Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins

Significance Plants biosynthesize their own proteinogenic aromatic l-amino acids, namely l-phenylalanine, l-tyrosine, and l-tryptophan, not only for building proteins but also for the production of a plethora of aromatic amino acid-derived natural products. Pyridoxal 5′-phosphate (PLP)-dependent aromatic l-amino acid decarboxylase (AAAD) family enzymes play important roles in channeling various aromatic l-amino acids into diverse downstream specialized metabolic pathways. Through comparative structural analysis of four functionally divergent plant AAAD proteins together with biochemical characterization and molecular dynamics simulations, we reveal the structural and mechanistic basis for the rich divergent and convergent evolutionary development within the plant AAAD family. Knowledge learned from this study aids our ability to engineer high-value aromatic l-amino acid-derived natural product biosynthesis in heterologous chassis organisms. Radiation of the plant pyridoxal 5′-phosphate (PLP)-dependent aromatic l-amino acid decarboxylase (AAAD) family has yielded an array of paralogous enzymes exhibiting divergent substrate preferences and catalytic mechanisms. Plant AAADs catalyze either the decarboxylation or decarboxylation-dependent oxidative deamination of aromatic l-amino acids to produce aromatic monoamines or aromatic acetaldehydes, respectively. These compounds serve as key precursors for the biosynthesis of several important classes of plant natural products, including indole alkaloids, benzylisoquinoline alkaloids, hydroxycinnamic acid amides, phenylacetaldehyde-derived floral volatiles, and tyrosol derivatives. Here, we present the crystal structures of four functionally distinct plant AAAD paralogs. Through structural and functional analyses, we identify variable structural features of the substrate-binding pocket that underlie the divergent evolution of substrate selectivity toward indole, phenyl, or hydroxyphenyl amino acids in plant AAADs. Moreover, we describe two mechanistic classes of independently arising mutations in AAAD paralogs leading to the convergent evolution of the derived aldehyde synthase activity. Applying knowledge learned from this study, we successfully engineered a shortened benzylisoquinoline alkaloid pathway to produce (S)-norcoclaurine in yeast. This work highlights the pliability of the AAAD fold that allows change of substrate selectivity and access to alternative catalytic mechanisms with only a few mutations.
Using an Accelerometer-Based Step Counter in Post-Stroke Patients: Validation of a Low-Cost Tool †

Monitoring the real-life mobility of stroke patients could be extremely useful for clinicians. Step counters are a widely accessible, portable, and cheap technology that can be used to monitor patients in different environments. The aim of this study was to validate a low-cost commercial tri-axial accelerometer-based step counter for stroke patients and to determine the best positioning of the step counter (wrists, ankles, and waist). Ten healthy subjects and 43 post-stroke patients were enrolled and performed four validated clinical tests (10 m, 50 m, and 6 min walking tests and timed up and go tests) while wearing five step counters in different positions while a trained operator counted the number of steps executed in each test manually. Data from step counters and those collected manually were compared using the intraclass coefficient correlation and mean average percentage error. The Bland–Altman plot was also used to describe agreement between the two quantitative measurements (step counter vs. manual counting). During walking tests in healthy subjects, the best reliability was found for lower limbs and waist placement (intraclass coefficient correlations (ICCs) from 0.46 to 0.99), and weak reliability was observed for upper limb placement in every test (ICCs from 0.06 to 0.38). On the contrary, in post-stroke patients, moderate reliability was found only for the lower limbs in the 6 min walking test (healthy ankle ICC: 0.69; pathological ankle ICC: 0.70). Furthermore, the Bland–Altman plot highlighted large average discrepancies between methods for the pathological group. However, while the step counter was not able to reliably determine steps for slow patients, when applied to the healthy ankle of patients who walked faster than 0.8 m/s, it counted steps with excellent precision, similar to that seen in the healthy subjects (ICCs from 0.36 to 0.99). These findings show that a low-cost accelerometer-based step counter could be useful for measuring mobility in select high-performance patients and could be used in clinical and real-world settings.
Novel Applications of Mesenchymal Stem Cell-Derived Exosomes for Myocardial Infarction Therapeutics

