Miracle-dz/UniFAR-FTUs huggingface dataset:
NONSTOP GLUMES1 Encodes a C2H2 Zinc Finger Protein That Regulates Spikelet Development in Rice[OPEN]

NSG1, encoding a member of the C2H2 zinc finger protein family, plays a pivotal role in maintaining organ identities in the spikelet by repressing the expression of LHS1, DL, and MFO1. The spikelet is an inflorescence structure unique to grasses. The molecular mechanisms underlying spikelet development and evolution are unclear. In this study, we characterized three allelic recessive mutants in rice (Oryza sativa): nonstop glumes 1-1 (nsg1-1), nsg1-2, and nsg1-3. In these mutants, organs such as the rudimentary glume, sterile lemma, palea, lodicule, and filament were elongated and/or widened, or transformed into lemma- and/or marginal region of the palea–like organs. NSG1 encoded a member of the C2H2 zinc finger protein family and was expressed mainly in the organ primordia of the spikelet. In the nsg1-1 mutant spikelet, LHS1 DL, and MFO1 were ectopically expressed in two or more organs, including the rudimentary glume, sterile lemma, palea, lodicule, and stamen, whereas G1 was downregulated in the rudimentary glume and sterile lemma. Furthermore, the NSG1 protein was able to bind to regulatory regions of LHS1 and then recruit the corepressor TOPLESS-RELATED PROTEIN to repress expression by downregulating histone acetylation levels of the chromatin. The results suggest that NSG1 plays a pivotal role in maintaining organ identities in the spikelet by repressing the expression of LHS1, DL, and MFO1.
Effects of hop bitter acids, bitter components in beer, on cognition in healthy adults: a randomized controlled trial.

The present study aimed to investigate the effects of matured hop bitter acids (MHBAs) on human cognition, mental fatigue, and mood state. In this randomized double-blind placebo-controlled study, 60 healthy adults (age 45-64 years) with self-awareness of cognitive decline were randomly divided into 2 groups and received either orally administered MHBAs (35 mg/day) or placebo for 12 weeks. Cognitive functions and mental states were assessed using neuropsychological tests or questionnaires at baseline and weeks 6 and 12 of the intervention. The change in verbal fluency score at week 6 compared with that at baseline was significantly higher in the MHBAs-treated group compared with the placebo group (P = 0.034), and Stroop test score at week 12 was significantly higher in the MHBAs-treated group compared with the placebo group (P = 0.019). Furthermore, subjective fatigue and anxiety at week 12 were significantly improved in the MHBAs-treated group (P = 0.008 and 0.043, respectively) compared with the placebo group. This is the first study to evaluate the effects of bitter ingredients in beer on cognition, subjective mood, and mental fatigue in a clinical trial. Our findings suggest that hop-derived bitter acids might be beneficial for cognition and mood state.
Metallopeptidase Stp1 activates the transcription factor Sre1 in the carotenogenic yeast Xanthophyllomyces dendrorhous[S]

Xanthophyllomyces dendrorhous is a basidiomycete yeast known as a natural producer of astaxanthin, a carotenoid of commercial interest because of its antioxidant properties. Recent studies indicated that X. dendrorhous has a functional SREBP pathway involved in the regulation of isoprenoid compound biosynthesis, which includes ergosterol and carotenoids. SREBP is a major regulator of sterol metabolism and homeostasis in mammals; characterization in fungi also provides information about its role in the hypoxia adaptation response and virulence. SREBP protease processing is required to activate SREBP pathway functions in fungi. Here, we identified and described the STP1 gene, which encodes a metallopeptidase of the M50 family involved in the proteolytic activation of the transcription factor Sre1 of the SREBP pathway, in X. dendrorhous. We assessed STP1 function in Δstp1 strains derived from the wild-type and a mutant of ergosterol biosynthesis that overproduces carotenoids and sterols. Bioinformatic analysis of the deduced protein predicted the presence of characteristic features identified in homologs from mammals and fungi. The Δstp1 mutation decreased yeast growth in the presence of azole drugs and reduced transcript levels of Sre1-dependent genes. This mutation also negatively affected the carotenoid- and sterol-overproducing phenotype. Western blot analysis demonstrated that Sre1 was activated in the yeast ergosterol biosynthesis mutant and that the Δstp1 mutation introduced in this strain prevented Sre1 proteolytic activation. Overall, our results demonstrate that STP1 encodes a metallopeptidase involved in proteolytic activation of Sre1 in X. dendrorhous, contributing to our understanding of fungal SREBP pathways.
Serving as a bedside surgeon before performing robotic radical prostatectomy improves surgical outcomes

