julilili42/papers huggingface dataset:
pyOpenMS-viz: Streamlining Mass Spectrometry Data Visualization with pandas
2024-10-03

<title>Abstract</title> Mass spectrometry data visualization is essential for a wide range of applications, such as validation of workflows and results, benchmarking new algorithms, and creating comprehensive quality control reports. Python offers a popular and powerful framework for analyzing and visualizing multidimensional data; however, generating commonly used mass spectrometry plots in Python can be cumbersome. Here we present pyOpenMS-viz, a versatile, unified framework for generating mass spectrometry plots. pyOpenMS-viz directly extends pandas DataFrame plotting for generating figures in a single line of code. This implementation enables easy integration across various Python-based mass spectrometry tools that already use pandas DataFrames to store MS data. pyOpenMS-viz is open-source under a BSD 3-Clause license and freely available at https://github.com/OpenMS/pyopenms_viz.
Detection of <em>Phakopsora pachyrhizi</em> Infestation in Soybean via Hyperspectral Imaging and Data Analysis
2024-10-03

Phakopsora pachyrhizi, the causative agent of the Asian Soybean Rust, is one of the most prominent causes of yield loss in soybean production worldwide. In this study, a combination of hyperspectral imaging with advanced data analysis methodology is shown to accurately detect soybean rust symptoms in early stages and differentiate them from other factors at leaf scale. Data analysis was performed with neural networks based on training data from a small subset of the respective experiments and compared with classical machine learning methods for its accuracy and early disease detection capabilities. Results show that even with a comparably small subset of training data the analysis through neural networks can outperform classical machine learning methods in a complex dataset with high variability in the designated classes. In two separate experiments it was possible to accurately detect disease in inoculated leaves before symptoms were visible to the human eye. These results do not only show the potential of this methodology for precision farming applications, but also allow accurate and objective assessment of symptom severity and development for scientific studies and resistance breeding.
Integrative nursing interventions: knowledge, attitudes and practice in home nursing services in Germany—a quantitative and qualitative online survey
2024-10-03

Introduction Integrative nursing interventions (INI) play a significant role in healthcare, particularly in the prevention and treatment of chronic diseases. Integrating evidence-based INI into healthcare aligns with global initiatives such as the WHO’s Decade of Healthy Aging 2020–2030. Many INI are low-threshold practices, empowering patients to independently manage health. However, the extent to which INI are used by home-care nursing-services (HNS) remains largely unknown. This study aims to explore the field of INI in German HNS regarding nurses’ use of INI as well as attitudes, subjective knowledge, and information needs on the subject. Methods A cross-sectional anonymous online survey with 29 Likert scale items and two open-ended questions was conducted between April 2023 and July 2023. The survey targeted nurse managers of HNS in Baden-Württemberg, Germany. Descriptive analysis was performed for quantitative data, while content analysis according to Kuckartz was applied to analyze open-ended text responses. Results In total, n = 68 out of n = 1,331 HNS took part in the survey yielding a response rate of 5.1%. Their overall attitude toward INI was clearly positive (10-point Likert scale M ± SD: 8.37 ± 2.22). The average self-assessed knowledge level about INI was moderate (M ± SD: 5.39 ± 2.76). Almost half of the participants (45.6%) declared to incorporate INI in patient care. Most participants (84.2%) lacked employees with additional qualifications in INI. The INI used most were medicinal herbal teas (61%), compresses (57%), and aromatherapy (48%). Acupressure showed the greatest disparity between actual use in participating HNS (4.3%) and interest in further education (61%). The most common symptoms for which INI are used are pain, respiratory problems, anxiety, and palliative care. The main challenges reported for the use of INI in HNS are financial aspects, qualification and limited resources (staff and time). Discussion This exploratory study provides the first insights into nurses’ attitudes, self-assessed knowledge, and utilization of INI in German HNS. Overall response rate was low (5.1%), therefore, the results should be interpreted with caution. Urgent action is needed to address financial aspects and further education on INI, to promote integration of INI in HNS to the best possible extent.
A generalized spectral concentration problem and the varying masks algorithm
2024-10-03

In this paper we generalize the spectral concentration problem as formulated by Slepian, Pollak and Landau in the 1960s. We show that a generalized version with arbitrary space and Fourier masks is well-posed, and we prove some new results concerning general quadratic domains and gaussian filters. We also propose a more general splitting representation of the spectral concentration operator allowing to construct quasi-modes in some situations. We then study its discretization and we illustrate the fact that standard eigen-algorithms are not robust because of a clustering of eigenvalues. We propose a new alternative algorithm that can be implemented in any dimension and for any domain shape, and that gives very efficient results in practice.
A chromatic feature detector in the retina signals visual context changes
2024-10-04

