julilili42/papers huggingface dataset:
The MARC SE-Africa Dashboard: Joining Forces to Counteract Emerging Antimalarial Resistance in South and East Africa
2025-01-08

Abstract Regions within eastern and southern Africa (SE-Africa) carry some of the highest malaria burdens. Understanding the spatiotemporal changes in the emergence and spread of artemisinin (partial) resistance (ART-R) and how to mitigate ART-R is therefore of paramount importance in these areas. Here, we present a dashboard developed by the Mitigating Antimalarial Resistance Consortium for SE-Africa in collaboration with nineteen national control malaria programs (NCMPs) and their partners. The dashboard supports NCMPs’ decision-making by providing curated information on the latest antimalarial resistance data available. We systematically reviewed, collated, and visualized antimalarial resistance information from therapeutic efficacy studies, molecular surveillance for Pfkelch13 ART-R genetic markers, current in-country malaria treatment policies, and reported malaria cases and deaths. We identified evidence gaps in therapeutic efficacy and molecular surveillance, particularly in southern Africa. Five countries, Angola, the Democratic Republic of Congo, Kenya, Tanzania and Uganda, reported artemether-lumefantrine treatment failures above the WHO threshold of 10% after correcting for reinfections. The A675V, R561H, P574L, and C469F Pfkelch13 markers were highly prevalent in cross-border regions of several East African countries, with the C469Y marker rapidly spreading across Uganda. The dashboard provides an interactive platform for data sharing at a regional level. We discuss the implications of these findings for policy, practice, and research. Author Summary We introduce the MARC SE-Africa Dashboard, an innovative tool developed at the request of national malaria control programs to enhance the management of malaria through data-driven insights into antimalarial drug resistance in Southern and Eastern Africa. This interactive dashboard compiles and visualizes data from multiple sources, offering an up-to-date overview of resistance patterns and treatment efficacy. With its interactive maps and user-defined parameters, the dashboard enables detailed multinational and cross-border analysis, which is invaluable for identifying and monitoring emerging hotspots of resistance. This allows health professionals, researchers, and policymakers to target interventions effectively and adapt strategies in response to the evolving landscape of malaria resistance. The information visualized on the dashboard includes updated information on molecular markers of resistance, therapeutic efficacy outcomes, and national treatment policies for 19 malaria-endemic countries. The dashboard aims to facilitate regional cooperation in malaria management, which proves essential for proactive combat against malaria in high-risk areas. We discuss the insights gained from the curated and collated data and the manner in which this data and dashboard can support national malaria control programs and researchers.
Cardiotoxicity as important differential diagnosis for reduced myocardial blood flow during Rubidium cardiac PET/CT
2025-01-08

Abstract A 65-year-old woman with a history of ductal mammary carcinoma and recent autonomic dysfunction underwent a Rb-82 chloride (RbCl) cardiac PET/CT scan that showed no ischemia or scarring, but significantly reduced myocardial flow reserve (MFR) (global: 1.5) and a CAC-Score of 0. The patient’s chemotherapy history (paclitaxel, carboplatin, epirubicin, pembrolizumab 2 years before) with elevated Troponin T and NT-pro-BNP levels at that time, and now reduced MFR with 0 CAC suggests cancer-therapy-related cardiotoxicity. An important differential diagnosis to the more common CAD-associated microvascular disease. Furthermore, tumor recurrence with a PET-avid lymph node metastasis was found additionally.
PTMVision: An Interactive Visualization Webserver for Post-translational Modifications of Proteins
2025-01-08