Cardiovascular diseases (CVDs) are the leading cause of mortality and morbidity globally, representing approximately a third of all deaths every year. The greater part of these cases is represented by myocardial infarction (MI), or heart attack as it is better known, which occurs when declining blood flow to the heart causes injury to cardiac tissue. Mesenchymal stem cells (MSCs) are multipotent stem cells that represent a promising vector for cell therapies that aim to treat MI due to their potent regenerative effects. However, it remains unclear the extent to which MSC-based therapies are able to induce regeneration in the heart and even less clear the degree to which clinical outcomes could be improved. Exosomes, which are small extracellular vesicles (EVs) known to have implications in intracellular communication, derived from MSCs (MSC-Exos), have recently emerged as a novel cell-free vector that is capable of conferring cardio-protection and regeneration in target cardiac cells. In this review, we assess the current state of research of MSC-Exos in the context of MI. In particular, we place emphasis on the mechanisms of action by which MSC-Exos accomplish their therapeutic effects, along with commentary on the current difficulties faced with exosome research and the ongoing clinical applications of stem-cell derived exosomes in different medical contexts.
Recent advances in landmarks research

Recently, most the state of the art heuristics utilize landmarks to estimate the path from current state to the goal. In this paper, we summarize many types of landmarks, the techniques for finding ordered landmarks, the approaches to exploit landmarks, analysis their differences, advantages and disadvantages, and discuss the future research with landmarks, and the trends of planning with landmarks.
The effectiveness of Kinesio Taping® for mobility and functioning improvement in knee osteoarthritis: a randomized, double-blind, controlled trial

Objective: To evaluate the effectiveness of the Kinesio Taping® method for mobility and functioning improvement for patients with knee osteoarthritis (KO). Design: Randomized, double-blinded, controlled trial. Setting: Outpatient rehabilitation department. Subjects: A total of 187 subjects with symptomatic I–III grade KO participated; of these, 157 subjects were included in the analyses (intervention group, n = 81 (123 knees); control group, n = 76 (114 knees). Intervention: The intervention group received a specific Kinesio Taping application, and the control group received non-specific knee taping for a month. Main measures: Changes in Knee injury and Osteoarthritis Outcome Scores (KOOS), knee active range of motion, 10-Meter Walk, and the five times sit to stand tests (5xSST) were assessed at baseline, after four weeks of taping, and a month post taping intervention. Subjective participants’ experiences and opinions on the effect of knee taping were evaluated. The chosen level of significance was p < 0.05. Results: The mean age of participants was 68.7 ± 9.9 in intervention group and 70.6 ± 8.3 in control group (p > 0.05). The change from baseline in gait speed in the intervention group after taping month was +0.04 ± 0.1 m/s, at follow-up +0.06 ± 0.1 m/s; in control group +0.07 ± 0.1 m/s, and +0.09 ± 0.1 m/s; the change in time needed to accomplish 5xSST was –2.2 ± 3.2 seconds, at follow-up –2.4 ± 3.1 seconds; in control group –2.8 ± 3.6 seconds, and –2.4 ± 4 seconds. Improved knee flexion and enhancement in functioning assessed by KOOS were noticed in both groups, with lasting improvement to follow up. No difference in the change in the above-mentioned outcomes was found between groups (p > 0.05). Fewer subjects (6.2% (5) vs. 21.1% (16), χ2 = 7.5, df = 2, p = 0.024) from Kinesio Taping group were unsure if taping alleviated their mobility and more intervention group patients indicated higher subjective satisfaction with the effect of knee taping to symptom and mobility alleviation than control group (p < 0.005). Conclusion: Investigated Kinesio Taping technique did not produce better results in mobility and functioning improvement over non-specific knee taping; however, it had higher patient-reported subjective value for symptom attenuation and experienced mobility enhancement.
Multiple growth of graphene from a pre-dissolved carbon source

