julilili42/papers huggingface dataset:
52,000 years of woolly rhinoceros population dynamics reveal extinction mechanisms
2024-06-03

The extinction of the woolly rhinoceros ( Coelodonta antiquitatis ) at the onset of the Holocene remains an enigma, with conflicting evidence regarding its cause and spatiotemporal dynamics. This partly reflects challenges in determining demographic responses of late Quaternary megafauna to climatic and anthropogenic causal drivers with available genetic and paleontological techniques. Here, we show that elucidating mechanisms of ancient extinctions can benefit from a detailed understanding of fine-scale metapopulation dynamics, operating over many millennia. Using an abundant fossil record, ancient DNA, and high-resolution simulation models, we untangle the ecological mechanisms and causal drivers that are likely to have been integral in the decline and later extinction of the woolly rhinoceros. Our 52,000-y reconstruction of distribution-wide metapopulation dynamics supports a pathway to extinction that began long before the Holocene, when the combination of cooling temperatures and low but sustained hunting by humans trapped woolly rhinoceroses in suboptimal habitats along the southern edge of their range. Modeling indicates that this ecological trap intensified after the end of the last ice age, preventing colonization of newly formed suitable habitats, weakening stabilizing metapopulation processes, triggering the extinction of the woolly rhinoceros in the early Holocene. Our findings suggest that fragmentation and resultant metapopulation dynamics should be explicitly considered in explanations of late Quaternary megafauna extinctions, sending a clarion call to the fragility of the remaining large-bodied grazers restricted to disjunct fragments of poor-quality habitat due to anthropogenic environmental change.
Type 1 Myocardial Infarction in Patients With Acute Ischemic Stroke
2024-06-03

Importance Elevated values of high-sensitivity cardiac troponin (hs-cTn) are common in patients with acute ischemic stroke and are associated with poor prognosis. However, diagnostic and therapeutic implications in patients with ischemic stroke remain unclear. Objective To identify factors indicative of myocardial infarction (MI) in patients with acute ischemic stroke and hs-cTn elevation. The primary hypothesis was that a dynamic change of hs-cTn values (&amp;amp;gt;50% change) in patients with acute ischemic stroke indicates MI. Design, Setting, and Participants This cross-sectional study was a prospective, observational study with blinded end-point assessment conducted across 26 sites in Germany. Patients were included if they had acute ischemic stroke within 72 hours and either (1) highly elevated hs-cTn values on admission (&amp;amp;gt;52 ng/L) or (2) hs-cTn levels above the upper limit of normal and a greater than 20% change at repeated measurements. Patients were enrolled between August 2018 and October 2020 and had 1 year of follow-up. Statistical analysis was performed between April 2022 and August 2023. Exposure Standardized electrocardiography, echocardiography, and coronary angiography. Main Outcome and Measures Diagnosis of MI as adjudicated by an independent end-point committee based on the findings of electrocardiography, echocardiography, and coronary angiography. Results In total, 254 patients were included. End points were adjudicated in 247 patients (median [IQR] age, 75 [66-82] years; 117 were female [47%] and 130 male [53%]). MI was present in 126 of 247 patients (51%) and classified as type 1 MI in 50 patients (20%). Dynamic change in hs-cTn value was not associated with MI in univariable (32% vs 38%; χ 2 ﻿ P = .30) or adjusted comparison (odds ratio, 1.05; 95% CI, 0.31-3.33). The baseline absolute hs-cTn value was independently associated with type 1 MI. The best cutoffs for predicting type 1 MI were at hs-cTn values 5 to 10 times the upper limit normal. Conclusions and Relevance This study found that in patients with acute ischemic stroke, a dynamic change in hs-cTn values did not identify MI, underscoring that dynamic changes do not identify the underlying pathophysiological mechanism. In exploratory analyses, very high absolute hs-cTn values were associated with a diagnosis of type 1 MI. Further studies are needed how to best identify patients with stroke who should undergo coronary angiography.
Evidence for dynastic succession among early Celtic elites in Central Europe
2024-06-03

Abstract The early Iron Age (800 to 450 BCE) in France, Germany and Switzerland, known as the ‘West-Hallstattkreis’, stands out as featuring the earliest evidence for supra-regional organization north of the Alps. Often referred to as ‘early Celtic’, suggesting tentative connections to later cultural phenomena, its societal and population structure remain enigmatic. Here we present genomic and isotope data from 31 individuals from this context in southern Germany, dating between 616 and 200 BCE. We identify multiple biologically related groups spanning three elite burials as far as 100 km apart, supported by trans-regional individual mobility inferred from isotope data. These include a close biological relationship between two of the richest burial mounds of the Hallstatt culture. Bayesian modelling points to an avuncular relationship between the two individuals, which may suggest a practice of matrilineal dynastic succession in early Celtic elites. We show that their ancestry is shared on a broad geographic scale from Iberia throughout Central-Eastern Europe, undergoing a decline after the late Iron Age (450 BCE to ~50 CE).
ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization
2024-06-03

