julilili42/papers huggingface dataset:
Systems of Precision: Coherent Probabilities on Pre-Dynkin Systems and Coherent Previsions on Linear Subspaces
2023-08-31

In the literature on imprecise probability, little attention is paid to the fact that imprecise probabilities are precise on a set of events. We call these sets systems of precision. We show that, under mild assumptions, the system of precision of a lower and upper probability form a so-called (pre-)Dynkin system. Interestingly, there are several settings, ranging from machine learning on partial data over frequential probability theory to quantum probability theory and decision making under uncertainty, in which, a priori, the probabilities are only desired to be precise on a specific underlying set system. Here, (pre-)Dynkin systems have been adopted as systems of precision, too. We show that, under extendability conditions, those pre-Dynkin systems equipped with probabilities can be embedded into algebras of sets. Surprisingly, the extendability conditions elaborated in a strand of work in quantum probability are equivalent to coherence from the imprecise probability literature. On this basis, we spell out a lattice duality which relates systems of precision to credal sets of probabilities. We conclude the presentation with a generalization of the framework to expectation-type counterparts of imprecise probabilities. The analogue of pre-Dynkin systems turns out to be (sets of) linear subspaces in the space of bounded, real-valued functions. We introduce partial expectations, natural generalizations of probabilities defined on pre-Dynkin systems. Again, coherence and extendability are equivalent. A related but more general lattice duality preserves the relation between systems of precision and credal sets of probabilities.
Contralateral delay activity as a marker of visual working memory capacity: a multi-site registered replication
2023-08-31

Visual working memory (VWM) is a temporary storage system capable of retaining information that can be accessed and manipulated by higher cognitive processes, thereby facilitating a wide range of cognitive functions. Electroencephalography (EEG) is used to understand the neural correlates of VWM with high temporal precision, and one commonly used EEG measure is an event-related potential called the contralateral delay activity (CDA). In a landmark study by Vogel and Machizawa (2004), the authors found that the CDA amplitude increases with the number of items stored in VWM and plateaus around three to four items, which is thought to represent the typical adult working memory capacity. Critically, this study also showed that the increase in CDA amplitude between two-item and four-item arrays correlated with individual subjects’ VWM performance. Although these results have been supported by subsequent studies, a recent study suggested that the number of subjects used in experiments investigating the CDA may not be sufficient to detect differences in set size and to provide a reliable account of the relationship between behaviorally measured VWM capacity and the CDA amplitude. To address this, the current study, as part of the #EEGManyLabs project, aims to conduct a multi-site replication of Vogel and Machizawa's (2004) seminal study on a large sample of participants, with a pre-registered analysis plan. Through this, our goal is to contribute to deepening our understanding of the neural correlates of visual working memory.
The geometry of the hot corona in MCG-05-23-16 constrained by X-ray polarimetry
2023-09-01

ABSTRACT We report on the second observation of the radio-quiet active galactic nucleus MCG-05-23-16 performed with the Imaging X-ray Polarimetry Explorer (IXPE). The observation started on 2022 November 6 for a net observing time of 640 ks, and was partly simultaneous with NuSTAR (86 ks). After combining these data with those obtained in the first IXPE pointing on 2022 May (simultaneous with XMM–Newton and NuSTAR) we find a 2–8 keV polarization degree Π = 1.6 ± 0.7 (at 68 per cent confidence level), which corresponds to an upper limit Π = 3.2 per cent (at 99 per cent confidence level). We then compare the polarization results with Monte Carlo simulations obtained with the monk code, with which different coronal geometries have been explored (spherical lamppost, conical, slab, and wedge). Furthermore, the allowed range of inclination angles is found for each geometry. If the best-fitting inclination value from a spectroscopic analysis is considered, a cone-shaped corona along the disc axis is disfavoured.
Machine Learning-Boosted Docking Enables the Efficient Structure-Based Virtual Screening of Giga-Scale Enumerated Chemical Libraries
2023-09-01