Recent improvements in methods and instruments used in mass spectrometry have greatly enhanced the detection of protein post-translational modifications (PTMs). On the computational side, the adoption of open modification search strategies now allows for the identification of a wide variety of PTMs, potentially revealing hundreds to thousands of distinct modifications in biological samples. While the observable part of the proteome is continuously growing, the visualization and interpretation of this vast amount of data in a comprehensive fashion is not yet possible. There is a clear need for methods to easily investigate the PTM landscape and to thoroughly examine modifications on proteins of interest from acquired mass spectrometry data. We present PTMVision, a web server providing an intuitive and simple way to interactively explore PTMs identified in mass spectrometry-based proteomics experiments and to analyze the modification sites of proteins within relevant context. It offers a variety of tools to visualize the PTM landscape from different angles and at different levels, such as 3D structures and contact maps, UniMod classification summaries, and site specific overviews. The web server's user-friendly interface ensures accessibility across diverse scientific backgrounds. PTMVision is available at https://ptmvision-tuevis.cs.uni-tuebingen.de/.
Combining disparate lines of evidence in the study of the history of language isolates, exemplified with Mochica from Northern Peru
2025-01-08

Abstract This article provides a synthesizing discussion of different lines of evidence for the linguistic history of the Mochica language (Northern Peru). Among the topics discussed are the inference of the former geographic extension through toponymic study; the study of indigenous personal names as a fertile source of information on grammatical structure, particularly the genesis and nature of an unusual numeral classifier system; internal reconstruction; local as well as rather spectacular cases of long-distance language contact; areal typology; sociolinguistic typology; the reconstruction of outlines of the social ecology of the language in its pre-Columbian context; and the interdisciplinary contextualization of linguistic data with that of other disciplines that study human prehistory. Thus, the article provides an exemplary case study of the richly textured picture which a multi-pronged approach can paint on the history of isolates.
Western disturbances and climate variability: a review of recent developments
2025-01-09

Abstract. Western disturbances (WDs) are synoptic-scale weather systems embedded within the subtropical westerly jet. Manifesting as upper-level troughs often associated with a lower-tropospheric low over western or northern India, they share some dynamical features with extratropical cyclones. WDs are most common during the boreal winter (December to March), during which they bring the majority of precipitation – both rain and snow – to the western Himalaya, as well as to surrounding areas of north India, Pakistan, and the Tibetan Plateau. WDs are also associated with weather hazards such as heavy snowfall, hailstorms, fog, cloudbursts, avalanches, frost, and cold waves. In this paper, we review recent developments in understanding WDs and their impacts. Over the last decade, recent studies have collectively made use of novel data, novel analysis techniques such as tracking algorithms, and the increasing availability of high-resolution weather and climate models. This review is separated into six main sections – structure and thermodynamics, precipitation and impacts, teleconnections, modelling experiments, forecasting at a range of scales, and paleoclimate and climate change – each motivated with a brief discussion of the accomplishments and limitations of previous research. A number of step changes in understanding are synthesised. Use of new modelling frameworks and tracking algorithms has significantly improved knowledge of WD structure and variability, and a more frequentist approach can now be taken. Improved observation systems have helped quantification of water security over the western Himalaya. Convection-permitting models have improved our understanding of how WDs interact with the Himalaya to trigger natural hazards. Improvements in paleoclimate and future climate modelling experiments have helped to explain how WDs and their impacts over the Himalaya respond to large-scale natural and anthropogenic forcings. We end by summarising unresolved questions and outlining key future WD research topics.
A BODIPY‐Containing Covalent Organic Framework as a Highly Porous Photosensitizer for Environmental Remediation and Pollutants Adsorption
2025-01-09

Abstract The direct incorporation of borondipyrromethene (BODIPY) subunits into the structural backbone of covalent organic frameworks (COFs) gives facile access to porous photosensitizers but is still a challenging task. Here, we introduce β ‐ketoenamine‐linked BDP‐TFP‐COF , which crystallizes in AA‐stacking mode with hcb topology. A comprehensive characterization reveals high crystallinity and enhanced stability in a variety of solvents, excellent mesoporosity (SA BET =1042 m 2 g −1 ), broad light absorption in the visible region, and red emission upon the exfoliation of few‐layer COF nanosheets. The versatility of multifunctional BODIPY‐COFs is highlighted in various applications. Pollutants Bisphenol A (BPA, q max =426 mg g −1 ) and Methylene Blue (MB, q max =96 mg g −1 ) have been efficiently removed from H 2 O. Fluorescence quenching or enhancement of exfoliated BDP‐TFP‐COF nanosheets have been utilized for dual‐mode sensing of MB or NEt 3 , respectively. Ultimately, the photosensitizing effect of the BODIPY units is retained in the COF. Thus, BPD‐TFP‐COF was established as a metal‐free triplet photosensitizer, which efficiently oxidized a mustard gas simulant under visible light irradiation.
Relative Energy Deficiency in Sport—Multidisciplinary Treatment in Clinical Practice
2025-01-09

