Miracle-dz/UniFAR-FTUs huggingface dataset:
Convergent Biochemical Pathways for Xanthine Alkaloid Production in Plants Evolved from Ancestral Enzymes with Different Catalytic Properties

Abstract Convergent evolution is widespread but the extent to which common ancestral conditions are necessary to facilitate the independent acquisition of similar traits remains unclear. In order to better understand how ancestral biosynthetic catalytic capabilities might lead to convergent evolution of similar modern-day biochemical pathways, we resurrected ancient enzymes of the caffeine synthase (CS) methyltransferases that are responsible for theobromine and caffeine production in flowering plants. Ancestral CS enzymes of Theobroma, Paullinia, and Camellia exhibited similar substrate preferences but these resulted in the formation of different sets of products. From these ancestral enzymes, descendants with similar substrate preference and product formation independently evolved after gene duplication events in Theobroma and Paullinia. Thus, it appears that the convergent modern-day pathways likely originated from ancestral pathways with different inferred flux. Subsequently, the modern-day enzymes originated independently via gene duplication and their convergent catalytic characteristics evolved to partition the multiple ancestral activities by different mutations that occurred in homologous regions of the ancestral proteins. These results show that even when modern-day pathways and recruited genes are similar, the antecedent conditions may be distinctive such that different evolutionary steps are required to generate convergence.
Evaluation of the Adsorption of Aquatic Humic Substances in Batch and Column Experiments by Thermally Modified Activated Carbons

Two commercially available granular activated carbons (GACs) were thermally modified and evaluated for their adsorption properties in batch and column mode experiments. The widely used and well characterized aquatic humic substances were used as adsorbate. The aim was to relate the adsorption properties of GAC with their physicochemical properties and also evaluate the impact of heat treatment under nitrogen atmosphere on the performance of the adsorbent in both batch and column operation modes. Heat treatment had a qualitatively similar effect on surface basicity and pore volume of both adsorbents. However, in quantitative terms, significant differences were reported. Heat-treatment enhanced batch adsorption capacity only for GAC-A. Surface available in pores within 12−15 A width was strongly correlated to the NOM adsorption capacity. Benefits of thermal treatment were more evident at high initial solute concentrations. Results from batch adsorption did not have a straightforward relationship with column.
Determination and Isotope-Ratio Analysis of Different Forms of Nitrogen in Soils: 3. Exchangeable Ammonium, Nitrate, and Nitrite by Extraction-Distillation Methods1

Methods of determining exchangeable ammonium, nitrate, and nitrite in soils are described. They involve extraction of the soil sample with 2M KCl (10 ml/g of soil) and analysis of the extract by steam-distillation methods in which magnesium oxide is used for distillation of ammonium, ball-milled Devarda alloy for reduction of nitrate and nitrite to ammonium, and sulfamic acid for destruction of nitrite. The distillation methods are rapid, accurate, and precise, have high specificity, and are applicable to turbid, colored, and unfiltered soil extracts. They give quantitative recovery of ammonium, nitrate, and nitrite added to soil extracts and permit nitrogen isotope-ratio analysis of these forms of nitrogen in N-tracer studies of nitrogen transformations in soils. View complete article To view this complete article, insert Disc 3 then click button8
Construction of engineered RuBisCO Kluyveromyces marxianus for a dual microbial bioethanol production system

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) genes play important roles in CO2 fixation and redox balancing in photosynthetic bacteria. In the present study, the kefir yeast Kluyveromyces marxianus 4G5 was used as host for the transformation of form I and form II RubisCO genes derived from the nonsulfur purple bacterium Rhodopseudomonas palustris using the Promoter-based Gene Assembly and Simultaneous Overexpression (PGASO) method. Hungateiclostridium thermocellum ATCC 27405, a well-known bacterium for its efficient solubilization of recalcitrant lignocellulosic biomass, was used to degrade Napier grass and rice straw to generate soluble fermentable sugars. The resultant Napier grass and rice straw broths were used as growth media for the engineered K. marxianus. In the dual microbial system, H. thermocellum degraded the biomass feedstock to produce both C5 and C6 sugars. As the bacterium only used hexose sugars, the remaining pentose sugars could be metabolized by K. marxianus to produce ethanol. The transformant RubisCO K. marxianus strains grew well in hydrolyzed Napier grass and rice straw broths and produced bioethanol more efficiently than the wild type. Therefore, these engineered K. marxianus strains could be used with H. thermocellum in a bacterium-yeast coculture system for ethanol production directly from biomass feedstocks.
Apolipoprotein E genotype-dependent nutrigenetic effects to prebiotic inulin for modulating systemic metabolism and neuroprotection in mice via gut-brain axis

