julilili42/papers huggingface dataset:
A Photoreactive Iron(II) Complex Luminophore
2022-01-13

Controlling the order and lifetimes of electronically excited states is essential to effective light-to-potential energy conversion by molecular chromophores. This work reports a luminescent and photoreactive iron(II) complex, the first performant group homologue of prototypical sensitizers of ruthenium. Double cyclometalation of a phenylphenanthroline framework at iron(II) favors the population of a triplet metal-to-ligand charge transfer (3MLCT) state as the lowest energy excited state. Near-infrared (NIR) luminescence exhibits a monoexponential decay with τ = 2.4 ns in the solid state and 1 ns in liquid phase. Lifetimes of 14 ns at 77 K are in line with a narrowing of the NIR emission band at λem,max = 1170-1230 nm. Featuring a 3MLCT excited-state redox potential of -2 V vs the ferrocene/ferrocenium couple, the use of the Fe(II) chromophore as a sensitizer for light-driven synthesis is exemplified by the radical cross-coupling of 4-chlorobromobenzene and benzene.
nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning
2022-01-13

Abstract The analysis of shotgun metagenomic data provides valuable insights into microbial communities, while allowing resolution at individual genome level. In absence of complete reference genomes, this requires the reconstruction of metagenome assembled genomes (MAGs) from sequencing reads. We present the nf-core/mag pipeline for metagenome assembly, binning and taxonomic classification. It can optionally combine short and long reads to increase assembly continuity and utilize sample-wise group-information for co-assembly and genome binning. The pipeline is easy to install-all dependencies are provided within containers-portable and reproducible. It is written in Nextflow and developed as part of the nf-core initiative for best-practice pipeline development. All codes are hosted on GitHub under the nf-core organization https://github.com/nf-core/mag and released under the MIT license.
Immune pathway upregulation and lower genomic instability distinguish EBV-positive nodal T/NK-cell lymphoma from ENKTL and PTCL-NOS
2022-01-13

Primary Epstein-Barr virus (EBV)-positive nodal T/NK-cell lymphoma (PTCL-EBV) is a poorly understood disease which shows features resembling extranodal NK/T-cell lymphoma (ENKTL) and is currently not recognized as a distinct entity but categorized as a variant of primary T-cell lymphoma not otherwise specified (PTCL-NOS). Herein, we analyzed copynumber aberrations (n=77) with a focus on global measures of genomic instability and homologous recombination deficiency and performed gene expression (n=84) and EBV miRNA expression (n=24) profiling as well as targeted mutational analysis (n=16) to further characterize PTCL-EBV in relation to ENKTL and PTCL-NOS. Multivariate analysis revealed that patients with PTCL-EBV had a significantly worse outcome compared to patients with PTCL-NOS (P=0.002) but not to those with ENKTL. Remarkably, PTCL-EBV exhibited significantly lower genomic instability and homologous recombination deficiency scores compared to ENKTL and PTCL-NOS. Gene set enrichment analysis revealed that many immune-related pathways, interferon α/γ response, and IL6_JAK_STAT3 signaling were significantly upregulated in PTCLEBV and correlated with lower genomic instability scores. We also identified that NFκB-associated genes, BIRC3, NFKB1 (P50) and CD27, and their proteins are upregulated in PTCL-EBV. Most PTCL-EBV demonstrated a type 2 EBV latency pattern and, strikingly, exhibited downregulated expression of most EBV miRNA compared to ENKTL and their target genes were also enriched in immune-related pathways. PTCL-EBV also showed frequent mutations of TET2, PIK3CD and STAT3, and are characterized by microsatellite stability. Overall, poor outcome, low genomic instability, upregulation of immune pathways and downregulation of EBV miRNA are distinctive features of PTCL-EBV. Our data support the concept that PTCL-EBV could be considered as a distinct entity, provide novel insights into the pathogenesis of the disease and offer potential new therapeutic targets for this tumor.
Biogels in Soils: Plant Mucilage as a Biofilm Matrix That Shapes the Rhizosphere Microbial Habitat
2022-01-13

