julilili42/papers huggingface dataset:
The Measurement, Application, and Effect of Oxygen in Microbial Fermentations: Focusing on Methane and Carboxylate Production
2022-03-22

Oxygen is considered detrimental to anaerobic fermentation processes by many practitioners. However, deliberate oxygen sparging has been used successfully for decades to remove H2S in anaerobic digestion (AD) systems. Moreover, microaeration techniques during AD have shown that small doses of oxygen may enhance process performance and promote the in situ degradation of recalcitrant compounds. However, existing oxygen dosing techniques are imprecise, which has led to inconsistent results between studies. At the same time, real-time oxygen fluxes cannot be reliably quantified due to the complexity of most bioreactor systems. Thus, there is a pressing need for robust monitoring and process control in applications where oxygen serves as an operating parameter or an experimental variable. This review summarizes and evaluates the available methodologies for oxygen measurement and dosing as they pertain to anaerobic microbiomes. The historical use of (micro-)aeration in anaerobic digestion and its potential role in other anaerobic fermentation processes are critiqued in detail. This critique also provides insights into the effects of oxygen on these microbiomes. Our assessment suggests that oxygen dosing, when implemented in a controlled and quantifiable manner, could serve as an effective tool for bioprocess engineers to further manipulate anaerobic microbiomes for either bioenergy or biochemical production.
Controversial Aspects of Diagnostics and Therapy of Arthritis of the Temporomandibular Joint in Rheumatoid and Juvenile Idiopathic Arthritis—An Analysis of Evidence- and Consensus-Based Recommendations Based on an Interdisciplinary Guideline Project
2022-03-22

Introduction: Due to potentially severe sequelae (impaired growth, condylar resorption, and ankylosis) early diagnosis of chronic rheumatic arthritis of the temporomandibular joint (TMJ) and timely onset of therapy are essential. Aim: Owing to very limited evidence the aim of the study was to identify and discuss controversial topics in the guideline development to promote further focused research. Methods: Through a systematic literature search, 394 out of 3771 publications were included in a German interdisciplinary guideline draft. Two workgroups (1: oral and maxillofacial surgery, 2: interdisciplinary) voted on 77 recommendations/statements, in 2 independent anonymized and blinded consensus phases (Delphi process). Results: The voting results were relatively homogenous, except for a greater proportion of abstentions amongst the interdisciplinary group (p &lt; 0.001). Eighty-four percent of recommendations/statements were approved in the first round, 89% with strong consensus. Fourteen recommendations/statements (18.2%) required a prolonged consensus phase and further discussion. Discussion: Contrast-enhanced MRI was confirmed as the method of choice for the diagnosis of TMJ arthritis. Intraarticular corticosteroid injection is to be limited to therapy-refractory cases and single injection only. In adults, alloplastic joint replacement is preferable to autologous replacement. In children/adolescents, autologous reconstruction may be performed lacking viable alternatives. Alloplastic options are currently still considered experimental.
Regional Right Ventricular Function Assessed by Intraoperative Three-Dimensional Echocardiography Is Associated With Short-Term Outcomes of Patients Undergoing Cardiac Surgery
2022-03-22