ABSTRACT Introduction: To evaluate the influence of previous experience as bedside assistants on patient selection, perioperative and pathological results in robot assisted laparoscopic radical prostatectomy. Materials and Methods: The first 50 cases of two robotic surgeons were reviewed retrospectively. Group 1 consisted of the first 50 cases of the surgeon with previous experience as a robotic bedside assistant between September 2016-July 2018, while Group 2 included the first 50 cases of the surgeon with no bedside assistant experience between February 2009-December 2009. Groups were examined in terms of demographics, prostate volume, presence of median lobe, prostate specific antigen (PSA), preoperative Gleason score, positive core number, clinical stage, console surgery time, estimated blood loss, postoperative Gleason score, pathological stage, positive surgical margin rate, postoperative complications, length of hospital stay and biochemical recurrence rate. Results: Previous abdominal surgery and the presence of median lobe hypertrophy rates were higher in Group 1 than in Group 2 (20% vs. 4%, p=0.014; 24% vs. 6%, p=0.012; respectively). In addition, patients in Group 1 were in a higher clinical stage than those in Group 2 (cT2: 70% vs. 28%, p=0.001). Median console surgery time and median length of hospital stay was significantly shorter in Group 1 than in Group 2 (170 min vs. 240 min, p=0.001; 3 vs. 4, p=0.022; respectively). Clavien grade 3 complication rate was higher in Group 2 but was statistically insignificant. Conclusion: Our findings might reflect that previous bedside assistant experience led to an increase in self-confidence and the ability to manage troubleshooting and made it more likely for surgeons to start with more difficult cases with more challenging patients. It is recommended that novice surgeons serve as bedside assistants before moving on to consoles.
MRIgRT Head and Neck Anthropomorphic QA Phantom: Design, Development, Reproducibility and Feasibility Study.

PURPOSE The purpose of this paper was to design, manufacture, and evaluate a tissue equivalent, dual MR/CT visible anthropomorphic Head and Neck (H&N) phantom. This phantom was specially designed as an end-to-end quality assurance (QA) tool for magnetic resonance (MR) imaging guided radiotherapy (MRIgRT) systems participating in NCI-sponsored clinical trials. METHOD The MRIgRT H&N phantom was constructed using a water-fillable acrylic shell and a custom insert that mimics an organ at risk (OAR) and target structures. The insert consists of a primary and secondary PTV manufactured of a synthetic Clear Ballistic gel, an acrylic OAR and surrounding tissue fabricated using melted Superflab. Radiochromic EBT3 film and TLDs were used to measure the dose distribution and absolute dose, respectively. The phantom was evaluated by conducting an end-to-end test that included: imaging on a GE Lightspeed CT simulator, planning on Monaco treatment planning software (TPS), verifying treatment setup with MR and irradiating on Elekta's 1.5T Unity MR linac system. The phantom was irradiated three times using the same plan to determine reproducibility. Three institutions, equipped with either ViewRay MRIdian 60 Co or ViewRay MRIdian Linac, were used to conduct a feasibility study by performing independent end-to-end studies. TLDs were evaluated in both reproducibility and feasibility studies by comparing ratios of measured TLD to reported TPS calculated values. Radiochromic film was used to compare measured planar dose distributions to expected TPS distributions. Film was evaluated by using an in-house gamma analysis software to measure the discrepancies between film and TPS. RESULTS The MRIgRT H&N phantom on the Unity system resulted in reproducible TLD doses (SD < 1.5%). The measured TLD to calculated dose ratios for the Unity system ranged from 0.94 to 0.98. The Viewray dose result comparisons had a larger range (0.95-1.03) but these depended on the TPS dose calculations from each site. Using a 7%/4mm gamma analysis, Viewray institutions had average axial and sagittal passing rates of 97.3% and 96.2% and the Unity system had average passing rates of 97.8% and 89.7%, respectively. All of the results were within the Imaging and Radiation Oncology Core in Houston (IROC-Houston) standard credentialing criteria of 7% on TLDs, and > 85% of pixels passing gamma analysis using 7%/4mm on films. CONCLUSIONS An MRIgRT H&N phantom that is tissue equivalent and visible on both CT and MR was developed. The results from initial reproducibility and feasibility testing of the MRIgRT H&N phantom using the tested MGIgRT systems suggests the phantom's potential utility as a credentialing tool for NCI-clinical trials.
Jodindtagelse i Danmark

