julilili42/papers huggingface dataset:
Roles of second messengers in the regulation of cyanobacterial physiology: the carbon-concentrating mechanism and beyond
2023-01-01

Abstract Second messengers are a fundamental category of small molecules and ions that are involved in the regulation of many processes in all domains of life. Here we focus on cyanobacteria, prokaryotes playing important roles as primary producers in the geochemical cycles due to their capability of oxygenic photosynthesis and carbon and nitrogen fixation. Of particular interest is the inorganic carbon-concentrating mechanism (CCM), which allows cyanobacteria to concentrate CO2 near RubisCO. This mechanism needs to acclimate toward fluctuating conditions, such as inorganic carbon availability, intracellular energy levels, diurnal light cycle, light intensity, nitrogen availability, and redox state of the cell. During acclimation to such changing conditions, second messengers play a crucial role, particularly important is their interaction with the carbon control protein SbtB, a member of the PII regulator protein superfamily. SbtB is capable of binding several second messengers, uniquely adenyl nucleotides, to interact with different partners in a variety of responses. The main identified interaction partner is the bicarbonate transporter SbtA, which is regulated via SbtB depending on the energy state of the cell, the light conditions, and different CO2 availability, including cAMP signaling. The interaction with the glycogen branching enzyme, GlgB, showed a role for SbtB in the c-di-AMP-dependent regulation of glycogen synthesis during the diurnal life cycle of cyanobacteria. SbtB has also been shown to impact gene expression and metabolism during acclimation to changing CO2 conditions. This review summarizes the current knowledge about the complex second messenger regulatory network in cyanobacteria, with emphasis on carbon metabolism.
Metacognitive Information Theory
2023-01-01

Abstract The capacity that subjects have to rate confidence in their choices is a form of metacognition, and can be assessed according to bias, sensitivity and efficiency. Rich networks of domain-specific and domain-general regions of the brain are involved in the rating, and are associated with its quality and its use for regulating the processes of thinking and acting. Sensitivity and efficiency are often measured by quantities called meta–d′ and the M-ratio that are based on reverse engineering the potential accuracy of the original, primary, choice that is implied by the quality of the confidence judgements. Here, we advocate a straightforward measure of sensitivity, called meta–I, which assesses the mutual information between the accuracy of the subject’s choices and the confidence reports, and two normalized versions of this measure that quantify efficiency in different regimes. Unlike most other measures, meta–I-based quantities increase with the number of correctly assessed bins with which confidence is reported. We illustrate meta–I on data from a perceptual decision-making task, and via a simple form of simulated second-order metacognitive observer.
Clinical outcome of biomarker-guided therapies in adult patients with tumors of the nervous system
2023-01-01

Abstract Background The clinical utility of molecular profiling and targeted therapies for neuro-oncology patients outside of clinical trials is not established. We aimed at investigating feasibility and clinical utility of molecular profiling and targeted therapy in adult patients with advanced tumors in the nervous system within a prospective observational study. Methods molecular tumor board (MTB)@ZPM (NCT03503149) is a prospective observational precision medicine study for patients with advanced tumors. After inclusion of patients, we performed comprehensive molecular profiling, formulated ranked biomarker-guided therapy recommendations based on consensus by the MTB, and collected prospective clinical outcome data. Results Here, we present initial data of 661 adult patients with tumors of the nervous system enrolled by December 31, 2021. Of these, 408 patients were presented at the MTB. Molecular-instructed therapy recommendations could be made in 380/408 (93.1%) cases and were prioritized by evidence levels. Therapies were initiated in 86/380 (22.6%) cases until data cutoff. We observed a progression-free survival ratio &amp;gt;1.3 in 31.3% of patients. Conclusions Our study supports the clinical utility of biomarker-guided therapies for neuro-oncology patients and indicates clinical benefit in a subset of patients. Our data might inform future clinical trials, translational studies, and even clinical care.
Embodied Processing at Six Linguistic Granularity Levels: A Consensus Paper
2023-01-01