ABSTRACT Objective The goal of the study was to identify the potential nutrigenetic effects to inulin, a prebiotic fiber, in mice with different human apolipoprotein E (APOE) genetic variants. Specifically, we compared responses to inulin for the potential modulation of the systemic metabolism and neuroprotection via gut-brain axis in mice with human APOE ϵ3 and ϵ4 alleles. Method We performed experiments with young mice expressing the human APOE3 (E3FAD mice and APOE4 gene (E4FAD mice). We fed mice with either inulin or control diet for 16 weeks starting from 3 months of age. We determined gut microbiome diversity and composition using16s rRNA sequencing, systemic metabolism using in vivo MRI and metabolomics, and blood–brain barrier (BBB) tight junction expression using Western blot. Results In both E3FAD and E4FAD mice, inulin altered the alpha and beta diversity of the gut microbiome, increased beneficial taxa of bacteria and elevated cecal short chain fatty acid and hippocampal scyllo-inositol. E3FAD mice had altered metabolism related to tryptophan and tyrosine, while E4FAD mice had changes in the tricarboxylic acid cycle, pentose phosphate pathway, and bile acids. Differences were found in levels of brain metabolites related to oxidative stress, and levels of Claudin-1 and Claudin-5 BBB tight junction expression. Discussion We found that inulin had many similar beneficial effects in the gut and brain for both E3FAD and E4FAD mice, which may be protective for brain functions and reduce risk for neurodegeneration. E3FAD and E4FAD mice also had distinct responses in several metabolic pathways, suggesting an APOE-dependent nutrigenetic effects in modulating systemic metabolism and neuroprotection.
Translational and Rotational Motion of Probes in Supercooled 1,3,5-Tris(naphthyl)benzene

Measurements of the rotational and translational motion of several probe molecules in supercooled 1,3-bis(1-naphthyl)-5-(2-naphthyl)benzene (ααβ-TNB) are reported. Rotational correlation times from 10-10 to 103 s were measured in the temperature range from 341 to 515 K (Tg = 343.5 K). Translational diffusion coefficients ranged from 10-6 to 10-15 cm2/s over a similar temperature range. The rotational correlation times of all probes have essentially the same temperature dependence as the viscosity of TNB. In contrast, the translational diffusion of the smallest probe, tetracene, is observed to have a significantly weaker temperature dependence. At Tg, the translational diffusion coefficient of tetracene is 300 times larger than expected based on its rotational correlation time. Similar enhancements of translational diffusion near Tg have recently been observed in other glass-forming liquids. These observations suggest that dynamics in TNB and other supercooled liquids are spatially heterogeneous. The probe.
Social Support, Sense of Coherence, and Self-Management among Hemodialysis Patients

Self-management is essential for patients who require regular hemodialysis treatment. This study aimed to explore the relationships between social support, sense of coherence (SOC), and self-management in hemodialysis patients and to examine whether SOC plays a mediating role. In a cross-sectional study, 402 hemodialysis patients from four tertiary hospitals were recruited. Data were analyzed using structural equation modeling. Social support, SOC, and self-management were significantly correlated with each other. The proposed model provided a good fit to the data. Social support had a direct effect on self-management and SOC, partially mediated the effect of social support on self-management (β = 0.248, p = 0.001). Social support and SOC explained 69% of the variance in self-management. Our findings indicate that health care providers can enhance social support with an emphasis on strengthening SOC strategies to better improve self-management in hemodialysis patients.
Integrative Proteomic Analysis of Posttranslational Modification in The Inflammatory Response