Mono- to few-layer graphene materials are successfully synthesized multiple times using Cu-Ni alloy as a catalyst after a single-chemical vapor deposition (CVD) process. The multiple synthesis is realized by extracting carbon source pre-dissolved in the catalyst substrate. Firstly, graphene is grown by the CVD method on Cu-Ni catalyst substrates. Secondly, the same Cu-Nicatalyst foils are annealed, in absence of any external carbon precursor, to grow graphene using the carbon atoms pre-dissolved in the catalyst during the CVD process. This annealing process is repeated to synthesize graphene successfully until carbon is exhausted in the Cu-Ni foils. After the CVD growth and each annealing growth process, the as-grown graphene is removed using a bubbling transfer method. A wide range of characterizations are performed to examine the quality of the obtained graphene material and to monitor the carbon concentration in the catalyst substrates. Results show that graphene from each annealing growth process possesses a similar quality, which confirmed the good reproducibility of the method. This technique brings great freedom to graphene growth and applications, and it could be also used for other 2D material synthesis.
Bacterial Diversity within Feedlot Manure

In this study, we identified the predominant culturable anaerobic bacteria and enumerated the total culturable anaerobic bacterial population present in samples of feedlot manure from Southern Queensland. Sixteen bacterial isolates were cultured from feedlot pad material with species of Lactobacillus, Clostridium and Bacillus predominating. From a library of 123 clones, produced by the amplification, cloning and partial DNA sequencing of the 16S rRNA gene, only 3% were closely related to previously described species and 21% to known genera. Of the total clone library, 96% were apparently Gram-positive and fell within families whose members were generally anaerobes. The majority (71%) of the clone library was related to either members of the family Clostridiaceae or lactic acid-producing bacteria (Lactobacillus or Lactosphaera). It was concluded that Gram-positive clostridial and lactic acid-producing bacteria predominate in feedlot pad manure. The overwhelming majority of species are novel and have not been obtained in culture. It would appear that the most likely source of the sickly-sweet nuisance odours (particularly from butyric acid) that emanate from feedlots is the by-product of anaerobic fermentation by clostridia. Gut-inhabiting and Gram-negative bacteria do not appear to survive for lengthy periods of time under the environmental conditions present in feedlot manure.
Atmospheric Chemistry of Enols: The Formation Mechanisms of Formic and Peroxyformic Acids in Ozonolysis of Vinyl Alcohol.

Vinyl alcohol (VA), for a long time, is thought to be a missing source of formic acid (FA) in the atmospheric models. However, a recent study has shown that FA is just a by-product in the OH-initiated oxidation of VA, which stimulates investigation on the other sinks of VA in the atmosphere. In this study, the detailed ozonolysis mechanism of VA was investigated theoretically for the first time. The results show that two primary ozonides (syn- and anti-POZ) can be formed in the ozonolysis of VA and that FA coupled with the simplest Criegee intermediate (CH2OO) can be produced as the main nascent products. Thus, the ozonolysis of VA is predicted to be a more efficient process to produce FA in the atmosphere compared with its OH-initiated oxidation. Moreover, it's found that the syn-POZ can directly decompose to peroxyformic acid plus formaldehyde breaking the known "Criegee mechanism" to form carbonyl oxide with carbonyl compound. This special mechanism by providing a new source of peroxy acids in the atmosphere enriches the atmospheric chemistry of enols. The atmospheric lifetime of VA by ozonolysis is predicted to be 30 h, comparable with its prevalent reaction with the OH radical. Therefore, the obtained theoretical results can be usefully incorporated into future modeling study of enols.
Ruminal fermentation characteristics and protein fraction effects on metabolizable protein synthesis of beef cattle fed different levels of crude protein