Language processing is influenced by sensorimotor experiences. Here, we review behavioral evidence for embodied and grounded influences in language processing across six linguistic levels of granularity. We examine (a) sub-word features, discussing grounded influences on iconicity (systematic associations between word form and meaning); (b) words, discussing boundary conditions and generalizations for the simulation of color, sensory modality, and spatial position; (c) sentences, discussing boundary conditions and applications of action direction simulation; (d) texts, discussing how the teaching of simulation can improve comprehension in beginning readers; (e) conversations, discussing how multi-modal cues improve turn taking and alignment; and (f) text corpora, discussing how distributional semantic models can reveal how grounded and embodied knowledge is encoded in texts. These approaches are converging on a convincing account of the psychology of language, but at the same time, there are important criticisms of the embodied approach and of specific experimental paradigms. The surest way forward requires the adoption of a wide array of scientific methods. By providing complimentary evidence, a combination of multiple methods on various levels of granularity can help us gain a more complete understanding of the role of embodiment and grounding in language processing.
A comparative study of microsurgery and gamma knife radiosurgery in vestibular schwannoma evaluating tumor control and functional outcome
2023-01-01

Abstract Background Both stereotactic radiosurgery (SRS) and microsurgical resection (SURGERY) are available as treatment options for sporadic vestibular schwannoma (VS). There are very few direct comparative studies comparing both treatment modalities in large cohorts allowing detailed subgroup analysis. This present study aimed to compare the nuances in the treatment of VS by SURGERY and SRS in 2 highly specialized neurosurgical centers. Methods This is a retrospective bicentric cohort study. Data from patients treated between 2005 and 2011 were collected retrospectively. Recurrence-free survival (RFS) was assessed radiographically by contrast-enhanced magnetic resonance imaging. Results The study population included N = 901 patients with a mean follow-up of 7 years. Overall, the incidence of recurrence was 7% after SURGERY, and 11% after SRS with superior tumor control in SURGERY in the Kaplan–Meier-analysis (P = 0.031). In small tumors (Koos I and II), tumor control was equivalent in both treatment arms. In large VS (Koos III and IV), however, RFS was superior in SURGERY. The extent of resection correlated with RFS (P &amp;lt; .001). Facial and hearing deterioration was similar in both treatment arms in small VS, but more pronounced in SURGERY of large VS. Tinnitus, vertigo, imbalance, and trigeminal symptoms were more often improved by SURGERY than SRS. Conclusions SRS can achieve similar tumor control compared to SURGERY in smaller VS (Koos I and II)—with similar postinterventional morbidities. In large VS (Koos III and IV), long-term tumor control of SRS is inferior to SURGERY. Based on these results, we suggest that if combination therapy is chosen, the residual tumor should not exceed the size of Koos II.
What resources do high school students activate to link energetic and structural changes in chemical reactions? – A qualitative study
2023-01-01

Recent progress in elucidating chemical reactions allows to explain chemistry by the potential energy of the involved chemical structures. Nevertheless, from an educational point of view, empirical results indicate that students often do not connect the core idea of energy with other chemical concepts. From a resource-oriented perspective, students do not draw on a coherent concept of chemistry to solve a problem but rather activate diverse cognitive resources, crucially depending on the context. It is thus of interest which resources high school students activate to reflect on energetic aspects of a chemical reaction. In this study, 38 German high school students in 16 focus groups were asked to explain kinetic and thermodynamic aspects of the reaction between hydrogen and chlorine. The unguided focus group phase and the following semistructured qualitative interview were analysed by qualitative content analysis. Results show that students have a diverse network of cognitive resources on energetic aspects. However, this network's structure seems to be dominated by terminology and a few prominent ideas such as activation energy. In contrast, students seldom drew connections between bond-making and energy release. Many students mainly argued on a macroscopic level and relied heavily on technical terms. If they argued on the sub-microscopic scale, however, they often focussed on the whole system rather than on specific molecules and their structure. Hence, students interpreted concepts like activation energy or reaction coordinate diagrams on the system level leading to unproductive reasoning. Overall, it seems that students seldom activate resources on molecular structures to argue about energetic changes in chemical reactions. Also, they rarely refer to the fundamental principle of energy minimisation to reason about the driving force of reactions. These results suggest that chemical reactions should be explained already in high schools on a molecular level providing a more explicit reference to energy as a function of chemical structures.
Longitudinal clinical, cognitive and biomarker profiles in dominantly inherited versus sporadic early-onset Alzheimer’s disease
2023-01-01

