julilili42/papers huggingface dataset:
Missing what’s right under your nose: failed appetitive and aversive audio-olfactory conditioning in humans
2024-12-20

Abstract The comparison of physiological mechanisms underlying appetitive and aversive conditioning is often challenging due to the involvement of stimuli from different modalities with potentially disparate effective mechanisms (e.g., pain stimuli versus monetary rewards). The olfactory system offers a unique opportunity to examine both types of conditioning in humans, as isointense odors can serve as comparably pleasant and unpleasant stimuli. To study physiological and behavioral responses during appetitive and aversive learning, we employed odors as unconditioned stimuli (US) in a within-subjects design, measuring various conditioned physiological responses including skin conductance, heart rate, pulse wave amplitude, respiration, fear-potentiated startle, postauricular reflex, facial electromyography as well as event-related potentials, and auditory steady-state responses (ASSR) derived from electroencephalography. We conducted four experiments with a total of 95 participants, presenting three neutral sounds paired with either a pleasant odor, unpleasant odor, or odorless air. The first experiment involved uninstructed participants and frequency-modulated conditioned stimuli (CS) for ASSR analysis. In the second experiment, we omitted the frequency modulation and startle probe. The third experiment included pre-experiment instruction on CS-US contingencies, while the fourth employed a delayed conditioning paradigm in contrast to the other three experiments. Our results revealed differences between CS+ and CS-only in the fear-potentiated startle response in Experiment 3. No other effects were found. The minimal or absent learning effects observed across multiple peripheral and neural physiological measures may be attributed to the extra-thalamic nature of olfactory pathways and the subsequent difficulty in forming associations with auditory stimuli. Impact statement In a series of 4 experiments, we explored the neurophysiological differences between appetitive and aversive conditioning. Yet, none of the experiments showed effective conditioning. We hypothesize that the lack of learning effects is attributed to the inherent difficulty in forming associations between auditory and olfactory inputs.
A haplotype-based evolutionary history of barley domestication
2024-12-21

Barley is an old crop with a complex history. Its evolution and the molecular basis of domestication have been intensely studied. This research has ruled out a single origin of the crop and motivated a model of mosaic genomics ancestry. As more and better genome sequences have become available, this concept can be refined: where do the building blocks of the mosaic, that is, the haplotypes come from? Were all cultivated barleys created equal or did some wild barley populations contribute more to some domesticated lineages? To answer these and other questions, we pursue a haplotype-based approach to connect diversity and population structure in wild and domesticated barley. We sequence the genomes of 628 genebank accessions and 23 archaeological specimens. Using these data, we infer the spatiotemporal origins of haplotypes and map the contributions of different wild barley populations either during the initial phase of domestication or through later gene flow. Ancient DNA sequences corroborate our genome-wide analysis in present-day samples. Our results indicate that an early domesticated founder population formed in the Fertile Crescent during an extended period of pre-domestication cultivation. A practical implication of our findings is that the high haplotype differentiation between barley populations, which arose possibly without, and most likely on top of, selective forces, complicates the mapping of adaptive loci.
Pediatric lymphomas: overview and diagnostic challenges
2024-12-21

Abstract Only 10% of new lymphoma diagnoses in the USA occur in children &lt; 15 years. Although the same diagnostic criteria apply to both adult and pediatric lymphomas, there are important differences in some lymphoma subtypes. These differences are recognized by the World Health Organization (WHO) with the recent 2022 classification of pediatric tumors including pediatric hematopoietic tumors. Here, we review the WHO classification scheme for pediatric lymphomas and summarize the diagnostic criteria, recent genetic findings, and differences from their adult counterparts for some subtypes including those yet to be included as a definitive subtype. In general, there are differences in relatively frequency, genetic mutation, and prognosis with the pediatric counterpart often having better prognosis. Emerging B-cell lymphomas with recurrent gene alterations such as IRF4 rearrangement and 11q gain/loss chromosomal alterations will be reviewed. The overlapping pathological, clinical, and molecular features between pediatric-type follicular lymphoma (PTFL) and pediatric nodal marginal zone lymphoma (PNMZL) suggesting one disease with broad morphological spectrum will be discussed. The pathogenetic role of EBV in subclassifying Burkitt lymphoma is highlighted. The revised classification of the EBV-positive lymphoproliferative disorders in children is discussed. This review will focus on novel findings, areas of special interest, and diagnostic challenges in pediatric lymphomas.
The Effect of Plant Food Treatment on Stable Isotopes and Their Relevance for Archaeological Studies: A Methodological Pilot Study
2024-12-21