Untargeted tandem mass spectrometry (MS/MS) has become a high-throughput method to measure small molecules in complex samples. One key goal is the transformation of these MS/MS spectra into chemical structures. Computational techniques such as MS/MS library search have enabled the reidentification of known compounds. Analog library search and molecular networking extend this identification to unknown compounds. While there have been advancements in metrics for the similarity of MS/MS spectra of structurally similar compounds, there is still a lack of automated methods to provide site specific information about structural modifications. Here we introduce ModiFinder which leverages the alignment of peaks in MS/MS spectra between structurally related known and unknown small molecules. Specifically, ModiFinder focuses on shifted MS/MS fragment peaks in the MS/MS alignment. These shifted peaks putatively represent substructures of the known molecule that contain the site of the modification. ModiFinder synthesizes this information together and scores the likelihood for each atom in the known molecule to be the modification site. We demonstrate in this manuscript how ModiFinder can effectively localize modifications which extends the capabilities of MS/MS analog searching and molecular networking to accelerate the discovery of novel compounds.
Gender Bias Detection in Court Decisions: A Brazilian Case Study
2024-06-03

Data derived from the realm of the social sciences is often produced in digital text form, which motivates its use as a source for natural language processing methods. Researchers and practitioners have developed and relied on artificial intelligence techniques to collect, process, and analyze documents in the legal field, especially for tasks such as text summarization and classification. While increasing procedural efficiency is often the primary motivation behind natural language processing in the field, several works have proposed solutions for human rights-related issues, such as assessment of public policy and institutional social settings. One such issue is the presence of gender biases in court decisions, which has been largely studied in social sciences fields; biased institutional responses to gender-based violence are a violation of international human rights dispositions since they prevent gender minorities from accessing rights and hamper their dignity. Natural language processing-based approaches can help detect these biases on a larger scale. Still, the development and use of such tools require researchers and practitioners to be mindful of legal and ethical aspects concerning data sharing and use, reproducibility, domain expertise, and value-charged choices. In this work, we (a) present an experimental framework developed to automatically detect gender biases in court decisions issued in Brazilian Portuguese and (b) describe and elaborate on features we identify to be critical in such a technology, given its proposed use as a support tool for research and assessment of court~activity.
Insights From Insurance for Fair Machine Learning
2024-06-03

We argue that insurance can act as an analogon for the social situatedness of machine learning systems, hence allowing machine learning scholars to take insights from the rich and interdisciplinary insurance literature. Tracing the interaction of uncertainty, fairness and responsibility in insurance provides a fresh perspective on fairness in machine learning. We link insurance fairness conceptions to their machine learning relatives, and use this bridge to problematize fairness as calibration. In this process, we bring to the forefront two themes that have been largely overlooked in the machine learning literature: responsibility and aggregate-individual tensions.
Effect of Multiantibiotic-Loaded Bone Cement on the Treatment of Periprosthetic Joint Infections of Hip and Knee Arthroplasties—A Single-Center Retrospective Study
2024-06-03

Background: Two-stage septic revision is the prevailing method for addressing late periprosthetic infections. Using at least dual-antibiotic-impregnated bone cement leads to synergistic effects with a more efficient elution of individual antibiotics. Recent data on the success rates of multiantibiotic cement spacers in two-stage revisions are rare. Methods: We conducted a retrospective follow-up single-center study involving 250 patients with late periprosthetic hip infections and 95 patients with prosthetic knee infections who underwent septic two-stage prosthesis revision surgery between 2017 and 2021. In accordance with the antibiotic susceptibility profile of the microorganisms, a specific mixture of antibiotics within the cement spacer was used, complemented by systemic antibiotic treatment. All patients underwent preoperative assessments and subsequent evaluations at 3, 6, 9, 12, 18, and 24 months post operation and at the most recent follow-up. Results: During the observation period, the survival rate after two-step septic revision was 90.7%. Although survival rates tended to be slightly lower for difficult-to-treat (DTT) microorganism, there was no difference between the pathogen groups (easy-to-treat (ETT) pathogens, methicillin-resistant staphylococci (MRS), and difficult-to-treat (DTT) pathogens). Furthermore, there were no differences between monomicrobial and polymicrobial infections. No difference in the survival rate was observed between patients with dual-antibiotic-loaded bone cement without an additional admixture (Copal® G+C and Copal® G+V) and patients with an additional admixture of antibiotics to proprietary cement. Conclusion: Employing multiple antibiotics within spacer cement, tailored to pathogen susceptibility, appears to provide reproducibly favorable success rates, even in instances of infections with DTT pathogens and polymicrobial infections.
Human Placental Schistosomiasis—A Systematic Review of the Literature
2024-06-03