Abstract Approximately 5% of Alzheimer’s disease cases have an early age at onset (&amp;lt;65 years), with 5–10% of these cases attributed to dominantly inherited mutations and the remainder considered as sporadic. The extent to which dominantly inherited and sporadic early-onset Alzheimer’s disease overlap is unknown. In this study, we explored the clinical, cognitive and biomarker profiles of early-onset Alzheimer’s disease, focusing on commonalities and distinctions between dominantly inherited and sporadic cases. Our analysis included 117 participants with dominantly inherited Alzheimer’s disease enrolled in the Dominantly Inherited Alzheimer Network and 118 individuals with sporadic early-onset Alzheimer’s disease enrolled at the University of California San Francisco Alzheimer’s Disease Research Center. Baseline differences in clinical and biomarker profiles between both groups were compared using t-tests. Differences in the rates of decline were compared using linear mixed-effects models. Individuals with dominantly inherited Alzheimer’s disease exhibited an earlier age-at-symptom onset compared with the sporadic group [43.4 (SD ± 8.5) years versus 54.8 (SD ± 5.0) years, respectively, P &amp;lt; 0.001]. Sporadic cases showed a higher frequency of atypical clinical presentations relative to dominantly inherited (56.8% versus 8.5%, respectively) and a higher frequency of APOE-ε4 (50.0% versus 28.2%, P = 0.001). Compared with sporadic early onset, motor manifestations were higher in the dominantly inherited cohort [32.5% versus 16.9% at baseline (P = 0.006) and 46.1% versus 25.4% at last visit (P = 0.001)]. At baseline, the sporadic early-onset group performed worse on category fluency (P &amp;lt; 0.001), Trail Making Test Part B (P &amp;lt; 0.001) and digit span (P &amp;lt; 0.001). Longitudinally, both groups demonstrated similar rates of cognitive and functional decline in the early stages. After 10 years from symptom onset, dominantly inherited participants experienced a greater decline as measured by Clinical Dementia Rating Sum of Boxes [3.63 versus 1.82 points (P = 0.035)]. CSF amyloid beta-42 levels were comparable [244 (SD ± 39.3) pg/ml dominantly inherited versus 296 (SD ± 24.8) pg/ml sporadic early onset, P = 0.06]. CSF phosphorylated tau at threonine 181 levels were higher in the dominantly inherited Alzheimer’s disease cohort (87.3 versus 59.7 pg/ml, P = 0.005), but no significant differences were found for t-tau levels (P = 0.35). In summary, sporadic and inherited Alzheimer’s disease differed in baseline profiles; sporadic early onset is best distinguished from dominantly inherited by later age at onset, high frequency of atypical clinical presentations and worse executive performance at baseline. Despite these differences, shared pathways in longitudinal clinical decline and CSF biomarkers suggest potential common therapeutic targets for both populations, offering valuable insights for future research and clinical trial design.
The impact of corruption in climate finance on achieving net zero emissions
2023-01-01

The study’s primary purpose is to assess the probabilistic impact of corruption in climate finance on achieving zero emissions. This scientific problem is highly relevant since the largest recipients of international climate assistance are countries with significant corruption in the public sector. Thus, it is necessary to increase the transparency in the use of international assistance funds and strengthen accountability. The study used the methods of survival analysis, namely the Kaplan-Meier approach and the Cox proportional hazards regression model, to investigate 114 countries that received international climate assistance during 2005-2021. The empirical analysis showed that the most probable time frame for achieving 5% reduction in greenhouse gas emissions is five years. Moreover, the response of climate finance to reducing greenhouse emissions is faster in countries with medium levels of corruption than in countries with high and very high levels of corruption. Two covariates (the level of corruption and the volume of climate finance) likely to affect the achievement of net zero emissions were chosen to build the Cox proportional hazards model. The study empirically confirms that with a 1-point increase in the Corruption Perceptions Index, the probability of reducing emissions increases by 2.4581%, while the volume of climate finance does not have a statistically significant impact on the performance indicator. It suggests that current climate investment in underdeveloped countries is incapable of mitigating the negative impact of climate change.
Transparency and Corruption Prevention in Financing Climate Action
2023-01-01