The retina transforms patterns of light into visual feature representations supporting behaviour. These representations are distributed across various types of retinal ganglion cells (RGCs), whose spatial and temporal tuning properties have been studied extensively in many model organisms, including the mouse. However, it has been difficult to link the potentially nonlinear retinal transformations of natural visual inputs to specific ethological purposes. Here, we discover a nonlinear selectivity to chromatic contrast in an RGC type that allows the detection of changes in visual context. We trained a convolutional neural network (CNN) model on large-scale functional recordings of RGC responses to natural mouse movies, and then used this model to search in silico for stimuli that maximally excite distinct types of RGCs. This procedure predicted centre colour opponency in transient suppressed-by-contrast (tSbC) RGCs, a cell type whose function is being debated. We confirmed experimentally that these cells indeed responded very selectively to Green-OFF, UV-ON contrasts. This type of chromatic contrast was characteristic of transitions from ground to sky in the visual scene, as might be elicited by head or eye movements across the horizon. Because tSbC cells performed best among all RGC types at reliably detecting these transitions, we suggest a role for this RGC type in providing contextual information (i.e. sky or ground) necessary for the selection of appropriate behavioural responses to other stimuli, such as looming objects. Our work showcases how a combination of experiments with natural stimuli and computational modelling allows discovering novel types of stimulus selectivity and identifying their potential ethological relevance.
Coronary artery disease detection using deep learning and ultrahigh-resolution photon-counting coronary CT angiography
2024-10-04

Automated deep learning shows remarkable performance for the diagnosis of significant CAD on non-UHR PC-CCTA images. AI pre-reading may be of supportive value to the human reader in daily clinical practice to target and validate coronary artery stenosis using UHR PC-CCTA.
Humanlike manual activities in Australopithecus
2024-10-04

The evolution of the human hand is a topic of great interest in paleoanthropology. As the hand can be involved in a vast array of activities, knowledge regarding how it was used by early hominins can yield crucial information on the factors driving biocultural evolution. Previous research on early hominin hands focused on the overall bone shape. However, while such approaches can inform on mechanical abilities and the evolved efficiency of manipulation, they cannot be used as a definite proxy for individual habitual activity. Accordingly, it is crucial to examine bone structures more responsive to lifetime biomechanical loading, such as muscle attachment sites or internal bone architecture. In this study, we investigate the manual entheseal patterns of Australopithecus afarensis, Australopithecus africanus, and Australopithecus sediba through the application of the validated entheses-based reconstruction of activity method. Using a comparative sample of later Homo and three great ape genera, we analyze the muscle attachment site proportions on the thumb, fifth ray, and third intermediate phalanx to gain insight into the habitual hand use of Australopithecus. We use a novel statistical procedure to account for the effects of interspecies variation in overall size and ray proportions. Our results highlight the importance of certain muscles of the first and fifth digits for humanlike hand use. In humans, these muscles are required for variable in-hand manipulation and are activated during stone-tool production. The entheses of A. sediba suggest muscle activation patterns consistent with a similar suite of habitual manual activities as in later Homo. In contrast, A. africanus and A. afarensis display a mosaic entheseal pattern that combines indications of both humanlike and apelike manipulation. Overall, these findings provide new evidence that some australopith species were already habitually engaging in humanlike manipulation, even if their manual dexterity was likely not as high as in later Homo.
Site-specific sulfations regulate the physicochemical properties of papillomavirus–heparan sulfate interactions for entry
2024-10-04

Certain human papillomaviruses (HPVs) are etiological agents for several anogenital and oropharyngeal cancers. During initial infection, HPV16, the most prevalent cancer-causing type, specifically interacts with heparan sulfates (HSs), not only enabling initial cell attachment but also triggering a crucial conformational change in viral capsids termed structural activation. It is unknown, whether these HPV16-HS interactions depend on HS sulfation patterns. Thus, we probed potential roles of HS sulfations using cell-based functional and physicochemical assays, including single-molecule force spectroscopy. Our results demonstrate that N-sulfation of HS is crucial for virus binding and structural activation by providing high-affinity sites, and that additional 6O-sulfation is required to mechanically stabilize the interaction, whereas 2O-sulfation and 3O-sulfation are mostly dispensable. Together, our findings identify the contribution of HS sulfation patterns to HPV16 binding and structural activation and reveal how distinct sulfation groups of HS synergize to facilitate HPV16 entry, which, in turn, likely influences the tropism of HPVs.
Targeting CD276 for T cell-based immunotherapy of breast cancer
2024-10-04