The effects of nitrogen levels of protein supplements were evaluated on the concentrations of ammonical nitrogen (N-NH3), volatile fatty acids (VFA's) concentrations and pH in beef cattle grazing Brachiaria brizantha cv. Marandu. The microbial protein synthesis, ruminal undegradable protein (RUP) and endogenous crude protein (ECP) and their contributions to the pool of metabolizable protein (MP). Four Nelore steer, 395 ± 9 kg, fitted with ruminal cannulas, were used to evaluate ruminal parameters, degradability, ruminal kinetics and microbial synthesis in a 4 ×4 Latin square design. The animals were supplied with 400g/head/day of supplements containing 30, 40, and 50% crude protein (CP) for comparison with a control group without protein supplementation (C). The animals grazed Brachiaria brizantha cv Marandu, distributed in four one-hectare paddocks where the supplements were offered and the orts removed daily. The N-NH3 levels in the animals that received 50% CP were higher than those observed in animals receiving 40% CP and C, but were similar to the levels observed in the animals supplemented with 30% CP. The VFA concentrations in the group supplemented with 30% PB were higher than the control treatment (C) and similar to those obtained with 40 and 50% CP supplementation. The pH did not differ among the groups. The microbial synthesis and RUP were greater for the animals that received protein supplementation compared to the control treatment.
Vascular pathways in the gill of ling cod, Ophiodon elongatus

Corrosion plastic casts were made of the gill vasculature in ling cod (Ophiodon elongatus) using methyl methacrylate. The vessels afferent and efferent to the gills are described, as well as the microvasculature of the filament. There is a respiratory network and a venolymphatic network. The venolymphatic network is derived from efferent arteries and thus all cardiac output must pass through the gill lamellae.
Effects of risk factors related to computer use on musculoskeletal pain in office workers

Purpose. Work-related musculoskeletal disorders (WMSDs) are increasing due to overuse of desktop computers. This investigation examined musculoskeletal pain in office workers. Methods. Sociodemographic factors were recorded for 362 participants (female, 50.8%; male, 49.2%; mean age 37.35 ± 8.43 years). Participants were questioned for their daily working time, computer usage time and years, whether musculoskeletal pain was related to their job and whether pain disturbed their activities of daily living (ADLs). Working postures were observed and pain severity was evaluated by visual analog scale. Results. Participants more frequently had upper back pain (69.6%), neck pain (65.2%) and lower back pain (LBP) (64.1%) during the last 12 months; 60.5% of participants reported pain after they started work. LBP (32.9%), back pain (28.2%) and neck pain (22.9%) restricted participants’ daily life. We found positive correlations between daily computer use and neck/upper back, and LBP. Conclusions. The most painful areas of participants using desktop computers were the upper back, neck, lower back and shoulder, and the pain in these regions affected ADLs negatively. This pain mostly occurred after the current job and these individuals experience more intense pain. Ergonomic approaches could reduce WMSDs and make workers more independent in ADLs and prevent chronicity.
Structural Transitions in Ge2Sb2Te5 Phase Change Memory Thin Films Induced by Nanosecond UV Optical Pulses

Ge-Sb-Te-based phase change memory alloys have recently attracted a lot of attention due to their promising applications in the fields of photonics, non-volatile data storage, and neuromorphic computing. Of particular interest is the understanding of the structural changes and underlying mechanisms induced by short optical pulses. This work reports on structural changes induced by single nanosecond UV laser pulses in amorphous and epitaxial Ge2Sb2Te5 (GST) thin films. The phase changes within the thin films are studied by a combined approach using X-ray diffraction and transmission electron microscopy. The results reveal different phase transitions such as crystalline-to-amorphous phase changes, interface assisted crystallization of the cubic GST phase and structural transformations within crystalline phases. In particular, it is found that crystalline interfaces serve as crystallization templates for epitaxial formation of metastable cubic GST phase upon phase transitions. By varying the laser fluence, GST thin films consisting of multiple phases and different amorphous to crystalline volume ratios can be achieved in this approach, offering a possibility of multilevel data storage and realization of memory devices with very low resistance drift. In addition, this work demonstrates amorphization and crystallization of GST thin films by using only one UV laser with one single pulse duration and one wavelength. Overall, the presented results offer new perspectives on switching pathways in Ge-Sb-Te-based materials and show the potential of epitaxial Ge-Sb-Te thin films for applications in advanced phase change memory concepts.
MONOFUNCTIONAL COVALENT PHOTOBINDING OF DICTAMNINE, A FUROQUINOLINE ALKALOID, TO DNA AS TARGET IN VITRO