The emergence of ultra-large screening libraries, filled to the brim with billions of readily available compounds, poses a growing challenge for docking-based virtual screening. Machine learning (ML)-boosted strategies like the tool HASTEN combine rapid ML prediction with the brute-force docking of small fractions of such libraries to increase screening throughput and take on giga-scale libraries. In our case study of an anti-bacterial chaperone and an anti-viral kinase, we first generated a brute-force docking baseline for 1.56 billion compounds in the Enamine REAL lead-like library with the fast Glide high-throughput virtual screening protocol. With HASTEN, we observed robust recall of 90% of the true 1000 top-scoring virtual hits in both targets when docking only 1% of the entire library. This reduction of the required docking experiments by 99% significantly shortens the screening time. In the kinase target, the employment of a hydrogen bonding constraint resulted in a major proportion of unsuccessful docking attempts and hampered ML predictions. We demonstrate the optimization potential in the treatment of failed compounds when performing ML-boosted screening and benchmark and showcase HASTEN as a fast and robust tool in a growing arsenal of approaches to unlock the chemical space covered by giga-scale screening libraries for everyday drug discovery campaigns.
Cross-species communication via agr controls phage susceptibility in Staphylococcus aureus
2023-09-01

Bacteria use quorum sensing (QS) to coordinate group behavior in response to cell density, and some bacterial viruses (phages) also respond to QS. In Staphylococcus aureus, the agr-encoded QS system relies on accumulation of auto-inducing cyclic peptides (AIPs). Other staphylococci also produce AIPs of which many inhibit S. aureus agr. We show that agr induction reduces expression of tarM, encoding a glycosyltransferase responsible for α-N-acetylglucosamine modification of the major S. aureus phage receptor, the wall teichoic acids. This allows lytic phage Stab20 and related phages to infect and kill S. aureus. However, in mixed communities, producers of inhibitory AIPs like S. haemolyticus, S. caprae, and S. pseudintermedius inhibit S. aureus agr, thereby impeding phage infection. Our results demonstrate that cross-species interactions dramatically impact phage susceptibility. These interactions likely influence microbial ecology and impact the efficacy of phages in medical and biotechnological applications such as phage therapy.
Contingency and Landscape: Basic Considerations on Graphic and Cartographic Representations in Recourse to the Concept of Inverse Landscapes as a Contribution to Deviant Cartographies with Examples on Louisiana
2023-09-01

Abstract This paper deals with the possibilities of graphic and cartographic representation of landscapes that are always contingently constituted. The contingency of the representation of landscape is based on the contingency of understandings of landscape, the contingency of methods of (scientific) acquisition of knowledge about landscape, as well as the contingency of forms of representation, with which the present essay deals in a prominent way. If contingency is to be treated graphically and cartographically, this means to question widespread conventions, both regarding the choice of topics, the methodology of obtaining and ordering data, but also with regard to representation. This is—following the neopragmatic basic considerations—to be oriented strongly at the statement goal. Following these basic considerations, we have designed the cartographic representations in a strongly focused manner, graphic representations in parts in a manner borrowed from the comic style of the Ligne Claire . This type of representation is intended to create a meta-deviance that makes it easier for readers to develop contingent interpretations of the world. With our approach we follow neopragmatic basic considerations, which follows a postcritical cartographic perspective, not to seek the separative and discursively exclude the other, but to make other perspectives functionally available through integration, complementarity, and further development.
Molecular Dynamics in Rydberg Tweezer Arrays: Spin-Phonon Entanglement and Jahn-Teller Effect
2023-09-01

Atoms confined in optical tweezer arrays constitute a platform for the implementation of quantum computers and simulators. State-dependent operations are realized by exploiting electrostatic dipolar interactions that emerge, when two atoms are simultaneously excited to high-lying electronic states, so-called Rydberg states. These interactions also lead to state-dependent mechanical forces, which couple the electronic dynamics of the atoms to their vibrational motion. We explore these vibronic couplings within an artificial molecular system in which Rydberg states are excited under so-called facilitation conditions. This system, which is not necessarily self-bound, undergoes a structural transition between an equilateral triangle and an equal-weighted superposition of distorted triangular states (Jahn-Teller regime) exhibiting spin-phonon entanglement on a micrometer distance. This highlights the potential of Rydberg tweezer arrays for the study of molecular phenomena at exaggerated length scales.
Fiber deprivation and microbiome-borne curli shift gut bacterial populations and accelerate disease in a mouse model of Parkinson’s disease
2023-09-01