Mucilage is a gelatinous high-molecular-weight substance produced by almost all plants, serving numerous functions for plant and soil. To date, research has mainly focused on hydraulic and physical functions of mucilage in the rhizosphere. Studies on the relevance of mucilage as a microbial habitat are scarce. Extracellular polymeric substances (EPS) are similarly gelatinous high-molecular-weight substances produced by microorganisms. EPS support the establishment of microbial assemblages in soils, mainly through providing a moist environment, a protective barrier, and serving as carbon and nutrient sources. We propose that mucilage shares physical and chemical properties with EPS, functioning similarly as a biofilm matrix covering a large extent of the rhizosphere. Our analyses found no evidence of consistent differences in viscosity and surface tension between EPS and mucilage, these being important physical properties. With regard to chemical composition, polysaccharide, protein, neutral monosaccharide, and uronic acid composition also showed no consistent differences between these biogels. Our analyses and literature review suggest that all major functions known for EPS and required for biofilm formation are also provided by mucilage, offering a protected habitat optimized for nutrient mobilization. Mucilage enables high rhizo-microbial abundance and activity by functioning as carbon and nutrient source. We suggest that the role of mucilage as a biofilm matrix has been underestimated, and should be considered in conceptual models of the rhizosphere.
Human immunocompetent choroid-on-chip: a novel tool for studying ocular effects of biological drugs
2022-01-13

Abstract Disorders of the eye leading to visual impairment are a major issue that affects millions of people. On the other side ocular toxicities were described for e.g. molecularly targeted therapies in oncology and may hamper their development. Current ocular model systems feature a number of limitations affecting human-relevance and availability. To find new options for pharmacological treatment and assess mechanisms of toxicity, hence, novel complex model systems that are human-relevant and readily available are urgently required. Here, we report the development of a human immunocompetent Choroid-on-Chip (CoC), a human cell-based in vitro model of the choroid layer of the eye integrating melanocytes and microvascular endothelial cells, covered by a layer of retinal pigmented epithelial cells. Immunocompetence is achieved by perfusion of peripheral immune cells. We demonstrate controlled immune cell recruitment into the stromal compartments through a vascular monolayer and in vivo-like cytokine release profiles. To investigate applicability for both efficacy testing of immunosuppressive compounds as well as safety profiling of immunoactivating antibodies, we exposed the CoCs to cyclosporine and tested CD3 bispecific antibodies.
Operative Volume of Newborn Surgery in German University Hospitals: High Volume Versus Low Volume Centers
2022-01-13

Abstract Introduction Adequate patient volume is essential for the maintenance of quality, meaningful research, and training of the next generation of pediatric surgeons. The role of university hospitals is to fulfill these tasks at the highest possible level. Due to decentralization of pediatric surgical care during the last decades, there is a trend toward reduction of operative caseloads. The aim of this study was to assess the operative volume of the most relevant congenital malformations at German academic pediatric surgical institutions over the past years. Methods Nineteen chairpersons representing university-chairs in pediatric surgery in Germany submitted data on 10 index procedures regarding congenital malformations or neonatal abdominal emergencies over a 3-year period (2015 through 2017). All institutions were categorized according to the total number of respective cases into “high,” “medium,” and “low” volume centers by terciles. Some operative numbers were verified using data from health insurance companies, when available. Finally, the ratio of cumulative case load versus prevalence of the particular malformation was calculated for the study period. Results From 2015 through 2017, a total 2,162 newborns underwent surgery for congenital malformations and neonatal abdominal emergencies at German academic medical centers, representing 51% of all expected newborn cases nationwide. The median of cases per center within the study period was 101 (range 18–258). Four institutions (21%) were classified as “high volume” centers, four (21%) as “medium volume” centers, and 11 (58%) as “low volume” centers. The proportion of patients operated on in high-volume centers varied per disease category: esophageal atresia/tracheoesophageal fistula: 40%, duodenal atresia: 40%, small and large bowel atresia: 39%, anorectal malformations: 40%, congenital diaphragmatic hernia: 56%, gastroschisis: 39%, omphalocele: 41%, Hirschsprung disease: 45%, posterior urethral valves: 39%, and necrotizing enterocolitis (NEC)/focal intestinal perforation (FIP)/gastric perforation (GP): 45%. Conclusion This study provides a national benchmark for neonatal surgery performed in German university hospitals. The rarity of these cases highlights the difficulties for individual pediatric surgeons to gain adequate clinical and surgical experience and research capabilities. Therefore, a discussion on the centralization of care for these rare entities is necessary.
Impact of single-room contact precautions on acquisition and transmission of vancomycin-resistant enterococci on haematological and oncological wards, multicentre cohort-study, Germany, January−December 2016
2022-01-13