Abstract— The naturally occurring furoquinoline alkaloid, dictamnine, is phototoxic to Gram‐positive bacteria, yeasts and filamentous fungi in the presence of long‐wave UV light. Prior to photobinding to DNA dictamnine forms a complex with the macromolecule in the dark. Photobinding to DNA is shown with [3H]‐dictamnine. In contradiction to an earlier finding, dictamnine proved to be incapable of forming interstrand crossiinkages with native DNA. This fact was ascertained by the use of methods additional to hydroxyapatite column chromatography, e.g. alkaline sucrose gradient centrifugation and hyperchromicity tests. The alkaloid therefore represents a new monofunctional photoreagent towards DNA in vitro. It is assumed that it binds through its furyl‐C=C to DNA. The inability to form crosslinks may be attributed to the stability of the lateral aromatic nucleus. As no photoreactivity against human erythrocytes could be observed, it is possible that nucleic acids represent the major target of damage in vivo.
The influence of photoperiod on the Vrn-H2 locus (4H) which is a major determinant of plant development and reproductive fitness traits in a facultative × winter barley (Hordeum vulgare L.) mapping population

To determine the effect of Vrn-H2 locus on plant developmental and agronomic traits, detailed controlled environment tests involving a factorial set of vernalization and photoperiod treatments were carried out using doubled haploid lines developed from a facultative (Vrn-H2 - ) x winter (Vrn-H2 + ) barley cross. The allele phase at the Vrn-H2 locus influenced heading date as well as the developmental and agronomic traits. The performance of Vrn-H2 + lines was significantly influenced by vernalization: reproductive fitness traits showed significant decreases without vernalization. However, the effects of alleles at the Vrn-H2 locus extended beyond simple satisfaction of the vernalization requirement. Vrn-H2 + lines showed increased reproductive fitness compared with Vrn-H2 - lines when vernalization was followed by a long photoperiod. The responses of the two Vrn-H2 allele classes to photoperiod duration were quite different in terms of heading date, developmental and agronomic traits. These results suggest that alleles at the Vrn-H2 locus - and/or tightly linked gene(s) - respond primarily to the exogenous signal of vernalization (temperature), but when the vernalization requirement has been fulfilled, they also respond to photoperiod duration.
Normal human and sheep fetal vessel oxygen saturations by T2 magnetic resonance imaging

Human fetal Doppler ultrasound and invasive blood gas measurements obtained by cordocentesis or at the time of delivery reveal similarities with sheep (an extensively used model for human fetal cardiovascular physiology). Oxygen saturation (SO2) measurements in human fetuses have been limited to the umbilical and scalp vessels, providing little information about normal regional SO2 differences in the fetus. Blood T2 MRI relaxometry presents a non‐invasive measure of SO2 in the major fetal vessels. This study presents the first in vivo validation of fetal vessel T2 oximetry against the in vitro T2–SO2 relationship using catheterized sheep fetuses and compares the normal SO2 in the major vessels between the human and sheep fetal circulations. Human fetal vessel SO2 by T2 MRI confirms many similarities with the sheep fetal circulation and is able to demonstrate regional differences in SO2; in particular the significantly higher SO2 in the left versus right heart.
The fine structure of muscle fibres of roach, Rutilus rutilus (L.), and chub, Leuciscus cephalus (L.), Cyprinidae, Teleostei: interspecific differences and effects of habitat and season

Red and white axial muscle fibres from roach and chub were investigated by electron microscopy. Fish from three different localities were compared. Qualitative and quantitative analysis of myofibrils, mitochondria, lipid and subsarcolemmal cytoplasm with regard to muscle fibre type, species, season and habitat were made. Muscle fibre types differ significantly with the exception of the subsarcolemmal cytoplasm in roach. Within-species lipid content of red fibres differs between seasons. However, the most marked effect on red muscle fibres within species and season as regards volume density of lipid and mitochondria can be attributed to the different localities. The results are discussed in relation to mode of life and differences in habitat.