Miracle-dz/UniFAR-FTUs huggingface dataset:
The acclimation of leaf photosynthesis of wheat and rice to seasonal temperature changes in T‐FACE environments

Crops show considerable capacity to adjust their photosynthetic characteristics to seasonal changes in temperature. However, how photosynthesis acclimates to changes in seasonal temperature under future climate conditions has not been revealed. We measured leaf photosynthesis (An) of wheat (Triticum aestivum L.) and rice (Oryza sativa L.) grown under four combinations of two levels of CO2 (ambient and enriched up to 500 µmol/mol) and two levels of canopy temperature (ambient and increased by 1.5–2.0°C) in temperature by free‐air CO2 enrichment (T‐FACE) systems. Parameters of a biochemical C3‐photosynthesis model and of a stomatal conductance (gs) model were estimated for the four conditions and for several crop stages. Some biochemical parameters related to electron transport and most gs parameters showed acclimation to seasonal growth temperature in both crops. The acclimation response did not differ much between wheat and rice, nor among the four treatments of the T‐FACE systems, when the difference in the seasonal growth temperature was accounted for. The relationships between biochemical parameters and leaf nitrogen content were consistent across leaf ranks, developmental stages, and treatment conditions. The acclimation had a strong impact on gs model parameters: when parameter values of a particular stage were used, the model failed to correctly estimate gs values of other stages. Further analysis using the coupled gs–biochemical photosynthesis model showed that ignoring the acclimation effect did not result in critical errors in estimating leaf photosynthesis under future climate, as long as parameter values were measured or derived from data obtained before flowering.
A DAO1-Mediated Circuit Controls Auxin and Jasmonate Crosstalk Robustness during Adventitious Root Initiation in Arabidopsis

Adventitious rooting is a post-embryonic developmental program governed by a multitude of endogenous and environmental cues. Auxin, along with other phytohormones, integrates and translates these cues into precise molecular signatures to provide a coherent developmental output. Auxin signaling guides every step of adventitious root (AR) development from the early event of cell reprogramming and identity transitions until emergence. We have previously shown that auxin signaling controls the early events of AR initiation (ARI) by modulating the homeostasis of the negative regulator jasmonate (JA). Although considerable knowledge has been acquired about the role of auxin and JA in ARI, the genetic components acting downstream of JA signaling and the mechanistic basis controlling the interaction between these two hormones are not well understood. Here we provide evidence that COI1-dependent JA signaling controls the expression of DAO1 and its closely related paralog DAO2. In addition, we show that the dao1-1 loss of function mutant produces more ARs than the wild type, probably due to its deficiency in accumulating JA and its bioactive metabolite JA-Ile. Together, our data indicate that DAO1 controls a sensitive feedback circuit that stabilizes the auxin and JA crosstalk during ARI.
Orally-administered Outer-membrane vesicles from Helicobacter pylori reduce H. pylori infection via Th2-biased immune responses in mice.

As the trend of antibiotic resistance has increased, prevention and treatment of Helicobacter pylori infection have been challenged by the fact that no vaccines preventing H. pylori infection are available. Scientists continue to make sustained efforts to find better vaccine formulations and adjuvants to eradicate this chronic infection. In this study, we systemically analyzed the protein composition and potential vaccine function of outer-membrane vesicles (OMVs) derived from gerbil-adapted H. pylori strain 7.13. In total, we identified 169 proteins in H. pylori OMVs and found that outer-membrane, periplasmic, and extracellular proteins (48.9% of the total proteins) were enriched. Furthermore, we evaluated the immune protective response of H. pylori OMVs in a C57BL/6 mouse model, and mice were orally immunized with OMVs or the H. pylori whole cell vaccine (WCV) alone, with or without cholera toxin (CT) as an adjuvant. The data demonstrated that oral immunization with OMVs can elicit a strong humoral and significantly higher mucosal immune response than the group immunized with the WCV plus the CT adjuvant. Moreover, our results also confirmed that OMVs predominantly induced Th2-biased immune responses that can significantly reduce bacterial loads after challenging with the H. pylori Sydney Strain 1 (SS1). In summary, OMVs as new antigen candidates in vaccine design would be of great value in controlling H. pylori infection.
Myotendinous asymmetries derived from the prolonged practice of badminton in professional players