Iodine deficiency with a high frequency of goitre and, in severely affected areas, cretinism is common in some areas of the world. In Denmark the iodine intake as evaluated by urinary iodine excretion has been at a stable low level for many years, except for the part of the population now taking iodine supplementation as part of vitamin/ mineral preparations. The iodine intake is lowest in the western part of the country where an epidemiological study of elderly subjects has demonstrated a high frequency of goitre and hyperthyroidism in women. This supports the suggestion of a controlled moderate increase in iodine intake via an iodine supplementation program.
De Novo Genome Assembly of Populus simonii Further Supports That Populus simonii and Populus trichocarpa Belong to Different Sections

Populus simonii is an important tree in the genus Populus, widely distributed in the Northern Hemisphere and having a long cultivation history. Although this species has ecologically and economically important values, its genome sequence is currently not available, hindering the development of new varieties with wider adaptive and commercial traits. Here, we report a chromosome-level genome assembly of P. simonii using PacBio long-read sequencing data aided by Illumina paired-end reads and related genetic linkage maps. The assembly is 441.38 Mb in length and contain 686 contigs with a contig N50 of 1.94 Mb. With the linkage maps, 336 contigs were successfully anchored into 19 pseudochromosomes, accounting for 90.2% of the assembled genome size. Genomic integrity assessment showed that 1,347 (97.9%) of the 1,375 genes conserved among all embryophytes can be found in the P. simonii assembly. Genomic repeat analysis revealed that 41.47% of the P. simonii genome is composed of repetitive elements, of which 40.17% contained interspersed repeats. A total of 45,459 genes were predicted from the P. simonii genome sequence and 39,833 (87.6%) of the genes were annotated with one or more related functions. Phylogenetic analysis indicated that P. simonii and Populus trichocarpa should be placed in different sections, contrary to the previous classification according to morphology. The genome assembly not only provides an important genetic resource for the comparative and functional genomics of different Populus species, but also furnishes one of the closest reference sequences for identifying genomic variants in an F1 hybrid population derived by crossing P. simonii with other Populus species.
Has the long-predicted decline in consanguineous marriage in India occurred?

Abstract To an extent the question posed in the title of this paper can simply be answered in the affirmative. Based on the extensive data available from the National Family Health Survey-1 (NFHS-1) conducted in 1992–93 and NFHS-4 in 2015–16 there has been a significant overall decline of some 19% in the prevalence of consanguineous marriage in India. However, when examined at state level the picture is more complex, with large reductions in consanguinity in southern states where intra-familial marriage previously has been strongly favoured, whereas in some northern states in which close kin unions traditionally have been proscribed small increases were recorded. In a country such as India, comprising an estimated 18% of the current world population and with multiple ethnic, religious, geographical and social sub-divisions, apparently contrary findings of this nature are not unexpected – especially given the major shifts that are underway in family sizes, in education and employment, and with rapid urbanization. The changing health profile of the population also is an important factor, with non-communicable diseases now responsible for a majority of morbidity and premature mortality in adulthood. The degree to which future alterations in the prevalence and profile of consanguineous marriage occur, and at what rate, is difficult to predict – the more so given the markedly diverse cultural identities that remain extant across the Sub-Continent, and ongoing intra-community endogamy.
Specification of BMP Signaling