Background Evidence supporting the effectiveness of single-room contact precautions (SCP) in preventing in-hospital acquisition of vancomycin-resistant enterococci (haVRE) is limited. Aim We assessed the impact of SCP on haVRE and their transmission. Methods We conducted a prospective, multicentre cohort study in German haematological/oncological departments during 2016. Two sites performed SCP for VRE patients and two did not (NCP). We defined a 5% haVRE-risk difference as non-inferiority margin, screened patients for VRE, and characterised isolates by whole genome sequencing and core genome MLST (cgMLST). Potential confounders were assessed by competing risk regression analysis. Results We included 1,397 patients at NCP and 1,531 patients at SCP sites. Not performing SCP was associated with a significantly higher proportion of haVRE; 12.2% (170/1,397) patients at NCP and 7.4% (113/1,531) patients at SCP sites (relative risk (RR) 1.74; 95% confidence interval (CI): 1.35–2.23). The difference (4.8%) was below the non-inferiority margin. Competing risk regression analysis indicated a stronger impact of antimicrobial exposure (subdistribution hazard ratio (SHR) 7.46; 95% CI: 4.59–12.12) and underlying disease (SHR for acute leukaemia 2.34; 95% CI: 1.46–3.75) on haVRE than NCP (SHR 1.60; 95% CI: 1.14–2.25). Based on cgMLST and patient movement data, we observed 131 patient-to-patient VRE transmissions at NCP and 85 at SCP sites (RR 1.76; 95% CI: 1.33–2.34). Conclusions We show a positive impact of SCP on haVRE in a high-risk population, although the observed difference was below the pre-specified non-inferiority margin. Importantly, other factors including antimicrobial exposure seem to be more influential.
Neural Correlates of Cognitive Load While Playing an Emergency Simulation Game: A Functional Near-Infrared Spectroscopy (fNIRS) Study
2022-01-13

Functional near-infrared spectroscopy (fNIRS) provides reliable results for determining cognitive load based on averaged cortical blood flow during multiple repetitions of short cognitive tasks. At the same time, it remains unclear how to use this technique for assessing cognitive load during prolonged single-trial activity. In this study, we used a computer-based emergency simulation game for inducing different levels of cognitive load. We propose a novel approach to measure cognitive load using specific time slots, determined based on simulation log-data interpreted in light of Barrouillet's time-based resource-sharing model. To validate this approach, we compared cortical activity in dorsolateral prefrontal cortex (DLPFC) and left inferior frontal gyrus (IFG) regions measured at four specific time slots during a simulation. We found significant associations between cognitive load and neuronal activity within the DLPFC depending on the chosen time slot, whereas no such dependencies were found for the IFG. These results illustrate how knowledge of task structure could be used advantageously for the identification of cognitive load. Although requiring further investigation in terms of reliability and generalizability, the presented approach can be considered promising evidence that fNIRS might be suitable for more general reliable assessments of cognitive load during prolonged single-trial activities and for real-time adaptations in simulation-based learning environments.
Determination of Both TP53 Mutation Status and the Amount of p53Protein has Limited Diagnostic Importance for Patients with OvarianCancer
2022-01-13