Abstract Plants are a crucial part of the human diet, serving as a primary source of micronutrients, fiber, and carbohydrates, providing readily available energy. Beyond the consumption of cooked and raw edible plants, early humans also developed methods for plant processing for delayed consumption, to de-toxify/improve bioavailability, and perhaps for flavor. In later prehistory delayed consumption includes preservation processes for storage. The processing of plants through sprouting, fermentation, cooking, and roasting has not only expanded the variety of consumable plant species but also enhanced their nutritional value. There are few methods for detecting fermented foods in the early prehistoric diet. Based on the hypothesis that the microbes active in fermentation change the nitrogen and carbon isotope ratios of plant foods, our pilot study lays the groundwork for further research, offering a promising direction for understanding the complexities of human-plant interactions throughout history. This study focuses on these four plant treatment methods, which have both contemporary relevance and archaeobotanical evidence of use. We aimed to explore how these treatments might affect stable isotope values, such as carbon ( δ 13 C) and nitrogen ( δ 15 N), which are crucial for reconstructing ancient diets. Through an experimental approach involving 12 plant species, our findings suggest that while sprouting and roasting had minimal impact on isotopic values, fermentation and cooking showed more variable effects depending on the plant species. These preliminary results provide new insights into the influence of plant processing on isotopic compositions and underscore the importance of considering these factors in dietary reconstructions.
Contrasting genetic burden for bipolar disorder: Early onset versus late onset in an older adult bipolar disorder sample
2024-12-22

Older Adults with Bipolar Disorder (OABD) represent a heterogeneous group, including those with early and late onset of the disorder. Recent evidence shows both groups have distinct clinical, cognitive, and medical features, tied to different neurobiological profiles. This study explored the link between polygenic risk scores (PRS) for bipolar disorder (PRS-BD), schizophrenia (PRS-SCZ), and major depressive disorder (PRS-MDD) with age of onset in OABD. PRS-SCZ, PRS-BD, and PRS-MDD among early vs late onset were calculated. PRS was used to infer posterior SNP effect sizes using a fully Bayesian approach. Demographic, clinical, and cognitive variables were also analyzed. Logistic regression analysis was used to estimate the amount of variation of each group explained by standardized PRS-SCZ, PRS-MDD, and PRS-BD. A total of 207 OABD subjects were included (144 EOBD; 63 LOBD). EOBD showed higher PRS-BD compared to LOBD (p = 0.005), while no association was found between age of onset and PRS-SCZ or PRS-MDD. Compared to LOBD, EOBD individuals also showed a higher likelihood for suicide attempts (p = 0.01), higher presence of psychotic symptoms (p = 0.003), higher prevalence of BD-I (p = 0.002), higher rates of familiarity for any psychiatric disorder (p = 0.004), and lower processing speed measured with Trail-Making Test part A (p = 0.03). OABD subjects with an early onset showed a greater genetic burden for BD compared to subjects with a late onset. These findings contribute to the notion that EOBD and LOBD may represent different forms of OABD, particularly regarding the genetic predisposition to BD.
ORACLE: An analytical approach for T1, T2, proton density, and off‐resonance mapping with phase‐cycled balanced steady‐state free precession
2024-12-22