Background: Schistosome egg deposition in pregnant women may affect the placenta of infected mothers and cause placental schistosomiasis (PS). Histopathological examination of placental tissue is an inadequate detection method due to low sensitivity. So far, there has not been any systematic review on PS. Methods: We conducted a systematic literature search on PubMed, EMBASE, and Medline and included all publications that reported microscopically confirmed cases of PS, as well as the relevant secondary literature found in the citations of the primarily included publications. Results: Out of 113 abstracts screened we found a total of 8 publications describing PS with a total of 92 cases describing egg deposition of dead and/or viable eggs and worms of S. haematobium and S. mansoni in placental tissue. One cross-sectional study investigating the prevalence of PS and its association with adverse birth outcomes, found 22% of placentas to be infested using a maceration technique but only &lt;1% using histologic examination. Additionally, no direct link to deleterious pregnancy outcomes could be shown. Conclusions: PS is a highly unattended and underdiagnosed condition in endemic populations, due to a lack of awareness as well as low sensitivity of histopathological examinations. However, PS may play an important role in mediating or reinforcing adverse birth outcomes (ABO) such as fetal growth restriction (FGR) in maternal schistosomiasis, possibly by placental inflammation.
Testing the reliability of global surface temperature reconstructions of the last glacial cycle
2024-06-03

Abstract. Reconstructing past variations of the global mean surface temperature is used to characterise the Earth system response to perturbations as well as validate Earth system simulations. Reconstructing GMST beyond the instrumental period relies on algorithms aggregating local proxy temperature records. Here, we propose to establish standards for the evaluation of the performance of such reconstruction algorithms. Our framework relies on pseudo-proxy experiments. That is, we test the ability of the algorithm to reconstruct a simulated GMST, using artificially generated proxy data created from the same simulation. We apply the framework to an adapted version of the GMST reconstruction algorithm used in Snyder (2016), and the synthesis of marine proxy records for temperature of the last 130 kyr from Jonkers et al. (2020). We use an ensemble of 4 transient simulations of the last glacial cycle or the last 25 kyr for the pseudo-proxy experiments. We find the algorithm to be able to reconstruct timescales longer than 4 kyr over the last 25 kyr. However, beyond 40 kyr BP, age uncertainty limits the algorithm capability to timescales longer than 15 kyr. The main sources of uncertainty are a factor, that rescales near global mean sea surface temperatures to GMST, the proxy measurement, the specific set of record locations, and potential seasonal bias. Increasing the number of records significantly reduces all sources of uncertainty but the scaling. We also show that a trade-off exists between the inclusion of a large number of records, which reduces the uncertainty on long time scales, and of only records with low age uncertainty, high accumulation rate, and high resolution, which improves the reconstruction of the short timescales. Finally, the method and the quantitative results presented here can serve as a basis for future evaluations of reconstructions. We also suggest future avenues to improve reconstruction algorithms and discuss the key limitations arising from the proxy data properties.
Better source memory for remembered to-be-forgotten items than for remembered to-be-remembered items.
2024-06-03

When participants study items one-by-one and are directed to either remember or forget the respective item directly after its presentation, retention of to-be-forgotten items is regularly worse than of to-be-remembered items. We tested whether this directed forgetting effect which is regularly observed for item memory generalizes to source memory. In three experiments, participants studied items in two different source colors (<i>N</i> = 101) or at two different source locations (<i>N</i> = 64; <i>N</i> = 81). Sources were manipulated orthogonally to item type (remember vs. forget). At test, we asked participants to recognize all studied items and also to identify their source. We used a multinomial processing tree model to disentangle item memory, source memory, and guessing. In all three experiments, we replicated the directed forgetting effect in item memory. Source memory for to-be-forgotten items that were recognized despite the intention to forget, however, tended to be even better than source memory for to-be-remembered items that were recognized. These results suggest that the directed forgetting effect does not simply translate from item to source memory. Rather source memory seems to be disproportionally increased in to-be-forgotten items that are remembered. (PsycInfo Database Record (c) 2024 APA, all rights reserved).
Nanometer-scale electron beam shaping with thickness controlled and stacked nanostructured graphite
2024-06-03

The generation of small electron probes is the basis for various techniques in which such a probe is scanned across a sample, and special probe shapes like vortices can be desirable, e.g., to gain insight into magnetic properties. Micron-scale phase plates or holographic masks, in combination with demagnifying optics, are usually used for creating such special probe wave functions. Here, we present the fabrication of nanometer-sized phase plates based on thickness-selected and stacked graphite layers as well as an analysis of their performance. First, a spiral phase plate is demonstrated that creates a vortex beam with an orbital angular momentum of 1 and an outer radius of 2.5 nm. Second, a three-level Fresnel lens built from two nanopatterned graphite membranes is presented, which achieves a focal spot with a full width at half maximum of 5.5 nm. Third, an array of electron sieves is demonstrated, each of which creates a focal spot with a radius of 2 nm, and the array is applied as a Shack–Hartmann wavefront detector. These elements allow the generation of few-nanometer sized focused probes or vortices without the need for additional optical elements.
Sustained bias of spatial attention in a 3 T MRI scanner
2024-06-03