Background: Ovarian cancer is one of the most aggressive types of gynecologic cancers. Many patients have a relapse within two years after diagnosis and subsequent therapy. Among different genetic changes generally believed to be important for the development of cancer, TP53 is the most common mutation in the case of ovarian tumors. Objective: Our work aims to compare the outcomes of different comparisons based on the overall survival of ovarian cancer patients, determination of TP53 status, and amount of p53 protein in tumor tissues. Methods: We analyzed and compared a collective of 436 ovarian patient’s data. Extracted data include TP53 mutation status, p53 protein level, and information on the overall survival. Values for p53 protein level in dependence of TP53 mutation status were compared using the Independent-Samples t-Test. Survival analyses were displayed by Kaplan-Meier plots, using the log-rank test to check for statistical significance. Results: We have not found any statistically significant correlations between determination of TP53 status, amount of p53 protein in tumor tissues, and overall survival of ovarian cancer patients. Conclusion: In ovarian tumors both determination of TP53 status as well as p53 protein amount has only limited diagnostic importance.
Dissecting the interactions of PINK1 with the TOM complex in depolarized mitochondria
2022-01-13

Abstract Mitochondria dysfunction is involved in the pathomechanism of many illnesses including Parkinson’s disease. PINK1, which is mutated in some cases of familiar Parkinsonism, is a key component in the degradation of damaged mitochondria by mitophagy. The accumulation of PINK1 on the mitochondrial outer membrane (MOM) of compromised organelles is crucial for the induction of mitophagy, but the molecular mechanism of this process is still unresolved. Here, we investigate the association of PINK1 with the TOM complex. We demonstrate that PINK1 heavily relies on the import receptor TOM70 for its association with mitochondria and directly interacts with this receptor. The structural protein TOM7 appears to play only a moderate role in PINK1 association with the TOM complex, probably due to its role in stabilizing this complex. PINK1 requires the TOM40 pore lumen for its stable interaction with the TOM complex and apparently remains there during its further association with the MOM. Overall, this study provides new insights on the role of the individual TOM subunits in the association of PINK1 with the MOM of depolarized mitochondria.
Minimal genetically encoded tags for fluorescent protein labeling in living neurons
2022-01-14

Abstract Modern light microscopy, including super-resolution techniques, has brought about a demand for small labeling tags that bring the fluorophore closer to the target. This challenge can be addressed by labeling unnatural amino acids (UAAs) with bioorthogonal click chemistry. The minimal size of the UAA and the possibility to couple the fluorophores directly to the protein of interest with single-residue precision in living cells make click labeling unique. Here, we establish click labeling in living primary neurons and use it for fixed-cell, live-cell, dual-color pulse–chase, and super-resolution microscopy of neurofilament light chain (NFL). We also show that click labeling can be combined with CRISPR/Cas9 genome engineering for tagging endogenous NFL. Due to its versatile nature and compatibility with advanced multicolor microscopy techniques, we anticipate that click labeling will contribute to novel discoveries in the neurobiology field.
Quality beats frequency? Investigating students’ effort in learning when introducing technology in classrooms
2022-01-14