Abstract Purpose To develop and validate a novel analytical approach simplifying , , proton density (PD), and off‐resonance quantifications from phase‐cycled balanced steady‐state free precession (bSSFP) data. Additionally, to introduce a method to correct aliasing effects in undersampled bSSFP profiles. Theory and Methods Off‐resonant‐encoded analytical parameter quantification using complex linearized equations (ORACLE) provides analytical solutions for bSSFP profiles. which instantaneously quantify , , proton density (PD), and . An aliasing correction formalism was derived to allow undersampling of bSSFP profiles. ORACLE was used to quantify , , PD, /, and based on fully sampled () bSSFP profiles from numerical simulations and 3T MRI experiments in phantom and 10 healthy subjects' brains. Obtained values were compared with reference scans in the same scan session. Aliasing correction was validated in subsampled () bSSFP profiles in numerical simulations and human brains. Results ORACLE quantifications agreed well with input values from simulations and phantom reference values ( R 2 = 0.99). In human brains, and quantifications when compared with reference methods showed coefficients of variation below 2.9% and 3.9%, biases of 182 and 16.6 ms, and mean white‐matter values of 642 and 51 ms using ORACLE. The quantification differed less than 3 Hz between both methods. PD and maps had comparable histograms. The maps effectively identified cerebrospinal fluid. Aliasing correction removed aliasing‐related quantification errors in undersampled bSSFP profiles, significantly reducing scan time. Conclusion ORACLE enables simplified and rapid quantification of , , PD, and from phase‐cycled bSSFP profiles, reducing acquisition time and eliminating biomarker maps' coregistration issues.
A comparison study between liquid- and vapor-fed anode zero-gap bioelectrolysis cells
2024-12-22

Abstract Improving microbial electrosynthesis could be one solution for transitioning towards sustainable chemical production, offering a pathway to convert CO 2 into valuable commodities from renewable energy sources. Therefore, we examined the performance differences between liquid- and vapor-fed anode zero-gap bioelectrochemical cells for electromethanogenesis, utilizing a membrane electrode assembly to enhance mass and ohmic transport. Focusing on CH 4 and H 2 production, we compared two ion-exchange membranes with the liquid-fed anode system and selected the best performing ion-exchange membrane for the vapor-fed anode system. Liquid-fed anode systems did not show significant differences in volumetric CH4 production rates compared to vapor-fed anode systems, although the latter demonstrated advantages in reducing electrocatalyst degradation and maintaining stable cell voltages. The research underscores the need for further optimization to address performance losses and suggests potential for industrial applications of microbial electrosynthesis, highlighting the importance of catalyst protection.
VGLL fusions define a new class of intraparenchymal central nervous system schwannoma
2024-12-23

Abstract Background Intracerebral schwannomas are rare tumors resembling their peripheral nerve sheath counterparts but localized in the central nervous system (CNS). They are not classified as a separate tumor type in the 2021 World Health Organization classification. This study aimed to compile and characterize these rare neoplasms morphologically and molecularly. Methods We analyzed 20 tumor samples by histology, RNA next-generation sequencing, DNA-methylation profiling, copy number analyses, and single-nucleus RNA sequencing (snRNA-seq). Clinical data, including age, sex, and disease progression, were collected. Magnetic resonance imaging (MRI) series were included when available. Results All cases with tissue available for histology review (n = 13) were morphologically consistent with intracerebral schwannoma, but differed in their extent of glial fibrillary acidic protein staining. All (n = 20) shared DNA-methylation profiles distinct from other CNS tumors, as well as from Vestigial-like family (VGLL)-altered peripheral nerve sheath tumors. Most cases (n = 14/17) harbored fusions of either Vestigial-like family member 3 (VGLL3) or Vestigial-like Family member 1 (VGLL1) (CHD7::VGLL3 [n = 9/17] and EWSR1::VGLL1 [n = 5/17]). In 2 cases, the presence of a VGLL3 fusion was also confirmed by copy number analyses (n = 2/17). MRI (n = 4) showed well-defined, nodular tumors with strong, homogeneous enhancement and no diffusion restriction. Tumors were located throughout the neuroaxis (supratentorial [n = 15], infratentorial [n = 4], and spinal [n = 1]). snRNA-seq of a VGLL1-fused tumor indicated VGLL1 upregulation in 28.6% of tumor cells (n = 1). During a median follow-up of 1.8 years (range 3 months-9 years), none of the tumors recurred (n = 10). Conclusions We identify and define a new benign tumor class, designated VGLL-altered intraparenchymal CNS schwannomas. These tumors feature VGLL alterations and a specific DNA-methylation profile, with schwannoma-like histopathology and CNS localization, akin to previously classified intracerebral schwannomas.
Foveal action for the control of extrafoveal vision
2024-12-23