Parkinson's disease (PD) is a neurological disorder characterized by motor dysfunction, dopaminergic neuron loss, and alpha-synuclein (αSyn) inclusions. Many PD risk factors are known, but those affecting disease progression are not. Lifestyle and microbial dysbiosis are candidates in this context. Diet-driven gut dysbiosis and reduced barrier function may increase exposure of enteric neurons to toxins. Here, we study whether fiber deprivation and exposure to bacterial curli, a protein cross-seeding with αSyn, individually or together, exacerbate disease in the enteric and central nervous systems of a transgenic PD mouse model. We analyze the gut microbiome, motor behavior, and gastrointestinal and brain pathologies. We find that diet and bacterial curli alter the microbiome and exacerbate motor performance, as well as intestinal and brain pathologies, but to different extents. Our results shed important insights on how diet and microbiome-borne insults modulate PD progression via the gut-brain axis and have implications for lifestyle management of PD.
How Personality Matters for Education Research
2023-09-01

Abstract The field of personality psychology could contribute to the aims of educational research, but several misconceptions may hold back this synthesis. We address three “misconceptions” about personality psychology that are surprisingly pervasive outside of that field: that there are personality types, that personality is fixed, and that the existence of personality implies that situations are unimportant. We then cover four ways that personality psychology can assist educational aims: personality can be used to (1) boost our ability to accurately predict educational outcomes, (2) inform educational interventions, (3) support the academic development of all learners in personalised learning interventions, and (4) be employed as target outcomes for education. In the process, we show how personality relates to important educational outcomes, outline theoretical links with educationally relevant concepts like socio-emotional skills, and include an overview of current personality scales that can be used when getting started. Through this paper, we hope to stimulate and enthuse researchers to advance synthesis between the disciplines.
Treatment management forBRAF-mutant melanoma patients with tumor recurrence on adjuvant therapy: a multicenter study from the prospective skin cancer registry ADOREG
2023-09-01

Background Adjuvant therapy with immune-checkpoint inhibitors (CPI) or BRAF/MEK-directed targeted therapy (TT) improves recurrence-free survival (RFS) for patients with advanced, BRAF V600-mutant ( BRAF mut) resected melanoma. However, 40% of these patients will develop distant metastases (DM) within 5 years, which require systemic therapy. Little data exist to guide the choice of upfront adjuvant therapy or treatment management upon DM. This study evaluated the efficacy of subsequent treatments following tumor recurrence upon upfront adjuvant therapy. Methods For this multicenter cohort study, we identified 515 BRAF mut patients with resected stage III melanoma who were treated with PD-1 inhibitors (anti-PD1) or TT in the adjuvant setting. Disease characteristics, treatment regimens, details on tumor recurrence, subsequent treatment management, and survival outcomes were collected within the prospective, real-world skin cancer registry ADOReg. Primary endpoints included progression-free survival (PFS) following DM and best tumor response to first-line (1L) treatments. Results Among 515 eligible patients, 273 patients received adjuvant anti-PD1 and 242 adjuvant TT. At a median follow-up of 21 months, 54.6% of anti-PD1 patients and 36.4% of TT patients recurred, while 39.6% (anti-PD1) and 29.3% (TT) developed DM. Risk of recurrence was significantly reduced in patients treated with TT compared with anti-PD1 (adjusted HR 0.52; 95% CI 0.40 to 0.68, p&lt;0.001). Likewise, median RFS was significantly longer in TT-treated patients (31 vs 17 months, p&lt;0.001). Patients who received TT as second adjuvant treatment upon locoregional recurrence had a longer RFS2 as compared with adjuvant CPI (41 vs 6 months, p=0.009). Patients who recurred at distant sites following adjuvant TT showed favorable response rates (42.9%) after switching to 1L ipilimumab+nivolumab (ipi+nivo). Patients with DM during adjuvant anti-PD1 achieved response rates of 58.7% after switching to 1L TT and 35.3% for 1L ipi+nivo. Overall, median PFS was significantly longer in patients who switched treatments for stage IV disease (median PFS 9 vs 5 months, p=0.004). Conclusions BRAF mut melanoma patients who developed DM upon upfront adjuvant therapy achieve favorable tumor control and prolonged PFS after switching treatment modalities in the first-line setting of stage IV disease. Patients with locoregional recurrence benefit from complete resection of recurrence followed by a second adjuvant treatment with TT.
Sex Differences in Vestibular Schwannoma
2023-09-01