Background The assessment of right ventricular (RV) function in patients undergoing elective cardiac surgery is paramount for providing optimal perioperative care. The role of regional RV function assessment employing sophisticated state-of-the-art cardiac imaging modalities has not been investigated in this cohort. Hence, this study investigated the association of 3D echocardiography-based regional RV volumetry with short-term outcomes. Materials and Methods In a retrospective single-center study, patients undergoing elective cardiac surgery were included if they underwent 3D transesophageal echocardiography prior to thoracotomy. A dedicated software quantified regional RV volumes of the inflow tract, apical body and RV outflow tract employing meshes derived from 3D speckle-tracking. Echocardiographic, clinical and laboratory data were entered into univariable and multivariable logistic regression analyses to determine association with the endpoint (in-hospital mortality or the need for extracorporeal circulatory support). Results Out of 357 included patients, 25 (7%) reached the endpoint. Inflow RV ejection fraction (RVEF, 32 ± 8% vs. 37 ± 11%, p = 0.01) and relative stroke volume (rel. SV) were significantly lower in patients who reached the endpoint (44 ± 8 vs. 48 ± 9%, p = 0.02), while the rel. SV of the apex was higher (38 ± 10% vs. 33 ± 8%, p = 0.01). Global left and right ventricular function including RVEF and left ventricular global longitudinal strain did not differ. In univariable logistic regression, tricuspid regurgitation grade ≥ 2 [odds ratio (OR) 4.24 (1.66–10.84), p &amp;lt; 0.01], inflow RVEF [OR 0.95 (0.92–0.99), p = 0.01], inflow rel. SV [OR 0.94 (0.90–0.99), p = 0.02], apex rel. SV [OR 1.07 (1.02–1.13), p &amp;lt; 0.01] and apex to inflow rel. SV ratio [OR 5.81 (1.90–17.77), p &amp;lt; 0.01] were significantly associated with the endpoint. In a multivariable model, only the presence of tricuspid regurgitation [OR 4.24 (1.66–10.84), p &amp;lt; 0.01] and apex to inflow rel. SV ratio [OR 6.55 (2.09–20.60), p &amp;lt; 0.001] were independently associated with the endpoint. Conclusions Regional RV function is associated with short-term outcomes in patients undergoing elective cardiac surgery and might be helpful for optimizing risk stratification.
(Z)-Endoxifen and Early Recurrence of Breast Cancer: An Explorative Analysis in a Prospective Brazilian Study
2022-03-22

Adherence to treatment and use of co-medication, but also molecular factors such as CYP2D6 genotype, affect tamoxifen metabolism, with consequences for early breast cancer prognosis. In a prospective study of 149 tamoxifen-treated early-stage breast cancer patients from Brazil followed up for 5 years, we investigated the association between the active tamoxifen metabolite (Z)-endoxifen at 3 months and event-free survival (EFS) adjusted for clinico-pathological factors. Twenty-five patients (16.8%) had recurred or died at a median follow-up of 52.3 months. When we applied a putative 15 nM threshold used in previous independent studies, (Z)-endoxifen levels below the threshold showed an association with shorter EFS in univariate analysis (p = 0.045) and after adjustment for stage (HR 2.52; 95% CI 1.13–5.65; p = 0.024). However, modeling of plasma concentrations with splines instead of dichotomization did not verify a significant association with EFS (univariate analysis: p = 0.158; adjusted for stage: p = 0.117). Hence, in our small exploratory study, the link between impaired tamoxifen metabolism and early breast cancer recurrence could not be unanimously demonstrated. This inconsistency justifies larger modeling studies backed up by mechanistic pharmacodynamic analyses to shed new light on this suspected association and the stipulation of an appropriate predictive (Z)-endoxifen threshold.
Taxonomic and functional diversity of aquatic heterotrophs is sustained by dissolved organic matter chemodiversity
2022-03-22

Dissolved organic matter (DOM) is ubiquitous in aquatic ecosystems and fundamental for planetary processes and ecosystem functioning. While the link between microbial community composition and heterotrophic utilization of DOM has been recognized, the full diversity of organic compounds, their bioavailability, degradability and specific influences on the diversity and function of heterotrophs are still not clear. Here we experimentally investigate heterotrophic bacteria in thirty-three freshwater model communities. We identified 34 different heterotrophs growing in ambient lake DOM with taxonomic affiliations matching abundant freshwater bacterioplankton. We further describe 25 different heterotrophs growing in the phycosphere of M. Aeruginosa and 6 heterotrophs growing on the DOM produced by M. Aeruginosa with taxonomic affiliation in accord to phycosphere heterotrophs. In our experiment we observed that heterotrophs that live in the phycosphere remove more dissolved organic carbon than abundant freshwater heterotrophs. Moreover, phycosphere heterotrophs have bigger genomes than abundant lake bacteria. Altogether of the 4224 chemical features that were resolved by LC-MS, only 1229 were seen in all three treatments. None of the common/shared compounds were removed across all the model communities, suggesting contrasting niches of the studied taxa. Altogether our study highlights how each model community, with its unique taxonomic assemblages and organotroph functioning is upkept by the chemodiversity of DOM.
“We Want Good Education for All of Us” – A Participatory Quality Improvement Approach
2022-03-22