The posttranslational modification (PTM) of proteins, particularly acetylation, phosphorylation and ubiquitination, plays a critical role in the host innate immune response. PTMs’ dynamic changes and the crosstalk among them are complicated. To build a comprehensive dynamic network of inflammation related proteins, we integrated data from the whole cell proteome (WCP), acetylome, phosphoproteome and ubiquitinome of human and mouse macrophages. Our datasets of acetylation, phosphorylation and ubiquitination sites helped identify PTM crosstalk within and across proteins involved in the inflammatory response. Stimulation of macrophages by lipopolysaccharide (LPS) resulted in both degradative and non-degradative ubiquitination. Moreover, this study contributes to the interpretation of the roles of known inflammatory molecules and the discovery of novel inflammatory proteins.
Cell lineage‐ and expression‐based inference of the roles of forkhead box transcription factor Foxc2 in craniofacial development

Foxc2 is a member of the winged helix/forkhead (Fox) box family of transcription factors. Loss of function of Foxc2 causes craniofacial abnormalities such as cleft palate and deformed cranial base, but its role during craniofacial development remains to be elucidated.
A contact mechanics method for characterizing the elastic properties and permeability of gels

When a saturated gel immersed in the same liquid is suddenly brought into contact with a smooth rigid indenter, the liquid cannot immediately flow out of the pores, and so the gel initially behaves as an incompressible material. This gives rise to a pressure gradient in the liquid phase and the liquid flows until the pressure in it goes to zero everywhere, and all the stresses are transferred to the elastic network. As a result of the flow, the force needed to maintain a constant contact area relaxes with time. In this work, we study the feasibility of using an indentation test to measure this time-dependent force and to determine the elastic modulus, the Poisson's ratio, and the permeability, Dp, of the network. Specifically, we consider a two-dimensional Hertz contact problem of a rigid circular cylinder indenting on a half space consisting of an elastic gel. The network of the gel is assumed to be linearly elastic and isotropic, and liquid flow within the gel is assumed to obey Darcy's law, which states that the flux is proportional to the pressure gradient. Exact expressions are obtained for the initial and final force required to maintain a given contact length. These expressions allow us to determine the elastic constants of the network. The permeability of the network can be obtained from the time-dependent relaxation of the load, which is obtained by solving the exact continuum equations. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 359–370, 2006
"Young" soap films

If we pull out rapidly a metallic frame out of a surfactant solution, we arrive at a "young" soap film with relatively simple features, as noticed first by Lucassen. The weight of the film is equilibrated by a vertical gradient of surface tension. At each level, the local solution concentration equilibrates with the local monolayers. A detailed analysis of the young films was started by us in 1987. We present here an approach which is more illuminating a) the concentration profiles decay exponentially at large heights, with a characteristic length in the range of meters b) the surface is protected up to a different (larger) height c) we also review the dynamic requirements. The surfactant must reach the surface in a time shorter than the free fall time of a pure water film.
Binary surrogate endpoints in clinical trials from the perspective of case definitions

Introduction Surrogate endpoints are widely used in clinical trials, especially in situations where the endpoint of interest is not directly observable or to avoid long trial periods. A typical example for this case is frequently found in clinical trials in oncology, where overall survival (OS) as endpoint of interest and progression free survival (PFS) as surrogate endpoint are discriminated. Methods Based on the perspective of case definitions on surrogate endpoints, we provide a formal definition of such endpoints followed by a description of the structure of surrogate endpoints. Results Surrogate endpoints can be considered as case definitions for the endpoint of interest. Therefore, the performance of surrogate endpoints can be described using the classical terminology of diagnostic tests including sensitivity and specificity. Since such endpoints always focus on sensitivity with necessarily reduced specificity, efficacy estimates based on such endpoints are in general biased. Conclusion The abovementioned has to be taken into account while interpreting the results of clinical trials and should not be ignored while planning or conducting a study.
Posterior Circulation Endovascular Thrombectomy for Large-Vessel Occlusion: Predictors of Favorable Clinical Outcome and Analysis of First-Pass Effect