Background The continued practice of a sport linked to the unilateral predominance of the dominant side can provoke chronic asymmetric adaptations in the myotendinous structure and mechanical properties. Objectives: The main purpose was to determine whether asymmetry between the preferred and non-preferred lower limb is present in the lower limb tendon structure, muscle architecture and stiffness values of professional badminton players. Methods Sixteen male professional badminton players (age = 24.1 ± 6.7 years; body height = 177.90 ± 7.53 cm) participated in this study. The muscle architecture of the vastus lateralis (VL), medial gastrocnemius (MG) and lateral gastrocnemius (LG) and the structure of patellar and Achilles tendons were measured in the dominant and non-dominant lower limb with ultrasonography. Stiffness was also measured at the same points with a hand-held MyotonPro. Significant differences between the dominant and non-dominant lower limb were determined using Student’s t test for related samples. Results Bilateral differences were observed for thickness, width and cross-sectional area (CSA) in both tendons showing higher values for the dominant side: patellar tendon CSA (2.02 ± 0.64 vs. 1.51 ± 0.42 cm2; p < 0.05) and Achilles tendon CSA (1.12 ± 0.18 vs. 0.92 ± 0.28 cm2; p < 0.05). No significant differences were observed in muscle architecture and myotonic variables between the dominant and non-dominant lower limb. Conclusions The prolonged practice of badminton caused asymmetries in the CSA, width and thickness of the patellar and Achilles tendon between the dominant and non-dominant lower limbs. No bilateral differences were found in the muscle architecture of VL, MG and LG or in the stiffness of any muscle or tendon analyzed.
Phase transitions beyond post-perovskite in NaMgF3 to 160 GPa

Significance The high-pressure behavior of NaMgF3 is of interest due to its role as a low-pressure analog for phase transitions in the MgSiO3 system. In this work, we have used the diamond anvil cell and synchrotron X-ray diffraction techniques to study structural transitions in NaMgF3 to 1.6 Mbars. Our work has identified a sequence of high-pressure phases beyond post-perovskite in this ABX3 system. We report the presence of a post-post-perovskite phase, followed by a partial and then complete dissociation into binary fluorides. A similar sequence of high-pressure phase transitions in MgSiO3 at very high pressure-temperature conditions has implications for understanding the interiors of large rocky exoplanets. Neighborite, NaMgF3, is used as a model system for understanding phase transitions in ABX3 systems (e.g., MgSiO3) at high pressures. Here we report diamond anvil cell experiments that identify the following phases in NaMgF3 with compression to 162 GPa: NaMgF3 (perovskite) → NaMgF3 (post-perovskite) → NaMgF3 (Sb2S3-type) → NaF (B2-type) + NaMg2F5 (P21/c) → NaF (B2) + MgF2 (cotunnite-type). Our results demonstrate the existence of an Sb2S3-type post-post-perovskite ABX3 phase. We also experimentally demonstrate the formation of the P21/c AB2X5 phase which has been proposed theoretically to be a common high-pressure phase in ABX3 systems. Our study provides an experimental observation of the full sequence of phase transitions from perovskite to post-perovskite to post-post-perovskite followed by 2-stage breakdown to binary compounds. Notably, a similar sequence of transitions is predicted to occur in MgSiO3 at ultrahigh pressures, where it has implications for the mineralogy and dynamics in the deep interior of large, rocky extrasolar planets.
Molecular determinants of response to high dose androgen therapy in prostate cancer.