Introduction In ever changing conditions, medical faculties must face the challenge of preparing their medical students as best as possible for the demands of their future work. This requires involving all stakeholders, especially medical students in the constant redefinition of medical curricula. Using the idea of “Communities of Practice” as conceptual framework, this study looks at semester spokespeople as an example for participatory quality management. Methods We conducted focus-group interviews with semester spokespeople at a German Medical Faculty. Data was recorded, transcribed, and analysed using MAXQDA. The interviews were analysed using meaning condensation method. Results Eleven out of 48 semester spokespeople took part. We found seven topics that fell within three main categories: (1) role of the semester spokesperson, (2) role of the fixed meeting, and (3) contact and commitment. Communities of Practice principles could be aligned to topics and categories. Discussion The idea of semester spokespeople based on the concept of Communities of Practice are useful in the quality management processes of a medical school and lead to greater involvement of medical students, identifying their needs. The reciprocal commitment among all stakeholders fosters mutual understanding and collaboration. Future studies could investigate the underlying motivational factors of dedicated students and how to transfer these characteristics to a larger cohort.
Constraints on the 3-30 MeV emission of Seyfert galaxies
2022-03-22

Seyfert galaxies have not been detected by COMPTEL on the Compton Gamma Ray Observatory (CGRO) in the energy range 0.75-3 MeV, placing upper limits on their emission which are more than an order of magnitude below previously reported detections. Here, we extend our previous work to the energy range 3-30 MeV. Again, we find no evidence for emission from a cumulative sample of X-ray bright Seyfert galaxies. We use the recent results on the extragalactic background at MeV energies to constrain the possible emission of these sources and their contribution to the cosmic extragalactic background (CXB). The lack of -rays from Seyfert galaxies strongly argues against hadronic cascades as the underlying radiation mechanism and, consequently, against recent claims that Seyferts might produce a high-energy neutrino background with an energy flux similar to that of the CXB.
Magnetically supramassive neutron stars
2022-03-23

It is commonly believed that neutron stars exceeding the maximum mass limit\\nfor stability could be formed in the aftermath of binary neutron star mergers,\\nenjoying a short life of metastability before losing centrifugal support and\\ncollapsing to a black hole. It is suggested here that a similar scenario could\\ntake place when the remnant's excess mass is supported by an ultra-strong\\n magnetic field that could be generated during,\\nand shortly after, coalescence. We show that such 'magnetically supramassive'\\nneutron stars could stave off collapse and survive for a few years before their\\nmagnetic energy is sufficiently dissipated due to ambipolar diffusion. In\\naddition, we speculate on multi-messenger signatures of such objects and\\ndiscuss the robustness of our results against limitations placed by neutron\\nsuperfluidity and magneto-thermal evolution.\\n
European Academy of Neurology guidance for developing and reporting clinical practice guidelines on rare neurological diseases
2022-03-23

Abstract Background and purpose Rare diseases affect up to 29 million people in the European Union, and almost 50% of them affect the nervous system or muscles. Delays in diagnosis and treatment onset and insufficient treatment choices are common. Clinical practice guidelines (CPGs) may improve the diagnosis and treatment of patients and optimize care pathways, delivering the best scientific evidence to all clinicians treating these patients. Recommendations are set for developing and reporting high‐quality CPGs on rare neurological diseases (RNDs) within the European Academy of Neurology (EAN), through a consensus procedure. Methods A group of 27 experts generated an initial list of items that were evaluated through a two‐step Delphi consensus procedure and a face‐to‐face meeting. The final list of items was reviewed by an external review group of 58 members. Results The consensus procedure yielded 63 final items. Items are listed according to the domains of the AGREE instruments and concern scope and purpose, stakeholder involvement, rigour of development, and applicability. Additional items consider reporting and ethical issues. Recommendations are supported by practical examples derived from published guidelines and are presented in two tables: (1) items specific to RND CPGs, and general guideline items of special importance for RNDs, or often neglected; (2) items for guideline development within the EAN. Conclusions This guidance aims to provide solutions to the issues specific to RNDs. This consensus document, produced by many experts in various fields, is considered to serve as a starting point for further harmonization and for increasing the quality of CPGs in the field of RNDs.
Proteasomal turnover of the RhoGAP tumor suppressor DLC1 is regulated by HECTD1 and USP7
2022-03-23