Lower baseline NIHSS score and a higher MR imaging posterior circulation ASPECTS were predictors of good clinical outcome. The use of large-bore catheters was a positive predictor of first-pass modified TICI 2b/3; the use of a combined technique was a negative predictor. BACKGROUND AND PURPOSE: Successful vessel recanalization in posterior circulation large-vessel occlusion is considered crucial, though the evidence of clinical usefulness, compared with the anterior circulation, is not still determined. The aim of this study was to evaluate predictors of favorable clinical outcome and to analyze the effect of first-pass thrombectomy. MATERIALS AND METHODS: A retrospective, multicenter, observational study was conducted in 10 high-volume stroke centers in Europe, including the period from January 2016 to July 2019. Only patients with an acute basilar artery occlusion or a single, dominant vertebral artery occlusion (“functional” basilar artery occlusion) who had a 3-month mRS were included. Clinical, procedural, and radiologic data were evaluated, and the association between these parameters and both the functional outcome and the first-pass effect was assessed. RESULTS: A total of 191 patients were included. A lower baseline NIHSS score (adjusted OR, 0.77; 95% CI, 0.61–0.96; P = .025) and higher baseline MR imaging posterior circulation ASPECTS (adjusted OR, 3.01; 95% CI, 1.03–8.76; P = .043) were predictors of better outcomes. The use of large-bore catheters (adjusted OR, 2.25; 95% CI, 1.08–4.67; P = .030) was a positive predictor of successful reperfusion at first-pass, while the use of a combined technique was a negative predictor (adjusted OR, 0.26; 95% CI, 0.09–0.76; P = .014). CONCLUSIONS: The analysis of our retrospective series demonstrates that a lower baseline NIHSS score and a higher MR imaging posterior circulation ASPECTS were predictors of good clinical outcome. The use of large-bore catheters was a positive predictor of first-pass modified TICI 2b/3; the use of a combined technique was a negative predictor.
Near-Infrared Spectroscopy of the Bladder: New Parameters for Evaluating Voiding Dysfunction

We describe innovative methodology for monitoring alterations in bladder oxygenation and haemodynamics in humans using near-infrared spectroscopy (NIRS). Concentrations of the chromophores oxygenated (O2Hb) and deoxygenated (HHb) haemoglobin and their sum (total haemoglobin) differ during bladder contraction in health and disease. A wireless device that incorporates three paired light emitting diodes (wavelengths 760 and 850 nanometers) and silicon photodiode detector collects data transcutaneously (10 Hz) with the emitter/detector over the bladder during spontaneous bladder emptying. Data analysis indicates comparable patterns of change in chromophore concentration in healthy children and adults (positive trend during voiding, predominantly due to elevated O2Hb), but different changes in symptomatic subjects with characteristic chromophore patterns identified for voiding dysfunction due to specific pathophysiologies: bladder outlet obstruction (males), overactive bladder (females), and nonneurogenic dysfunction (children). Comparison with NIRS muscle data suggests altered bladder haemodynamics and/or oxygenation may underlie voiding dysfunction offering new insight into the causal physiology.
Limited evidence for executive function load impairing selective copying in a win-stay lose-shift task

The use of ‘explicitly metacognitive’ learning strategies has been proposed as an explanation for uniquely human capacities for cumulative culture. Such strategies are proposed to rely on explicit, system-2 cognitive processes, to enable advantageous selective copying. To investigate the plausibility of this theory, we investigated participants’ ability to make flexible learning decisions, and their metacognitive monitoring efficiency, under executive function (EF) load. Adult participants completed a simple win-stay lose-shift (WSLS) paradigm task, intended to model a situation where presented information can be used to inform response choice, by copying rewarded responses and avoiding those that are unrewarded. This was completed alongside a concurrent switching task. Participants were split into three conditions: those that needed to use a selective copying, WSLS strategy, those that should always copy observed information, and those that should always do the opposite (Expt 1). Participants also completed a metacognitive monitoring task alongside the concurrent switching task (Expt 2). Conditions demanding selective strategies were more challenging than those requiring the use of one rule consistently. In addition, consistently copying was less challenging than consistently avoiding observed stimuli. Differences between selectively copying and always copying were hypothesised to stem from working memory requirements rather than the concurrent EF load. No impact of EF load was found on participants’ metacognitive monitoring ability. These results suggest that copying decisions are underpinned by the use of executive functions even at a very basic level, and that selective copying strategies are more challenging than a combination of their component parts. We found minimal evidence that selective copying strategies relied on executive functions any more than consistent copying or deviation. However, task experience effects suggested that ceiling effects could have been masking differences between conditions which might be apparent in other contexts, such as when observed information must be retained in memory.
Engineering bioinks for 3D bioprinting