Abstract Microsaccades have been convincingly linked to extrafoveal covert attention shifts for more than two decades. However, the direction of causality between individual microsaccade generation and an alteration in both extrafoveal visual sensitivity and behavior remains debated: do microsaccades merely reflect, perhaps probabilistically, an altered extrafoveal sensitivity, or is the act of generating microsaccades sufficient to, on its own, modify such sensitivity? Using a novel exploitation of real-time retinal image stabilization, behavior, and neurophysiology in the superior colliculus, we show that exclusive experimental control over foveal oculomotor state is entirely sufficient to influence extrafoveal sensitivity. This happens for eccentricities as large as ∼50 times those associated with microsaccades, and it also takes place in the absence of any differential attentional demands. Most importantly, such influence is mediated through well-known, classic pre- and post-saccadic visual processing changes. Thus, seemingly-innocuous subliminal eye movements do constitute an integral component of cognitive processes like attention.
One direction? Cultural aspects of the mental number line beyond reading direction
2024-12-23

Abstract Spatial-Numerical Associations (SNAs) refer to the demonstrations of spatial processing of numbers. The Mental Number Line (MNL) is a representation model describing numbers as aligning left-to-right (LR) and was suggested to account for directional biases in participants’ responses during numerical tasks. One common behavioral demonstration of this is the Spatial-Numerical Associations of Response Codes (SNARC) effect, which describes faster left-/right-hand responses to smaller/larger numbers, respectively. The MNL, and, consequently, directional SNAs, show variabilities across different cultures. Reading direction is considered to be the main factor in explaining these differences. In line with this, individuals with right-to-left (RL) reading habits show a weaker or even reverse SNARC effect. In the present study, we investigated whether SNAs are influenced not only by reading direction, but also by cultural directional preferences such as drawing lines, arranging objects, imagining objects (i.e., rightward or leftward facing), or representing events in time (i.e., mentally representing the past/future on the left/right, respectively). To test this hypothesis, we measured the cultural directional preferences and the SNARC effect across three cultures in an online setup; German, Turkish, and Iranian. LR preferences in the Cultural Directional Preferences Questionnaire were most prominent in German participants, intermediate in Turkish participants, and least prominent in Iranian participants. In line with this, the LR SNARC effect was strongest in German, intermediate in Turkish, and weakest (but not RL) in Iranian culture. These findings suggest that cultural directional preferences are involved in the emergence of adult SNAs in addition to the reading direction.
Epidemiology and Genotype Dynamics of Dengue in Hospitalized Patients in Northern Vietnam Between 2020 and 2022
2024-12-23

Abstract Background Arboviruses, including Dengue (DENV), Zika, and chikungunya, cause recurrent outbreaks of varying intensity in tropical countries. This study aimed to investigate other arboviruses, including Zika and chikungunya, in patients clinically suspected of Dengue and to characterize the circulating Dengue serotypes and genotypes in Northern Vietnam from 2020 to 2022. To date, information on this topic in the region has been limited. Methods Multiplex real-time polymerase chain reaction (PCR) was used to detect Dengue, Zika, and chikungunya RNA, and DENV serotypes were identified via real-time reverse transcriptase PCR from 426 clinically Dengue suspected patients. Patients were screened for NS1 antigen and anti-DENV immunoglobulin (Ig) G/IgM antibodies. Phylogenetic analysis of DENV Capsid-premembrane gene sequences was performed to investigate genotype distribution. Results Dengue was confirmed in 95% of cases, with no Zika or chikungunya RNA detected. DENV-2 was the predominant serotype (61%), followed by DENV-1 (31%) and DENV-4 (7%). Coinfections were observed, with DENV-1 and DENV-2 being the most common. In 2022, a high incidence of Dengue cases with warning signs and severe Dengue was observed, accompanied by elevated liver enzyme levels and reduced platelet counts. Phylogenetic analysis revealed that the DENV-1 and DENV-4 serotypes clustered with previously reported regional virus, while DENV-2 showed a shift from genotype Asian I to Cosmopolitan over the study period. Conclusions This study underscores a significant rise in Dengue severity and shifts in DENV genotypes in recent years in Northern Vietnam, emphasizing the importance of understanding genotype dynamics and clinical dynamics for improving outbreak preparedness and response strategies.
Automated total nucleic acid extraction with magnetic beads for the detection of Plasmodium falciparum in large study cohorts
2024-12-23