Clinical trials of high-dose androgen therapy for prostate cancer have shown promising efficacy but are limited by lack of criteria to identify likely responders. To elucidate factors that govern the growth-repressive effects of high-dose androgens we applied an unbiased integrative approach utilizing genetic screens and transcriptional profiling of prostate cancer cells with or without demonstrated phenotypic sensitivity to androgen-mediated growth repression. Through this comprehensive analysis, we identified genetic events and related signaling networks that determine the response to both high-dose androgen and androgen withdrawal. We applied these findings to develop a gene signature that may serve as an early indicator of treatment response and identify men with tumors amenable to high dose androgen therapy.
Is the tumour microenvironment a critical prognostic factor in early-stage colorectal cancer?

a ‘learning health care system’. In general, there are no structured clinical data collections of the outcome of off-label use. In the Netherlands, this approach has been incorporated into a ‘Drug Rediscovery Protocol’ (acronym DRUP) study (ClinicalTrials.gov Identifier: NCT02925234). DRUP serves as a platform where patients can be treated with off-label targeted agents whilst collecting all relevant outcome data. This approach improves access to these off-label drugs, diminishing inequalities in care, ensures robust review of target and treatment selection, and prospectively collects outcome data to be shared with industry, payers and regulatory bodies. This study, initiated in 2016, now has over 26 approved targeted drugs at its disposal. Data from this study led to a pay-for-performance system [10] for nivolumab in patients with MSI-high tumors (no approved drug available in Europe for this indication) whereby the manufacturer provides nivolumab for free during the first 16 weeks of treatment with payer commitment to reimbursement for responding patients. Negative findings are shared with the scientific community in order to prevent repetitive treatments without the outlook of clinical benefit. Several countries are now using similar protocols [e.g. TAPUR (NCT02693535) and CAPTUR (NCT03297606)] which specifically allow data sharing. In conclusion, while we are grateful for all the novel drugs that have been developed for cancer, we have an obligation to maximize the clinical value for our patients and communities. These dual obligations require commitments to rational off-label use and to structured learning through data collection and sharing in order to identify those approaches that deserve to become licensed indications and to be reimbursed. Importantly, this allows us to distinguish them from those that are inadequately effective to justify licensing or clinical recommendation.
Syllable as a unit of information transfer in linguistic communication: The entropy syllable parsing model.

To understand human language-both spoken and signed-the listener or viewer has to parse the continuous external signal into components. The question of what those components are (e.g., phrases, words, sounds, phonemes? ) has been a subject of long-standing debate. We re-frame this question to ask: What properties of the incoming visual or auditory signal are indispensable to eliciting language comprehension? In this review, we assess the phenomenon of language parsing from modality-independent viewpoint. We show that the interplay between dynamic changes in the entropy of the signal and between neural entrainment to the signal at syllable level (4-5 Hz range) is causally related to language comprehension in both speech and sign language. This modality-independent Entropy Syllable Parsing model for the linguistic signal offers insight into the mechanisms of language processing, suggesting common neurocomputational bases for syllables in speech and sign language. This article is categorized under: Linguistics > Linguistic Theory Linguistics > Language in Mind and Brain Linguistics > Computational Models of Language Psychology > Language.
Comparative proteomic analysis of hen egg yolk plasma proteins during embryonic development.

Avian egg yolk provides essential nutrients and physiological support for the developing embryo. To reveal the dynamics of yolk proteins during the entire period of incubation, we analyzed the alterations of egg yolk plasma proteins at different times during incubation (day 0, 7, 14, and 18). Day 14 (D14) of incubation was considered as the key point on the alteration of egg yolk proteins according to the SDS-PAGE analysis. The two-dimensional electrophoresis-based comparative proteomic analysis was conducted, and 26 spots representing 13 proteins were detected with significant changes in abundance. An accelerating transfer of ovalbumin from egg white into egg yolk was observed at D14 in fertilized eggs but not detected in unfertilized eggs, indicating an unrevealed absorbing pathway for the egg proteins/peptides particularly in fertilized eggs. Meanwhile, the abundance of yolk riboflavin-binding protein constantly decreased after D14, which might meet the need for essential riboflavin during embryo development. PRACTICAL APPLICATIONS: These findings provide fundamental insight into the effects of incubation on egg yolk plasma protein alterations during the entire embryonic development for a better understanding of plasma protein biological functions, especially in nutrient transportations and the formation of embryonic organs.
An Evidence-Based Perspective on Movement and Activity Following Median Sternotomy.

