherosclerosis that are useful for studying both the genetics and the biology of atherosclerosis. Patients with very high plaque burden despite low levels of risk factors have an unexplained phenotype; those with little or no plaque despite high levels of risk factors are protected. Patients with unexplained atherosclerosis have higher plasma levels of toxic metabolites produced by the intestinal microbiome largely from egg yolk, red meat, and protein, and those metabolites are renally excreted. This has important dietary implications for stroke prevention. Lowering of plasma total homocysteine with B vitamins significantly reduces the risk of stroke. That was not apparent in early studies because harm from cyanocobalamin among participants with renal failure obscured the benefit among those with good renal function. We should be using B vitamins to prevent stroke but should use methylcobalamin or oxocobalamin instead of cyanocobalamin.
Two centuries of settlement and urban development in the United States

New spatiotemporal settlement data enable unprecedented examination of urban and regional change in the United States since 1810. Over the past 200 years, the population of the United States grew more than 40-fold. The resulting development of the built environment has had a profound impact on the regional economic, demographic, and environmental structure of North America. Unfortunately, constraints on data availability limit opportunities to study long-term development patterns and how population growth relates to land-use change. Using hundreds of millions of property records, we undertake the finest-resolution analysis to date, in space and time, of urbanization patterns from 1810 to 2015. Temporally consistent metrics reveal distinct long-term urban development patterns characterizing processes such as settlement expansion and densification at fine granularity. Furthermore, we demonstrate that these settlement measures are robust proxies for population throughout the record and thus potential surrogates for estimating population changes at fine scales. These new insights and data vastly expand opportunities to study land use, population change, and urbanization over the past two centuries.
On setting expectations for a SARS-CoV-2 Vaccine

Abstract The global coronavirus pandemic is unlike any other since 1918. A century of dramatic medical advances has produced a public expectation that the medical field will rapidly provide solutions to restore normalcy. In under 6 months, since SARS-CoV-2 was identified, the massive international effort to develop a SARS-CoV-2 vaccine has generated more than 140 vaccines in different stages of development with 9 already recruiting into clinical trials posted on clinicaltrials.gov. The long-term strategy to handle COVID-19 will almost certainly rely on vaccines. But, what type of protection can we realistically expect to achieve from vaccines and when?