The article summarises the arguments and counter-arguments within the scientific debate on enchancing the climate finance transparency. The main purpose of this study is to investigate the mechanism of climate finance and identify the key challenges that hinder the effective climate fund monitoring system. The relevance of addressing this research problem is due to the fact that the largest recipients of international climate finance are countries with high corruption risks, low standards in protection human rights, low trust in law enforcement and judicial authorities, etc. Therefore, the reporting and the quality of the reports prepared on the funds received under international assistance programmes is an important component of establishing long-term relations and trust between donor-countries or receipient-countries. The article examines the issue of climate finance transparency in the following logical sequence: analysed scientific publications on the issues of transparency and corruption in climate finance, examined the institutional mechanism of global climate finance, analysed the scale of climate finance in the world, and identified the main challenges in improving the transparency and efficiency of climate funds. The study was conducted using empirical (observation, description) and theoretical (grouping, synthesis, abstraction) research methods. The paper substantiates that the strengheting transparency of climate finance in developing countries requires a comprehensive approach - on the one hand, improving the level of justice, judiciary, enchancing the work of local regulatory authorities, developing legislation in recipient countries of international financial assistance, and on the other hand, improving the methodology of integrated accounting and reporting on the receipt and use of climate funds, as well as tracking the effects of project implementation. The study found that the key challenges that hinder the formation of an effective climate funds monitoring system are: a data collection and reporting system, an accounting and reporting system, and a coordination system.
Bioinformatics-guided discovery of biaryl-linked lasso peptides
2023-01-01

Genome mining enabled the discovery of a series of unique lasso peptides. They contain a P450-mediated C–N-based biarylic crosslink at the lasso ring and can in addition bear a unique sulfonium residue.
Co-reduction of Fe(III) and S0 drives Fe-S biomineral formation and phosphate mobilisation
2023-01-01

Microbially mediated iron and sulfur cycling have impacted redox transitions and the bioavailability of nutrients throughout Earth's history.Here, we incubated Geobacter sulfurreducens in the co-presence of ferrihydrite and S 0 at pH 6.5, 7.2 or 8.0.Microbial reduction of Fe(III) and S 0 resulted in a shift from ferruginous (Fe 2þ -rich) to sulfidic (sulfide-rich) conditions and the precipitation of mackinawite, greigite and vivianite.The initial pH controlled the timing of the ferruginous-sulfidic transition and the relative abundance and crystallinity of the formed minerals.Vivianite formation was attributed to phosphate initially added to the medium.Phosphate showed a dynamic cycle, with low dissolved concentrations initially due to sorption to ferrihydrite, followed by vivianite precipitation under ferruginous conditions, and a significant release under sulfidic conditions.Co-reduction of Fe(III) and S 0 therefore regulates Fe-S biomineral formation and P bioavailability, which could be particularly important to consider in microbial mats and the sulfate-poor Archean ocean.
Electrospinning of collagen: enzymatic and spectroscopic analyses reveal solvent-independent disruption of the triple-helical structure
2023-01-01

Electrospun collagen mats were analyzed using circular dichroism, enzymatic digestion, SDS-PAGE, western blotting, and Raman spectroscopy and compared to heat-denaturated and electrospun collagen in HFIP.
Technology acceptance of digital devices for home use: Qualitative results of a mixed methods study
2023-01-01