Background/Objectives: The primary aim of this study was to characterize athletes approaching an outpatient interdisciplinary and multidisciplinary consultation structure for athletes with a suspected relative energy deficiency in sport (REDs) cross-sectionally and longitudinally to prove treatment efficacy. Methods: Data of 58 athletes suspected of REDs were collected at the onset (t0) and completion (t1) of interdisciplinary and multidisciplinary REDs treatment (clinical practice) between January 2019 and December 2022. The data included extracted information from medical records, anthropometric characteristics, physical performance diagnostics, laboratory values, dietary records, and partially gynecological and psychosomatic diagnostics. Results: The sample primarily consisted of female athletes (97%) under 18 years of age (66%) who were underweight with a body mass index (BMI) &lt; 18.5 kg/m2 and BMI percentile below the 10th percentile for their age and gender-specific norms (59%), and experienced menstrual disorders (93%). The dietary behavior is characterized by plant-based and low-energy-dense foods. Eating disorders (anorexia nervosa and bulimia nervosa) were diagnosed in 40% of the athletes according to the International Statistical Classification of Diseases and Related Health Problems 11th revision criteria. During the program, 64% of the athletes exhibited a mean weight gain of 7 (±6) kg (p &lt; 0.001), excluding those still undergoing treatment (36%). Conclusions: The proposed interdisciplinary and multidisciplinary treatment approach proved effective and holds promise for future evidence-based developments in REDs treatment.
Atrial Fibrillation and Retinal Stroke
2025-01-09

Importance Atrial fibrillation (AF) is the most common, chronic, cardiac arrythmia in older US adults. It is not known whether AF is independently associated with increased risk of retinal stroke (central retinal artery occlusion), a subtype of ischemic stroke that causes severely disabling visual loss in most cases and is a harbinger of further vascular events. Objective To determine whether there is an association between AF and retinal stroke. Design, Setting, and Participants This retrospective cohort study was performed between July 2023 and May 2024 using computerized inpatient, outpatient, emergency department, and skilled nursing facility claims files for a 5% sample of US fee-for-service Medicare beneficiaries aged 66 years and older between 2000 and 2020. Follow-up ended at death, conclusion of fee-for-service Medicare coverage, end of the study period, or loss to follow-up of 85% of the study cohort. Exposure AF, based on validated International Classification of Diseases, Ninth Revision, Clinical Modification and International Statistical Classification of Diseases, Tenth Revision, Clinical Modification diagnosis codes. Main Outcomes and Measures The primary end point was incident retinal stroke in the primary diagnostic position of a single claim in any venue of care. Secondary end points included retinal stroke in any position of a single claim, 1 positive control end point (cerebral ischemic stroke), and 4 negative control end points (central retinal vein occlusion, urinary tract infection, humeral fracture, and cataract). Unadjusted and adjusted hazard ratios (HRs) and rate differences were computed across matched and overlap-weighted cohorts with and without AF (defined as 1 inpatient claim or 2 outpatient claims within a 365-day period). Results In total, 1 090 144 patients (591 400 female [54.3%]; mean [SD] age, 76.92 [7.09] years) were included in the study; 545 072 patients had AF and 545 072 were matched controls. The median (IQR) follow-up was 45 (18 to 90) months. In total, 1333 patients with AF (rate, 0.55 per 1000 person-years) and 1082 AF-free matched controls (rate, 0.50 per 1000 person-years) experienced retinal stroke. The cause-specific, adjusted HR of retinal stroke after overlap weighting was 1.14 (95% CI, 1.02 to 1.28; adjusted rate difference, 0.05 [95% CI, −0.01 to 0.11]). AF was associated with cerebral ischemic stroke (adjusted HR, 1.73 [95% CI, 1.69 to 1.76]; adjusted rate difference, 10.11 [95% CI, 9.72 to 10.49]). Of 4 prespecified negative control end points, AF was not associated with central retinal vein occlusion but was associated with urinary tract infection, cataract, and humeral fracture. Conclusions and Relevance In this cohort study of Medicare beneficiaries aged 66 years and older, AF was independently associated with retinal stroke. The magnitude of the association was small, and a contribution from residual, unmeasured confounding could not be excluded.
Revisiting the electrophysiological correlates of valence and expectancy in reward processing – A multi-lab replication
2025-01-09