Abstract The Rho GTPase activating protein Deleted in Liver Cancer 1 (DLC1) is frequently downregulated through genetic and epigenetic mechanisms in various malignancies, leading to aberrant Rho GTPase signaling and thus facilitating cancer progression. Here we show that in breast cancer cells, dysregulation of DLC1 expression occurs at the protein level through rapid degradation via the ubiquitin–proteasome system. Using mass spectrometry, we identify two novel DLC1 interaction partners, the ubiquitin-ligase HECTD1 and the deubiquitinating enzyme ubiquitin-specific-processing protease 7 (USP7). While DLC1 protein expression was rapidly downregulated upon pharmacological inhibition of USP7, siRNA-mediated knockdown of HECTD1 increased DLC1 protein levels and impaired its degradation. Immunofluorescence microscopy analyses revealed that the modulation of HECTD1 levels and USP7 activity altered DLC1 abundance at focal adhesions, its primary site of action. Thus, we propose opposing regulatory mechanisms of DLC1 protein homeostasis by USP7 and HECTD1, which could open up strategies to counteract downregulation and restore DLC1 expression in cancer.
Modeling the mind of a predator: Interactive cognitive maps support flexible avoidance of dynamic threats
2022-03-23

Successful avoidance of recurrent threats depends on inferring threatening agents’ preferences and predicting their movement patterns accordingly. However, it remains largely unknown how the human brain achieves this, despite the fact that many natural threats are posed by complex, dynamic agents that act according to their own goals. Here, we propose that humans exploit an interactive cognitive map of the social environment to infer threatening agents’ preferences and also to simulate their future behavior, providing for flexible, generalizable avoidance strategies. We tested this proposal across three preregistered experiments (total n=510) using a task in which participants collected rewards while avoiding one of several possible virtual threatening agents. A novel, model-based, hypothesis-testing inverse reinforcement learning computational model best explained participants’ inferences about threatening agents’ latent preferences, with participants using this inferred knowledge to enact generalizable, model-based avoidance strategies across different environments. Using tree-search planning models, we found that participants’ behavior was best explained by a planning algorithm that incorporated simulations of the threat’s goal-directed behavior, and that prior expectations about the threat’s predictability were linked to individual differences in avoidance. Together, our results indicate that humans use a cognitive map to determine threatening agents’ preferences, in turn facilitating generalized predictions of the threatening agent’s behavior and enabling flexible and effective avoidance.
Minimising inequality in multiagent resource allocation
2022-03-23

Abstract We analyse the problem of finding an allocation of resources in a multiagent system that is as fair as possible in terms of minimising inequality between the utility levels enjoyed by the individual agents. We use the well-known Atkinson index to measure inequality and we focus on the distributed approach to multiagent resource allocation, where new allocations emerge as the result of a sequence of local deals between groups of agents who agree on an exchange of some of the items in their possession. Our results show that it is possible to design systems that provide theoretical guarantees for optimal outcomes that minimise inequality, but also that there are significant computational hurdles to be overcome in the worst case. In particular, finding an optimal allocation is computationally intractable and under the distributed approach a large number of structurally complex deals, possibly involving many agents and items, may be required before convergence to a socially optimal allocation. This remains true even in severely restricted resource allocation scenarios where all agents have the same utility function. From a methodological point of view, while much work in multiagent resource allocation relies on combinatorial arguments, here we instead use insights from basic calculus.
Cortical softening elicits zygotic contractility during mouse preimplantation development
2022-03-24