Vestibular schwannoma (VS) are equally common in men and woman. A number of epidemiological studies have reported on sex-specific aspects of incidence, tumor size, tinnitus and hearing loss. However, data on sex-specific, pre- and post-surgically quality of life (QoL) are rare. The objective of the present study was to determine sex-specific aspects on QoL in VS. Health-related QoL was analyzed in 260 patients (112 male/148 female) with unilateral sporadic VS using general (SF-36: general Short-Form Health Survey), disease-specific (PANQOL: Penn Acoustic Neuroma Quality-of-Life Scale, PANQOL) and symptom-specific (DHI: Dizziness Handicap Inventory; HHI: Hearing Handicap Inventory; THI: Tinnitus Handicap Inventory; FDI: Facial Disability Index) QoL questionnaires. Sex differences were evaluated pre- and postoperative by multi- and univariate analyses based on 200 preoperative and 88 postoperative questionnaires. Female patients were significantly more affected by dizziness, headaches, reduced energy and anxiety. Energy and balance changed similarly in both sexes after surgery. However, postoperative women tended to be more affected by facial palsy and headaches than men. Despite the greater physical impairment, general health improved equivalently or even more in female patients than in males. In conclusion, self-rated QoL in VS is significantly affected by sex and surgery. This should be taken into account when counseling VS patients regarding observation, radiotherapy, and surgery.
Temperature and soil moisture change microbial allocation of pesticide‐derived carbon
2023-09-01

Abstract Temperature and soil moisture are known to control pesticide mineralization. Half‐life times () derived from pesticide mineralization curves generally indicate longer residence times at low soil temperature and moisture but do not consider potential changes in the microbial allocation of pesticide‐derived carbon (C). We aimed to determine carbon use efficiency (, formation of new biomass relative to total C uptake) to better understand microbial utilization of pesticide‐derived C under different environmental conditions and to support the conventional description of degradation dynamics based on mineralization. We performed a microcosm experiment at two MCPA (2‐methyl‐4‐chlorophenoxyacetic acid) concentrations (1 and 20 mg kg −1 ) and defined 20°C/pF 1.8 as optimal and 10°C/pF 3.5 as limiting environmental conditions. After 4 weeks, 70% of the initially applied MCPA was mineralized under optimal conditions but MCPA mineralization reached less than 25% under limiting conditions. However, under limiting conditions, an increase in was observed, indicating a shift towards anabolic utilization of MCPA‐derived C. In this case, increased C assimilation implied C storage or the formation of precursor compounds to support resistance mechanisms, rather than actual growth since we did not find an increase in the tfdA gene relevant to MCPA degradation. We were able to confirm the assumption that under limiting conditions, C assimilation increases relative to mineralization and that C redistribution, may serve as an explanation for the difference between mineralization and MCPA dissipation‐derived degradation dynamics. In addition, by introducing to the temperature‐ and moisture‐dependent degradation of pesticides, we can capture the underlying microbial constraints and adaptive mechanisms to changing environmental conditions.
JUNO sensitivity to the annihilation of MeV dark matter in the galactic halo
2023-09-01

Abstract We discuss JUNO sensitivity to the annihilation of MeV dark matter in the galactic halo via detecting inverse beta decay reactions of electron anti-neutrinos resulting from the annihilation. We study possible backgrounds to the signature, including the reactor neutrinos, diffuse supernova neutrino background, charged- and neutral-current interactions of atmospheric neutrinos, backgrounds from muon-induced fast neutrons and cosmogenic isotopes. A fiducial volume cut, as well as the pulse shape discrimination and the muon veto are applied to suppress the above backgrounds. It is shown that JUNO sensitivity to the thermally averaged dark matter annihilation rate in 10 years of exposure would be significantly better than the present-day best limit set by Super-Kamiokande and would be comparable to that expected by Hyper-Kamiokande.
The many faces of nodal and splenic marginal zone lymphomas. A report of the 2022 EA4HP/SH lymphoma workshop
2023-09-01