Abstract Background Breast cancer (BC) is the most common malignancy in women. Immunotherapy has revolutionized treatment options in many malignancies, and the introduction of immune checkpoint inhibition yielded beneficial results also in BC. However, many BC patients are ineligible for this T cell-based therapy, others do not respond or only briefly. Thus, there remains a high medical need for new therapies, particularly for triple-negative BC. CD276 (B7-H3) is overexpressed in several tumors on both tumor cells and tumor vessels, constituting a promising target for immunotherapy. Methods We analyzed tumor samples of 25 patients using immunohistochemistry to assess CD276 levels. The potential of CC-3, a novel bispecific CD276xCD3 antibody, for BC treatment was evaluated using various functional in vitro assays. Results Pronounced expression of CD276 was observed in all analyzed tumor samples including triple negative BC. In analyses with BC cells, CC-3 induced profound T cell activation, proliferation, and T cell memory subset formation. Moreover, treatment with CC-3 induced cytokine secretion and potent tumor cell lysis. Conclusion Our findings characterize CD276 as promising target and preclinically document the therapeutic potential of CC-3 for BC treatment, providing a strong rationale for evaluation of CC-3 in BC patients in a clinical trial for which the recruitment has recently started.
ExoplaNeT accRetion mOnitoring sPectroscopic surveY (ENTROPY)
2024-10-04

Context . Accretion among planetary mass companions is a poorly understood phenomenon, due to the lack of both observational and theoretical studies. The detection of emission lines from accreting gas giants facilitates detailed investigations into this process. Aims . This work presents a detailed analysis of Balmer lines from one of the few known young, planetary-mass objects with observed emission, the isolated L2 γ dwarf 2MASS J11151597+1937266 with a mass between 7 and 21 M Jup and an age of 5–45 Myr, located at 45 ± 2 pc. Methods . We obtained the first high-resolution ( R ~ 50 000) spectrum of the target with VLT/UVES, an echelle spectrograph operating in the near-ultraviolet to visible wavelengths (3200–6800 Å). Results . We report several resolved hydrogen (H I ; H3–H6) and helium (He I ; λ5875.6) emission lines in the spectrum. Based on the asymmetric line profiles of H α and H β , the 10% width of H α (199 ± 1 km s −1 ), tentative He I λ 6678 emission, and indications of a disk from mid-infrared excess, we confirm ongoing accretion at this object. Using the Gaia update of the parallax, we revise its temperature to 1816 ± 63 K and radius to 1.5 ± 0.1 R Jup . Analysis of observed H I profiles using a 1D planet-surface shock model implies a pre-shock gas velocity, v 0 = 120 −40 + 80 km s −1 , and a pre-shock density, log( n 0 /cm −3 ) = 14 −5 + 0 . The pre-shock velocity points to a mass, M p = 6 −4 + 8 M Jup , for the target. Combining H I line luminosities ( L line ) and planetary L line −L acc (accretion luminosity) scaling relations, we derived a mass accretion rate, Ṁ acc = 1.4 −0.9 + 2.8 × 10 −8 M Jup yr −1 . Conclusions . The line-emitting area predicted from the planet-surface shock model is very small (~0.03%), and points to a shock at the base of a magnetospherically induced funnel. The H α profile exhibits a much stronger flux than predicted by the model that best fits the rest of the H I profiles, indicating that another mechanism than shock emission contributes to the H α emission. Comparison of line fluxes and Ṁ acc from archival moderate-resolution SDSS spectra indicate variable accretion at 2MASS J11151597+1937266.
Whole-exome sequencing reveals the genetic causes and modifiers of moyamoya syndrome
2024-10-04