In recent years, three-dimensional (3D) bioprinting has attracted wide research interest in biomedical engineering and clinical applications. This technology allows for unparalleled architecture control, adaptability and repeatability that can overcome the limits of conventional biofabrication techniques. Along with the emergence of a variety of 3D bioprinting methods, bioinks have also come a long way. From their first developments to support bioprinting requirements, they are now engineered to specific injury sites requirements to mimic native tissue characteristics and to support biofunctionality. Current strategies involve the use of bioinks loaded with cells and biomolecules of interest, without altering their functions, to deliver in situ the elements required to enhance healing/regeneration. The current research and trends in bioink development for 3D bioprinting purposes is overviewed herein.
The Integrity of Motivated Vision: A Reply to Gilchrist, 2020

(1) Motivated perception is compromised by experimental demand: Results do not actually show motivated perception but instead reflect subjects’ desires to comply with inferred predictions. (2) Motivated perception studies use designs that make predictions obvious to subjects. These transparent designs conspire with experimental demand to yield confirmatory but compromised results. (3) Motivated perception research lacks guiding theory and cannot explain what appear to be contradictory results. (4) Motivated perception presents an unsupportable assault upon the impermeability of perception.
Evaluation of neonatal mortality data completeness and accuracy in Ghana

Background Cause-specific mortality data are required to set interventions to reduce neonatal mortality. However, in many developing countries, these data are either lacking or of low quality. We assessed the completeness and accuracy of cause of death (COD) data for neonates in Ghana to assess their usability for monitoring the effectiveness of health system interventions aimed at improving neonatal survival. Methods A lot quality assurance sampling survey was conducted in 20 hospitals in the public sector across four regions of Ghana. Institutional neonatal deaths (IND) occurring from 2014 through 2017 were divided into lots, defined as neonatal deaths occurring in a selected facility in a calendar year. A total of 52 eligible lots were selected: 10 from Ashanti region, and 14 each from Brong Ahafo, Eastern and Volta region. Nine lots were from 2014, 11 from 2015 and 16 each were from 2016 and 2017. The cause of death (COD) of 20 IND per lot were abstracted from admission and discharge (A&D) registers and validated against the COD recorded in death certificates, clinician’s notes or neonatal death audit reports for consistency. With the error threshold set at 5%, ≥ 17 correctly matched diagnoses in a sample of 20 deaths would make the lot accurate for COD diagnosis. Completeness of COD data was measured by calculating the proportion of IND that had death certificates completed. Results Nineteen out of 52 eligible (36.5%) lots had accurate COD diagnoses recorded in their A&D registers. The regional distribution of lots with accurate COD data is as follows: Ashanti (4, 21.2%), Brong Ahafo (7, 36.8%), Eastern (4, 21.1%) and Volta (4, 21.1%). Majority (9, 47.4%) of lots with accurate data were from 2016, followed by 2015 and 2017 with four (21.1%) lots. Two (10.5%) lots had accurate COD data in 2014. Only 22% (239/1040) of sampled IND had completed death certificates. Conclusion Death certificates were not reliably completed for IND in a sample of health facilities in Ghana from 2014 through 2017. The accuracy of cause-specific mortality data recorded in A&D registers was also below the desired target. Thus, recorded IND data in public sector health facilities in Ghana are not valid enough for decision-making or planning. Periodic data quality assessments can determine the magnitude of the data quality concerns and guide site-specific improvements in mortality data management.