Actomyosin contractility is a major engine of preimplantation morphogenesis, which starts at the 8-cell stage during mouse embryonic development. Contractility becomes first visible with the appearance of periodic cortical waves of contraction (PeCoWaCo), which travel around blastomeres in an oscillatory fashion. How contractility of the mouse embryo becomes active remains unknown. We have taken advantage of PeCoWaCo to study the awakening of contractility during preimplantation development. We find that PeCoWaCo become detectable in most embryos only after the second cleavage and gradually increase their oscillation frequency with each successive cleavage. To test the influence of cell size reduction during cleavage divisions, we use cell fusion and fragmentation to manipulate cell size across a 20- to 60-μm range. We find that the stepwise reduction in cell size caused by cleavage divisions does not explain the presence of PeCoWaCo or their accelerating rhythm. Instead, we discover that blastomeres gradually decrease their surface tensions until the 8-cell stage and that artificially softening cells enhances PeCoWaCo prematurely. We further identify the programmed down-regulation of the formin Fmnl3 as a required event to soften the cortex and expose PeCoWaCo. Therefore, during cleavage stages, cortical softening, mediated by Fmnl3 down-regulation, awakens zygotic contractility before preimplantation morphogenesis.
Phosphate addition enhances alkaline extraction of glyphosate from highly sorptive soils and aquatic sediments
2022-03-24

Abstract BACKGROUND Analytical constraints complicate environmental monitoring campaigns of the herbicide glyphosate and its major degradation product aminomethylphosphonic acid (AMPA): their strong sorption to soil minerals requires harsh extraction conditions. Coextracted matrix compounds impair downstream analysis and must be removed before analysis. RESULTS A new extraction method combined with subsequent capillary electrophoresis‐mass spectrometry for derivatization‐free analysis of glyphosate and AMPA in soil and sediment was developed and applied to a suite of environmental samples. It was compared to three extraction methods from literature. We show that no extraction medium reaches 100% recovery. The new phosphate‐supported alkaline extraction method revealed (1) high recoveries of 70–90% for soils and aquatic sediments, (2) limits of detections below 20 μg kg −1 , and (3) a high robustness, because impairing matrix components (trivalent cations and humic acids) were precipitated prior to the analysis. Soil and sediment samples collected around Tübingen, Germany, revealed maximum glyphosate and AMPA residues of 80 and 2100 μg kg −1 , respectively, with residues observed along a core of lake sediments. Glyphosate and/or AMPA were found in 40% of arable soils and 57% of aquatic sediment samples. CONCLUSION In this work, we discuss soil parameters that influence (de)sorption and thus extraction. From our results we conclude that residues of glyphosate in environmental samples are easily underestimated. With its possible high throughput, the method presented here can resolve current limitations in monitoring campaigns of glyphosate by addressing soil and aquatic sediment samples with critical sorption characteristics.
2H-Imidazol-2-oneO-Oxide: A Criegee Intermediate from a σ0π2Singlet Ground-State Carbene
2022-03-24

Triplet carbenes and triplet molecular oxygen can combine to form singlet carbonyl <i>O</i>-oxide Criegee intermediates in an overall spin-allowed transformation. While this reaction runs at the diffusion limit in the case of triplet carbenes, singlet carbenes are commonly more reluctant to bind <sup>3</sup>O<sub>2</sub>. In contradiction to this customarily encountered spin selectivity, the σ<sup>0</sup>π<sup>2</sup> singlet ground-state carbene 2<i>H</i>-imidazol-2-ylidene <b>1</b> reacts extremely rapidly with <sup>3</sup>O<sub>2</sub> at temperatures as low as 30 K. The product of this cryogenic reaction is singlet 2<i>H</i>-imidazol-2-one <i>O</i>-oxide <b>7</b>, an N-heterocyclic Criegee intermediate. The addition reaction becomes possible through the electrophilic activation of dioxygen in the triplet state, in which O<sub>2</sub> binding can initially proceed without a barrier. Criegee intermediate <b>7</b> exhibits an unprecedented high O-O stretching vibration at 1105 cm<sup>-1</sup>, which can be explained by a resonance structure with an O<sub>2</sub> double bond. Furthermore, 2<i>H</i>-imidazol-2-one <b>5</b> and spiro-dioxirane <b>6</b> could be identified as the photodecomposition products of the herein-reported carbonyl oxide.