Cardiac surgery via median sternotomy is performed in over 1 million patients per year worldwide. Despite evidence, sternal precautions in the form of restricted arm and trunk activity are routinely prescribed to patients following surgery to prevent sternal complications. Sternal precautions may exacerbate loss of independence and prevent patients from returning home directly after hospital discharge. In addition, immobility and deconditioning associated with restricting physical activity potentially contributes to the negative sequelae of median sternotomy on patient symptoms, physical and psychosocial function, and quality of life. Interpreting the clinical impact of sternal precautions is challenging due to inconsistent definitions and applications globally. Following median sternotomy, typical guidelines involve limiting arm movement during loaded lifting, pushing, and pulling for 6 to 8 weeks. In this perspective paper, we propose that there is robust evidence to support early implementation of upper body activity and exercise in patients recovering from median sternotomy while minimizing risk of complications. We advocate a clinical paradigm shift that encourages a greater amount of controlled upper body activity, albeit modified in some situations, and less restrictive sternal precautions. Early screening for sternal complication risk factors and instability followed by individualized progressive functional activity and upper body therapeutic exercise is likely to promote optimal and timely patient recovery. Substantial research documenting current clinical practice of sternal precautions, early physical therapy, and cardiac rehabilitation provides support and the context for understanding why a less restrictive and more active plan of care is warranted and recommended for patients following a median sternotomy.
Metatranscriptomics yields new genomic resources and sensitive detection of infections for diverse blood parasites.

Metatranscriptomics is a powerful method for studying the composition and function of complex microbial communities. The application of metatranscriptomics to multi-species parasite infections is of particular interest, as research on parasite evolution and diversification has been hampered by technical challenges to genome-scale DNA sequencing. In particular, blood parasites of vertebrates are abundant and diverse though they often occur at low infection intensities and exist as multi-species infections, rendering the isolation of genomic sequence data challenging. Here, we use birds and their diverse haemosporidian parasites to illustrate the potential for metatranscriptome sequencing to generate large quantities of genome-wide sequence data from multiple blood parasite species simultaneously. We used RNA-Seq on 24 blood samples from songbirds in North America to show that metatranscriptomes can yield large proportions of haemosporidian protein-coding gene repertoires even when infections are low-intensity (<0.1% red blood cells infected) and consist of multiple parasite taxa. By bioinformatically separating host and parasite transcripts and assigning them to the haemosporidian genus of origin, we found that transcriptomes detected ~23% more total parasite infections across all samples than were identified using microscopy and DNA barcoding. For single-species infections, we obtained data for upwards of 1,300 loci from samples with as low as 0.03% parasitemia, with the number of loci increasing with infection intensity. In total, we provide data for 1,502 single-copy orthologous loci from a phylogenetically-diverse set of 33 haemosporidian mitochondrial lineages. The metatranscriptomic approach described here has the potential to accelerate ecological and evolutionary research on haemosporidians and other diverse parasites.
The neural basis of semantic cognition in Mandarin Chinese: A combined fMRI and TMS study