Two event-related brain potential (ERP) components, the frontocentral feedback-related negativity (FRN) and the posterior P300, are key in feedback processing. The FRN typically exhibits greater amplitude in response to negative and unexpected outcomes, whereas the P300 is generally more pronounced for positive outcomes. In an influential ERP study, Hajcak et al., (2005) manipulated outcome valence and expectancy in a guessing task. They found the FRN was larger for negative outcomes regardless of expectancy, and the P300 larger for unexpected outcomes regardless of valence. These findings challenged the dominant Reinforcement Learning Theory of the ERN. We aimed to replicate these results within the #EEGManyLabs project (Pavlov et al., 2021) across thirteen labs. Our replication, including robustness tests, a PCA and Bayesian models, found that both FRN and P300 were significantly modulated by outcome valence and expectancy: FRN amplitudes (no-reward - reward) were largest for unexpected outcomes, and P300 amplitudes were largest for reward outcomes. These results were consistent across different methods and analyses. Although our findings only partially replicate the original study, they underscore the complexity of feedback processing and demonstrate how aspects of Reinforcement Learning Theory may apply to the P300 component, reinforcing the need for rigorous ERP research methodologies.
Recipient sex and donor leukemic cell characteristics determine leukemogenesis in patient-derived models
2025-01-09

In acute myeloid leukemia (AML), leukemogenesis depends on cell-intrinsic genetic aberrations and thus, studies on AML require investigations in an in vivo setting as provided by patient derived xenografts (PDX) models. Here we report that, next to leukemic cell characteristics, recipient sex highly influences the outgrowth of AML cells in PDX models, with females being much better repopulated than males in primary as well as secondary transplantation assays. Testosterone may be the more important player since, strikingly, better engraftment was seen in castrated versus control male recipients, while ovariectomy did not significantly impair engraftment in females. Shorter time-to-engraftment and mouse survival were observed with adverse molecular risk, and respectively with high FLT3-ITD ratio mutated AML cells. Adverse risk AML furthermore showed higher percentages of phenotypic leukemic stem cells (LSCs), suggesting impaired differentiation capacity in these AML subtypes. Overall, we achieved successful repopulation with 14/23 (61%) favorable, 18/30 (60%) intermediate and 4/8 (50%) adverse risk AML cases in female recipient PDX models. Our data identify recipient sex as an important experimental confounder in leukemia PDX models, and the contribution of the sex hormones to leukemogenesis as an intriguing, underexplored research area.
Overall survival and progression-free survival in pediatric meningiomas: a systematic review and individual patient-level meta-analysis
2025-01-09