Bone Morphogenetic Proteins (BMPs) together with the Growth and Differentiation Factors (GDFs) form the largest subgroup of the Transforming Growth Factor (TGF)β family and represent secreted growth factors, which play an essential role in many aspects of cell communication in higher organisms. As morphogens they exert crucial functions during embryonal development, but are also involved in tissue homeostasis and regeneration in the adult organism. Their involvement in maintenance and repair processes of various tissues and organs made these growth factors highly interesting targets for novel pharmaceutical applications in regenerative medicine. A hallmark of the TGFβ protein family is that all of the more than 30 growth factors identified to date signal by binding and hetero-oligomerization of a very limited set of transmembrane serine-threonine kinase receptors, which can be classified into two subgroups termed type I and type II. Only seven type I and five type II receptors exist for all 30plus TGFβ members suggesting a pronounced ligand-receptor promiscuity. Indeed, many TGFβ ligands can bind the same type I or type II receptor and a particular receptor of either subtype can usually interact with and bind various TGFβ ligands. The possible consequence of this ligand-receptor promiscuity is further aggravated by the finding that canonical TGFβ signaling of all family members seemingly results in the activation of just two distinct signaling pathways, that is either SMAD2/3 or SMAD1/5/8 activation. While this would implicate that different ligands can assemble seemingly identical receptor complexes that activate just either one of two distinct pathways, in vitro and in vivo analyses show that the different TGFβ members exert quite distinct biological functions with high specificity. This discrepancy indicates that our current view of TGFβ signaling initiation just by hetero-oligomerization of two receptor subtypes and transduction via two main pathways in an on-off switch manner is too simplified. Hence, the signals generated by the various TGFβ members are either quantitatively interpreted using the subtle differences in their receptor-binding properties leading to ligand-specific modulation of the downstream signaling cascade or additional components participating in the signaling activation complex allow diversification of the encoded signal in a ligand-dependent manner at all cellular levels. In this review we focus on signal specification of TGFβ members, particularly of BMPs and GDFs addressing the role of binding affinities, specificities, and kinetics of individual ligand-receptor interactions for the assembly of specific receptor complexes with potentially distinct signaling properties.
Cognitive Integration of Personal or Public Events Affects Mental Health: Examining Memory Networks in a Case of Natural Flooding Disaster.

OBJECTIVE The purpose of this research was to examine whether memories of personal or public events could affect mental health through the way those memories are integrated in memory networks. METHOD Participants from the general population (N = 224, age mean = 36.62 years, 74% female) were either directly or indirectly personally affected by a natural flooding disaster with moderate consequences or had simply learned about it. A prospective design (during the floods and two months later) was used to examine the impact that such a personal or public event memory could have on their mental health. RESULTS Results showed that flood-affected individuals reported poorer mental health compared to the unaffected. However, both affected and unaffected individuals who had encoded a current floods-related event in memory as need satisfying or who had embedded such an event in need satisfying memory networks showed better mental health over time. These results held after controlling for the effect of various demographics and dispositional emotion regulation styles. CONCLUSION Simply learning about public events can impact mental health through the way those events are integrated in memory, which appears as a critical individual difference.
Efficacy and Determinants of Response to HER Kinase Inhibition in HER2-Mutant Metastatic Breast Cancer.