While converging sources of evidence point to the possibility of a large‐scale distributed network for semantic cognition, a consensus regarding the underlying subregions and their specific function in this network has not been reached. In the current study, we combined functional magnetic resonance imaging (fMRI) and transcranial magnetic stimulation (TMS) methodology to investigate the neural basis of semantic cognition in Mandarin Chinese. In the fMRI experiment, strong activations were observed in left inferior frontal gyrus (IFG) and left middle temporal gyrus (MTG) for semantic judgment task. Moreover, functional connectivity was found from seed region left IFG to left MTG. Meanwhile, negative correlation between performance and extracted parameter estimates from left IFG to left MTG was detected in semantic task. Subsequent TMS stimulation over left IFG resulted in performance deficits in semantic judgment task, in contrast to other three sites: left MTG, right intraparietal sulcus (IPS) and a control site. We concluded that the neural basis of semantic processing for Mandarin Chinese closely resembled that for alphabetic languages such as English, supporting a language‐universal view on semantic cognition.
Error detection using an electromagnetic tracking system in multi-catheter breast interstitial brachytherapy

The hybrid treatment delivery system (HTDS) has been proposed as a possible option for a quality assurance in the multi-catheter interstitial brachytherapy for breast cancer patients. The system, which consists out of a prototype afterloader with an integrated electromagnetic tracking (EMT) sensor and an EMT system, allows the automatic measurement of implanted catheters. To test the feasibility of the system for error detection, possible treatment planning errors and treatment delivery errors were simulated. Planning errors such as an incorrect offset value, an incorrect indexer length, tip/connector end swaps, and partial swaps, and; treatment delivery errors such as catheter shifts and catheter connection swaps were manually simulated using phantoms. An in-house Matlab routine was used to assess geometrical deviations between the dwell positions defined based on CT and EMT measurement. Additionally, the influence of implant motion on the detection ability of the system was assessed. An algorithm for the detection and specification of errors based on the error simulation results was developed. At the University Hospital Erlangen, a patient study is ongoing, where errors in patient data were analyzed using the proposed algorithm. All simulated planning errors were detected. Catheter connection swaps can be detected 100% of the time. A shift detection rate of >97% was observed for shifts larger than 1.1 mm, both in the static and the motion measurements. Catheter reconstruction uncertainties and catheter shifts <2 mm were found to be the most common treatment planning and delivery errors in patient data. HTDS proved to be a reliable method for error detection.
Pharmacokinetics and Pharmacodynamics of Depot Medroxyprogesterone Acetate (DMPA) in African women receiving treatment for HIV and TB: Potential concern for standard dosing frequency.

BACKGROUND Effective contraception is critical to young women with HIV-associated tuberculosis (TB), as unintended pregnancy is associated with increased perinatal morbidity and mortality. The effects of co-administration of efavirenz and rifampicin on the pharmacokinetics of depot medroxyprogesterone acetate (DMPA) are unknown. We hypothesized that clearance of medroxyprogesterone acetate (MPA) would increase when given with rifampicin and efavirenz, thus increasing risk of ovulation. METHODS This pharmacokinetics study assessed DMPA among HIV/TB co-infected women on an efavirenz-based antiretroviral treatment (ART) and rifampicin-based TB treatment. Plasma MPA concentrations and progesterone were measured pre-dose (MPA only), 2, 4, 6, 8, 10 and 12 weeks after a single DMPA 150 mg intramuscular injection. The primary outcome measure, MPA concentration (<0.1 ng/mL) at week 12, was assessed using exact 95% Clopper-Pearson confidence intervals. MPA PK parameters were calculated using non-compartmental analysis. RESULTS Among 42 PK-evaluable women from five African countries, median age was 32 years and median CD4 was 414 cells/mm3. Five women [11.9% (95% CI 4.0-25.6%)] had MPA <0.1 ng/mL at week 12; of these, one had MPA <0.1 ng/mL at week 10. The median clearance of MPA was 19,681 L/week compared to 12,118 L/week for historical controls. There were no adverse events related to DMPA and progesterone concentrations were <1 ng/mL for all women for the study duration. CONCLUSIONS DMPA, when given with rifampicin and efavirenz, was safe. MPA clearance was higher than in women with HIV not on ART, leading to sub-therapeutic concentrations of MPA in 12% of women, suggesting that more frequent dosing might be needed.