Abstract Background Pediatric meningiomas (PMs) are rare central nervous system tumors, accounting for 1–5% of all meningiomas, and differ from adult meningiomas in clinical, histopathological, and molecular features. Current guidelines primarily focus on adults, leaving a gap in evidence-based management for PMs. This study presents the largest meta-analysis of longitudinal individual patient data (IPD) to date, addressing progression-free survival (PFS) and overall survival (OS) in pediatric patients. Methods Data from 20 studies (2011–2023), including 1010 pediatric meningioma cases, were analyzed to assess PFS and OS stratified by WHO grade, NF1/NF2 status, extent of resection (EOR), and adjuvant radiotherapy. Longitudinal survival data were reconstructed from Kaplan–Meier curves using IPD extraction methods. Results PMs affect males and females nearly equally (52.1% vs. 47.9%). WHO grade 3 tumors had significantly shorter PFS (72.1 months) compared to grades 1 (209.8 months) and 2 (137.5 months) ( p &lt; 0.001). No significant OS difference between WHO grades 1 and 2 PMs were observed. NF1- and NF2-associated tumors showed shorter PFS (59.7 and 138.4 months) than sporadic cases (180.6 months) ( p = 0.02). GTR significantly improved PFS (113.8 vs. 40.1 months, p &lt; 0.001) and OS (602.9 vs. 173.8 months, p &lt; 0.001). Radiotherapy enhanced PFS (72.5 vs. 23.8 months, p = 0.009) and OS (140.7 vs. 63.0 months, p = 0.002) in grade 3 tumors but not in WHO grade 2 PMs ( p = 0.43). Conclusions This largest meta-analysis highlights the critical roles of GTR and adjuvant radiotherapy in improving outcomes for high-grade PMs and underscores the urgent need for pediatric-specific management guidelines based on robust longitudinal data. Graphical Abstract
Nitric oxide modulates contrast suppression in a subset of mouse retinal ganglion cells
2025-01-09

Neuromodulators have major influences on the regulation of neural circuit activity across the nervous system. Nitric oxide (NO) has been shown to be a prominent neuromodulator in many circuits and has been extensively studied in the retina. Here, it has been associated with the regulation of light adaptation, gain control, and gap junctional coupling, but its effect on the retinal output, specifically on the different types of retinal ganglion cells (RGCs), is still poorly understood. In this study, we used two-photon Ca 2+ imaging and multi-electrode array (MEA) recordings to measure light-evoked activity of RGCs in the ganglion cell layer in the ex vivo mouse retina. This approach allowed us to investigate the neuromodulatory effects of NO on a cell type-level. Our findings reveal that NO selectively modulates the suppression of temporal responses in a distinct subset of contrast-suppressed RGC types, increasing their activity without altering the spatial properties of their receptive fields. Given that under photopic conditions, NO release is triggered by quick changes in light levels, we propose that these RGC types signal fast contrast changes to higher visual regions. Remarkably, we found that about one-third of the RGC types, recorded using two-photon Ca 2+ imaging, exhibited consistent, cell type-specific adaptational response changes throughout an experiment, independent of NO. By employing a sequential-recording paradigm, we could disentangle those additional adaptational response changes from drug-induced modulations. Taken together, our research highlights the selective neuromodulatory effects of NO on RGCs and emphasizes the need of considering non-pharmacological activity changes, like adaptation, in such study designs.
Girls and Boys Typically Have Similar Math Value Beliefs: Replication Evidence Across Historical Time, High School, and Racial/Ethnic Groups
2025-01-09

ABSTRACT Introduction Individuals' math value beliefs are theorized to influence who persists in STEM. However, the existing findings on gender differences in adolescents' math value beliefs are inconsistent. The goal of this study was to use three existing datasets to help clarify when gender differences emerge for high school adolescents and for whom (i.e., adolescents across historical time, grade level, and race/ethnicity). Specifically, we examined the extent to which gender differences in adolescents' math value beliefs (i.e., interest, utility, and attainment) replicated (1) across three datasets spanning the 1990s to 2010s, (2) from 9th–12th grade, and (3) within each of the four largest U.S. racial/ethnic groups (i.e., Asian, Black, Latine, and White adolescents). Methods We tested these aims with three existing longitudinal U.S. datasets: the California Achievement Motivation Project (CAMP) ( n = 8855), the Childhood and Beyond Study (CAB) ( n = 582), and the High School Longitudinal Study (HSLS) ( n = 21,000). Students were in high school (9th–12th grade) and half were girls (49%–53%). All three datasets included measures with the same or similar math value belief items, making conceptual replication possible. Results and Conclusions Overall, we did not find strong evidence for meaningful gender differences in adolescents' math value beliefs overall. We did find meaningful gender differences in the oldest data set (CAB). When examined within each racial/ethnic group, we found no evidence of gender differences in math value beliefs among Black or Latine adolescents, but some differences among Asian and White adolescents. The findings align with the gender similarities hypothesis, suggesting adolescent girls and boys had similar math value beliefs.