Abstract When lying inside a MRI scanner and even in the absence of any motion, the static magnetic field of MRI scanners induces a magneto-hydrodynamic stimulation of subjects’ vestibular organ (MVS). MVS thereby not only causes a horizontal vestibular nystagmus but also induces a horizontal bias in spatial attention. In this study, we aimed to determine the time course of MVS-induced biases in both VOR and spatial attention inside a 3 T MRI-scanner as well as their respective aftereffects after participants left the scanner. Eye movements and overt spatial attention in a visual search task were assessed in healthy volunteers before, during, and after a one-hour MVS period. All participants exhibited a VOR inside the scanner, which declined over time but never vanished completely. Importantly, there was also an MVS-induced horizontal bias in spatial attention and exploration, which persisted throughout the entire hour within the scanner. Upon exiting the scanner, we observed aftereffects in the opposite direction manifested in both the VOR and in spatial attention, which were statistically no longer detectable after 7 min. Sustained MVS effects on spatial attention have important implications for the design and interpretation of fMRI-studies and for the development of therapeutic interventions counteracting spatial neglect.
Cracking Under Pressure? Gender Role Attitudes Toward Maternal Employment During COVID-19 in Germany
2024-06-03

The COVID-19 pandemic posed unprecedented challenges to gender equality, particularly affecting working parents due to disruptions in daycare and school operations. It also impacted labor market opportunities for both men and women. This study investigates shifts in gender role attitudes toward maternal employment in Germany during pandemic lockdowns and subsequent periods of eased restrictions, using combined data from 2008 to early 2022. During the lockdown in early 2021, the study documents a significant decline in egalitarian attitudes, especially for men with dependent children and women without dependent children in the household. The results are discussed and interpreted against the background of various theoretical approaches. During periods of eased restrictions in early 2022, the trend reversed, and gender role attitudes recovered significantly for the same groups. The findings imply that pandemic-related changes in gender role attitudes toward maternal employment were largely transitory.
Functional Brain Networks Underlying Autobiographical Event Simulation: An Update
2024-06-03

Functional magnetic resonance imaging (fMRI) studies typically explore changes in the blood-oxygen-level-dependent (BOLD) signal underlying discrete cognitive processes that occur over milliseconds to a few seconds. However, autobiographical cognition is a more protracted process and requires fMRI tasks with longer trials to capture the temporal dynamics of the underlying brain networks. In the current study, we provide an updated analysis of the fMRI data obtained from a published autobiographical event simulation task, with a slow-event-related design (34-second trials), that involved participants recalling past autobiographical events, imagining past/future autobiographical events, and completing a semantic association control task. Our updated analysis using Constrained Principal Component Analysis for fMRI (fMRI-CPCA) retrieved two networks reported in the original results, including the Default Mode Network (DMN) which was activated in the autobiographical event simulation conditions but deactivated in the semantic association control condition, and the Multiple Demand Network (MDN) which peaked early during all conditions but was more sustained in the recall condition. Two novel networks emerged, including the Maintaining Internal Attention network (MAIN) which, while active for all conditions, was more strongly engaged during the imagination and semantic association control conditions than during the Recall condition, suggesting a role in constructing novel associations. These results suggest that the DMN does not support autobiographical simulation alone, but co-activates with the MDN and MAIN networks, with the timing of peak activations depending on evolving task demands during the simulation process.
Acute Encephalopathy in a Patient with Raoultella Ornithinolytica Infection: A Challenging Presentation.
2024-06-03

Raoultella ornithinolytica is a rare, gram-negative environmental enterobacterium. Although infections in humans caused by R. ornithinolytica are uncommon, there are increasing reports implicating it in urinary tract infections, hepatobiliary infections, and bacteremia, designating it as an emerging pathogen. Its habitat is primarily in aquatic environments and soil, with seafood frequently identified as a potential source of infection. While these infections have predominantly been described in immunocompromised patients previously, our case suggests that advanced age may be a significant risk factor. We describe a case of a 73-year-old man presenting with encephalopathy who then was found to have R. ornithinolytica bacteremia from a genitourinary source. Following antibiotic treatment, the infection resolved and the neurologic symptoms improved. To the best of our knowledge, this is the first documented case in the medical literature of R. ornithinolytica featuring a primary neurologic presentation.