Abstract Session 3 of the lymphoma workshop of the XXI joint meeting of the European Association for Haematopathology and the Society for Hematopathology took place in Florence, Italy, on September 22, 2022. The topics of this session were splenic and nodal marginal zone lymphomas, transformation in marginal zone lymphomas, and pediatric nodal marginal zone lymphomas and their differential diagnosis as well as related entities. Forty-two cases in these categories were submitted to the workshop, including splenic lymphomas (marginal zone and diffuse red pulp lymphomas), transformed marginal zone lymphomas (splenic and nodal), nodal marginal zone lymphomas with increased TFH-cells, and pediatric nodal marginal zone lymphomas. The case review highlighted some of the principal problems in the diagnosis of marginal zone lymphomas, including the difficulties in the distinction between splenic marginal zone lymphoma, splenic diffuse red pulp lymphoma, and hairy cell leukemia variant/splenic B-cell lymphoma with prominent nucleoli which requires integration of clinical features, immunophenotype, and morphology in blood, bone marrow, and spleen; cases of marginal zone lymphoma with markedly increased TFH-cells, simulating a T-cell lymphoma, where molecular studies (clonality and mutation detection) can help to establish the final diagnosis; the criteria for transformation of marginal zone lymphomas, which are still unclear and might require the integration of morphological and molecular data; the concept of an overlapping spectrum between pediatric nodal marginal zone lymphoma and pediatric-type follicular lymphoma; and the distinction between pediatric nodal marginal zone lymphoma and “atypical” marginal zone hyperplasia, where molecular studies are mandatory to correctly classify cases.
Defining benchmark outcomes for transsphenoidal surgery of pituitary adenomas: a multicenter analysis
2023-09-01

Abstract Importance Benchmarks aid in improve outcomes for surgical procedures. However, best achievable results that have been validated internationally for transsphenoidal surgery (TS) are not available. Objective We aimed to establish standardized outcome benchmarks for TS of pituitary adenomas. Design A total of 2685 transsphenoidal tumor resections from 9 expert centers in 3 continents were analyzed. Setting Patients were risk stratified, and the median values of each center's outcomes were established. The benchmark was defined as the 75th percentile of all median values for a particular outcome. The postoperative benchmark outcomes included surgical factors, endocrinology-specific values, and neurology-specific values. Results Of 2685 patients, 1149 (42.8%) defined the low-risk benchmark cohort. Within these benchmark cases, 831 (72.3%) patients underwent microscopic TS, and 308 (26.8%) patients underwent endoscopic endonasal resection. Of all tumors, 799 (29.8%) cases invaded the cavernous sinus. The postoperative complication rate was 19.6% with mortality between 0.0% and 0.8%. Benchmark cutoffs were ≤2.9% for reoperation rate, ≤1.9% for cerebrospinal fluid leak requiring intervention, and ≤15.5% for transient diabetes insipidus. At 6 months, benchmark cutoffs were calculated as follows: readmission rate: ≤6.9%, new hypopituitarism ≤6.0%, and tumor remnant ≤19.2%. Conclusions This analysis defines benchmark values for TS targeting morbidity and mortality and represents the best outcomes in the best patients in expert centers. These cutoffs can be used to assess different centers, patient populations, and novel surgical techniques. It should be noted that the benchmark values may influence each other and must be evaluated in their own context.
Assessment of the relevance of midwifery competencies in academic education in Germany from the midwives’ perspective: A structural analysis of cross-sectional survey data
2023-09-01

The adapted assessment tool can be used with minor modifications to reliably and validly measure the assessed relevance of academic competence from the midwives' perspective. Combined with data on the assessments of medical practitioners and laypersons, the assessment provides a substantial data basis for the development of a competence profile for academic midwifery education in Germany.