Objective Digital devices have demonstrated benefits to patients with chronic and neurodegenerative diseases. But when patients use medical devices in their homes, the technologies have to fit into their lives. We investigated the technology acceptance of seven digital devices for home use. Methods We conducted 60 semi-structured interviews with participants of a larger device study on their views on the acceptability of seven devices. Transcriptions were analysed using qualitative content analysis. Results Based on the unified theory of acceptance and use of technology, we evaluated effort, facilitating conditions, performance expectancy and social influence of each device. In the effort category, five themes emerged: (a) the hassle to use the device; (b) its usability; (c) comfort; (d) disturbance to daily life; and (e) problems during usage. Facilitating conditions consisted of five themes: (a) expectations regarding a device; (b) quality of the instructions; (c) insecurities with usage; (d) possibilities of optimization; and (e) possibilities to use the device longer. Regarding performance expectancy, we identified three themes: (a) insecurities with the performance of a device; (b) feedback; and (c) motivation for using a device. In the social influence category, three themes emerged: (a) reactions of peers; (b) concerns with the visibility of a device; and (c) concerns regarding data privacy. Conclusions We identify key factors that determine the acceptability of medical devices for home use from the participants’ perspective. These include low effort of use, minor disruptions to their daily lives and good support from the study team.
Premature termination, satisfaction with care, and shared decision-making during home treatment compared to inpatient treatment: A quasi-experimental trial
2023-01-01

Abstract Background Inpatient equivalent home treatment (IEHT), implemented in Germany since 2018, is a specific form of home treatment. Between 2021 and 2022, IEHT was compared to inpatient psychiatric treatment in a 12-months follow-up quasi-experimental study with two propensity score matched cohorts in 10 psychiatric centers in Germany. This article reports results on the treatment during the acute episode and focuses on involvement in decision-making, patient satisfaction, and drop-out rates. Methods A total of 200 service users receiving IEHT were compared with 200 matched statistical “twins” in standard inpatient treatment. Premature termination of treatment as well as reasons for this was assessed using routine data and a questionnaire. In addition, we measured patient satisfaction with care with a specific scale. For the evaluation of patient involvement in treatment decisions, we used the 9-item Shared Decision Making Questionnaire (SDM-Q-9). Results Patients were comparable in both groups with regard to sociodemographic and clinical characteristics. Mean length-of-stay was 37 days for IEHT and 28 days for inpatient treatment. In both groups, a similar proportion of participants stopped treatment prematurely. At the end of the acute episode, patient involvement in decision-making (SDM-Q-9) as well as treatment satisfaction scores were significantly higher for IEHT patients compared to inpatients. Conclusions Compared to inpatient care, IEHT treatment for acute psychiatric episodes was associated with higher treatment satisfaction and more involvement in clinical decisions.
Reduced 8-Gray Compared to Standard 12-Gray Total Body Irradiation for Allogeneic Transplantation in First Remission Acute Lymphoblastic Leukemia: A Study of the Acute Leukemia Working Party of the EBMT
2023-01-01

In this registry-based study, we compared outcomes of allogeneic hematopoietic cell transplantation (allo-HCT) in adult patients with acute lymphoblastic leukemia (ALL) transplanted in first complete remission (CR-1), following conditioning with total body irradiation (TBI) at a standard 12-Gray or at a lower 8-Gray total dose. Patients received fludarabine (flu) as the sole chemotherapy complementing TBI. Eight-Gray TBI/flu was used in 494 patients and 12-Gray TBI/flu in 145 patients. Eighty-eight (23.1%) and 36 (29%) of the patients had Ph-negative B-ALL, 222 (58.3%) and 53 (42.7%) had Ph-positive B-ALL, 71 (18.6%) and 35 (28.2%) T-ALL, respectively ( P = 0.008). Patients treated with 8-Gray were older than ones received 12-Gray (median 55.7 versus 40.3 years, P &lt; 0.0001) and were more frequently administered in vivo T-cell depletion (71% versus 40%, P &lt;0.0001). In a multivariate model adjusted for age, type of ALL, and other prognostic factors, leukemia-free survival (primary endpoint) as well as relapse, nonrelapse mortality, overall survival, and GVHD-free, relapse-free survival were not influenced by the TBI dose. These results were confirmed when we focused on patients &lt;55 years of age (median 47 years). Patients with Ph-positive ALL or T-ALL had significantly better survival outcomes than ones with Ph-negative B-ALL, mainly due to significantly fewer relapses. We conclude that 8-Gray TBI is sufficient for adult patients with ALL transplanted in CR-1 with no additional benefit of augmenting the conditioning intensity to 12-Gray.