Effort students put forth when learning (EFF) is paramount to high achievement in an academic context. However, EFF has been shown to decrease over the course of a student's school career. Using technology (i.e., computer-based technologies including digital [smart] devices like tablet computers) in classroom teaching might be a powerful way to cushion this effect as technology has the potential to promote effort-related learning processes. However, it is yet unclear how technology should be integrated into classroom teaching to promote sustainable effects because long-term studies in natural classroom scenarios are scarce. In this study, we analyzed both short-term (across 4 months) and long-term (across 16 months) changes in students' EFF in mathematics and German as a language in a context in which teachers had begun to integrate technology (i.e., tablet computers) into their teaching. We used data from N = 1,363 seventh- to eighth-grade students in 28 schools. The schools were randomly assigned to either a tablet condition (teachers and students were given the opportunity to use tablet computers for one-to-one computing for teaching and learning) or a non-tablet condition. Changes in students' EFF, assessed as cognitive engagement and academic effort, were analyzed with baseline latent change and multiple, multivariate linear regression models. In mathematics, short-term changes in EFF were more positive in the tablet than in the non-tablet condition and the higher the quality of technology integration in classrooms the more positive were long-term changes. In German, the more often tablet computers were used the more positive were short-term changes. The results underscore the importance of high-quality integration of technology in complex classroom environments but also demonstrate the need to examine domain-specific integration of technologies more intensively.
Single-boson exchange representation of the functional renormalization group for strongly interacting many-electron systems
2022-01-14

We present a reformulation of the functional renormalization group (fRG) for many-electron systems, which relies on the recently introduced single boson exchange (SBE) representation of the parquet equations [Phys. Rev. B 100, 155149 (2019)]. The latter exploits a diagrammatic decomposition, which classifies the contributions to the full scattering amplitude in terms of their reducibility with respect to cutting one interaction line, naturally distinguishing the processes mediated by the exchange of a single boson in the different channels. We apply this idea to the fRG by splitting the one-loop fRG flow equations for the vertex function into SBE contributions and a residual four-point fermionic vertex. Similarly as in the case of parquet solvers, recasting the fRG algorithm in the SBE representation offers both computational and interpretative advantages: the SBE decomposition not only significantly reduces the numerical effort of treating the high-frequency asymptotics of the flowing vertices, but it also allows for a clear physical identification of the collective degrees of freedom at play. We illustrate the advantages of an SBE formulation of fRG-based schemes, by computing through the merger of dynamical mean-field theory and fRG the susceptibilities and the Yukawa couplings of the two-dimensional Hubbard model from weak to strong coupling, for which we also present an intuitive physical explanation of the results. The SBE formulation of the one-loop flow equations paves a promising route for future multiboson and multiloop extensions of fRG-based algorithms.
Boromycin has Rapid-Onset Antibiotic Activity Against Asexual and Sexual Blood Stages of Plasmodium falciparum
2022-01-14

Boromycin is a boron-containing macrolide antibiotic produced by Streptomyces antibioticus with potent activity against certain viruses, Gram-positive bacteria and protozoan parasites. Most antimalarial antibiotics affect plasmodial organelles of prokaryotic origin and have a relatively slow onset of action. They are used for malaria prophylaxis and for the treatment of malaria when combined to a fast-acting drug. Despite the success of artemisinin combination therapies, the current gold standard treatment, new alternatives are constantly needed due to the ability of malaria parasites to become resistant to almost all drugs that are in heavy clinical use. In vitro antiplasmodial activity screens of tetracyclines (omadacycline, sarecycline, methacycline, demeclocycline, lymecycline, meclocycline), macrolides (oleandomycin, boromycin, josamycin, troleandomycin), and control drugs (chloroquine, clindamycin, doxycycline, minocycline, eravacycline) revealed boromycin as highly potent against Plasmodium falciparum and the zoonotic Plasmodium knowlesi . In contrast to tetracyclines, boromycin rapidly killed asexual stages of both Plasmodium species already at low concentrations (~ 1 nM) including multidrug resistant P. falciparum strains (Dd2, K1, 7G8). In addition, boromycin was active against P. falciparum stage V gametocytes at a low nanomolar range (IC 50 : 8.5 ± 3.6 nM). Assessment of the mode of action excluded the apicoplast as the main target. Although there was an ionophoric activity on potassium channels, the effect was too low to explain the drug ́s antiplasmodial activity. Boromycin is a promising antimalarial candidate with activity against multiple life cycle stages of the parasite.