HER2 mutations define a subset of metastatic breast cancers with a unique mechanism of oncogenic addiction to HER2 signaling. We explored activity of the irreversible pan-HER kinase inhibitor neratinib, alone or with fulvestrant, in 81 patients with HER2-mutant metastatic breast cancer. Overall response rate was similar with or without estrogen receptor (ER) blockade. By comparison, progression-free survival and duration of response appeared longer in ER+ patients receiving combination therapy, although the study was not designed for direct comparison. Pre-existent concurrent activating HER2 or HER3 alterations were associated with poor treatment outcome. Similarly, acquisition of multiple HER2-activating events, as well as gatekeeper alterations, were observed at disease progression in a high proportion of patients deriving clinical benefit from neratinib. Collectively these data define HER2 mutations as a therapeutic target in breast cancer and suggest that co-existence of additional HER signaling alterations may promote both de novo and acquired resistance to neratinib.
Spider Monkeys Rule the Roost: Ateline Sleeping Sites Influence Rainforest Heterogeneity

Simple Summary Spider monkeys are important dispersers of many hardwood trees that contribute greatly to the carbon sequestration of tropical forests. One way in which Spider monkeys influence tropical ecosystem structure and function is through the creation of visible terrestrial latrines beneath their “sleeping sites”—trees in which they frequently return to sleep. Spider monkey latrines are thought to create high quality resource patches for rainforest plants and other wildlife to exploit. We investigate this using camera traps placed in both the canopy and on the rainforest floor to determine which rainforest wildlife are attracted to the latrines beneath the sleeping sites of spider monkeys. We also assess the tree species and dung beetles found within the latrines compared with other areas of the forest. Our evidence suggests that spider monkey roosting sites are a hub of activity for other rainforest wildlife, and act as germinating beds for many rainforest trees. If rainforests were to lose spider monkeys, from intensive hunting for example, many other rainforest wildlife species would be affected, and forests would therefore be made up of different tree communities than landscapes where spider monkeys exist. Abstract The sleeping site behavior of Ateline primates has been of interest since the 1980s, yet limited focus has been given to their influence upon other rainforest species. Here, we use a combination of arboreal and terrestrial camera traps, and dung beetle pitfall traps, to characterize spider monkey sleeping site use and quantify the impact of their associated latrines on terrestrial vertebrate and dung beetle activity. We also characterize the physical characteristics of the sleeping sites and the floristic and soil composition of latrines beneath them. Spider monkey activity at sleeping sites peaked at dawn and dusk and group composition varied by sex of the adults detected. The habitat-use of terrestrial fauna (vertebrates and dung beetles) differed between latrine sites and non-latrine controls, underpinned by species-specific changes in the relative abundance of several seed-dispersing species (such as paca and great curassow). Seedling density was higher in latrines than in non-latrine controls. Although most soil properties were similar between latrines and controls, potassium and manganese concentrations were different. These results suggest that spider monkey sleeping site fidelity leads to a hotspot of ecological activity in latrines and downstream impacts on rainforest floristic composition and diversity.
From back to front: A functional model for the cerebellar modulation in the establishment of conditioned preferences for cocaine‐related cues

It is now increasingly clear that the cerebellum may modulate brain functions altered in drug addiction. We previously demonstrated that cocaine‐induced conditioned preference increased activity at the dorsal posterior cerebellar vermis. Unexpectedly, a neurotoxic lesion at this region increased the probability of cocaine‐induced conditioned preference acquisition. The present research aimed at providing an explanatory model for such as facilitative effect of the cerebellar lesion. First, we addressed a tracing study in which we found a direct projection from the lateral (dentate) nucleus to the ventral tegmental area (VTA) that also receives Purkinje axons from lobule VIII in the vermis. This pathway might control the activity and plasticity of the cortico‐striatal circuitry. Then we evaluated cFos expression in different regions of the medial prefrontal cortex and striatum after a lesion in lobule VIII before conditioning. Additionally, perineuronal net (PNN) expression was assessed to explore whether the cerebellar lesion might affect synaptic stabilization mechanisms in the medial prefrontal cortex (mPFC). Damage in this region of the vermis induced general disinhibition of the mPFC and striatal subdivisions that receive dopaminergic projections, mainly from the VTA. Moreover, cerebellar impairment induced an upregulation of PNN expression in the mPFC. The major finding of this research was to provide an explanatory model for the function of the posterior cerebellar vermis on drug‐related memory. In this model, damage of the posterior vermis would release striatum‐cortical networks from the inhibitory tonic control exerted by the cerebellar cortex over VTA, thereby promoting drug effects.