Abstract Background Molecular methods play an important role in clinical trials assessing anti-malarial drugs and vaccines, as well as in epidemiological studies aimed at detecting Plasmodium species, especially when dealing with large sample sizes. Molecular techniques are more sensitive and generally have a higher throughput compared to the gold standard microscopy. Further optimization can be achieved with automation of nucleic acid isolation, allowing for rapid and precise extraction. This study evaluated the isolation of total nucleic acids from Plasmodium falciparum mocked samples using an automated extraction method with a magnetic bead-based kit compared to a manual silica column-based kit. Additionally, two different RNA preservation solutions were compared. Methods Plasmodium falciparum Dd2 parasites were serially diluted and spiked into whole blood. The dilutions were stored in two different RNA preservation solutions and total nucleic acids extracted with an automated magnetic bead-based kit and a manual silica column-based kit. Subsequently, a reverse transcription (RT) qPCR for Plasmodium detection targeting Plasmodium 18S rRNA and DNA in a single reaction was performed and the quantification cycle (Cq) values across the different sample groups were compared. Results Comparable Cq values across the various sample preparations were obtained, suggesting minimal influence from RNA preservation solutions (p = 0.686) or extraction methods (p = 0.119) on RT-qPCR outcomes. Automated nucleic acids extraction allowed processing numerous samples in a shorter timeframe and showed similar efficiency in detecting Plasmodium in blood samples by RT-qPCR as manual extraction. Conclusions The automated method for nucleic acid isolation is a valuable tool for the detection of Plasmodium infections in large-scale studies. It is efficient, reliable, and cost-effective. Its potential applications extend to other molecular surveillance studies to support malaria control measures.
Enhancing intercultural competence of German medical students through innovative teaching on medical ethics with a focus on Muslim patients – a pilot study
2024-12-23

Abstract Background Effective healthcare delivery in today's diverse society necessitates healthcare providers' adeptness in navigating cultural and religious nuances in patient care. However, the integration of cultural competence training into medical education remains inadequate, particularly concerning the care of Muslim patients. In response, we introduce a novel educational intervention aimed at enhancing intercultural proficiency among medical students, emphasizing care for Muslim patients. Methods The intervention comprised interactive seminars and simulated patient sessions. With a bespoke and the Cross-Cultural Competence of Healthcare Professionals (CCCHP-27) questionnaire the pre- and post-course intercultural competencies of n = 31 medical students of the Medical Faculty of Jena University were assessed. Additionally, there was a control group consisting of 34 students. Statistical analyses including descriptive statistics, paired samples t-tests, Wilcoxon tests, correlation analysis, Mann–Whitney U-tests, and multiple regression analysis were employed for data analysis. Results Results of the bespoke questionnaire reveal significant improvements in intercultural knowledge (median pre 1.0 (0.6 – 1.6), median post 2.2 (2.4-2.8), p &lt; 0.001) and in knowledge regarding Muslim patients (median pre 1.0 (0.5 – 1.5), median post 2.5 (2-3), p &lt; 0.001) following the course. Regarding the CCCHP-27, students demonstrated a significant improvement in their skills, with pre-assessment score of 4.10 (± 0.47) and post-assessment score of 4.38 (± 0.40), p = 0.001. Female participants and those with limited prior experience demonstrated greater gains ( p = 0.005 and p = 0.053). Notably, the incorporation of a session with a simulated patient garnered favorable feedback, affirming the efficacy of practical application in consolidating learning outcomes. Discussion Our study emphasizes the importance of integrating intercultural competencies training into medical education and our findings underscore the efficacy of targeted educational interventions in enhancing intercultural competencies among medical students. For the assessment of intercultural competence, our bespoke questionnaire serves as a valuable addition to the German healthcare system. Conclusion Implementation of similar interventions into medical curricula nationwide is imperative to address the needs of diverse patient populations effectively.