Moyamoya vasculopathy secondary to various genetic disorders is classified as moyamoya syndrome (MMS). Recent studies indicate MMS occurs due to a combination of genetic modifiers and causative mutations for the primary genetic disorders. We performed whole-exome sequencing (WES) in 13 patients with various genetic disorders who developed MMS. WES successfully revealed the genetic diagnoses of neurofibromatosis type 1 (NF-1), Down syndrome, multisystemic smooth muscle dysfunction syndrome, Noonan syndrome, and alpha thalassemia. The previously reported modifier genes, RNF213 and MRVI1, were confirmed in the NF-1 and Down syndrome cases. Further analysis revealed rare hypomorphic variants in the causative genes of the primary disorders underlying MMS, such as Alagille syndrome and Rasopathies, conferred susceptibility to MMS. Genes involved in the development of pulmonary arterial hypertension (PAH), such as ABCC8 and BMPR2, were also identified as potential modifiers. The rare variants in the MMS and PAH genes were significantly enriched in the eight Japanese patients with MMS compared with the 104 Japanese individuals from the 1000 Genomes Project. Disease genes associated with the arterial occlusive conditions represented by those of Rasopathies and PAH may provide novel diagnostic markers and future therapeutic targets for MMS as well as moyamoya disease with an unknown cause.
Longitudinal multimodal monitoring of transplanted islet β-cells
2024-10-04

For the quantification of β-cell function, Mn-based contrast mechanisms between native and transplanted islets differ and require further studies for optimal biological readout. However, non-invasive PET/MRI nonetheless provides the tools to investigate the relationship between β-cell mass and function in pancreatic islets.
Microsaccadic suppression of peripheral perceptual detection performance as a function of foveated visual image appearance
2024-10-04

Microsaccades are known to be associated with a deficit in perceptual detection performance for brief probe flashes presented in their temporal vicinity. However, it is still not clear how such a deficit might depend on the visual environment across which microsaccades are generated. Here, and motivated by studies demonstrating an interaction between visual background image appearance and perceptual suppression strength associated with large saccades, we probed peripheral perceptual detection performance of human subjects while they generated microsaccades over three different visual backgrounds. Subjects fixated near the center of a low spatial frequency grating, a high spatial frequency grating, or a small white fixation spot over an otherwise gray background. When a computer process detected a microsaccade, it presented a brief peripheral probe flash at one of four locations (over a uniform gray background) and at different times. After collecting full psychometric curves, we found that both perceptual detection thresholds and slopes of psychometric curves were impaired for peripheral flashes in the immediate temporal vicinity of microsaccades, and they recovered with later flash times. Importantly, the threshold elevations, but not the psychometric slope reductions, were stronger for the white fixation spot than for either of the two gratings. Thus, like with larger saccades, microsaccadic suppression strength can show a certain degree of image dependence. However, unlike with larger saccades, stronger microsaccadic suppression did not occur with low spatial frequency textures. This observation might reflect the different spatiotemporal retinal transients associated with the small microsaccades in our study versus larger saccades.
Determination of double bond positions in unsaturated fatty acids by pre-column derivatization with dimethyl and dipyridyl disulfide followed by LC-SWATH-MS analysis
2024-10-05

Abstract Comprehensive in-depth structural characterization of free mono-unsaturated and polyunsaturated fatty acids often requires the determination of carbon-carbon double bond positions due to their impact on physiological properties and relevance in biological samples or during impurity profiling of pharmaceuticals. In this research, we report on the evaluation of disulfides as suitable derivatization reagents for the determination of carbon-carbon double bond positions of unsaturated free fatty acids by UHPLC-ESI-QTOF-MS/MS analysis and SWATH (sequential windowed acquisition of all theoretical mass spectra) acquisition. Iodine-catalyzed derivatization of C = C double bonds with dimethyl disulfide (DMDS) enabled detection of characteristic carboxy-terminal MS2 fragments for various fatty acids in ESI negative mode. The determination of double bond positions of fatty acids with up to three double bonds, the transfer of the method to plasma samples, and its limitations have been shown. To achieve charge-switching for positive ion mode MS-detection, derivatization with 2,2′-dipyridyldisulfide (DPDS) was investigated. It enabled detection of both corresponding characteristic omega-end- and carboxy-end-fragments for fatty acids with up to two double bonds in positive ion mode. It provides a straightforward strategy for designing MRM transitions for targeted LC–MS/MS assays. Both derivatization techniques represent a simple and inexpensive way for the determination of double bond positions in fatty acids with low number of double bonds. No adaptation of MS hardware is required and the specific isotopic pattern of resulting sulfur-containing products provides additional structural confirmation. This reaction scheme opens up the avenue of structural tuning of disulfide reagents beyond DMDS and DPDS using reagents like cystine and analogs to achieve enhanced performance and sensitivity. Graphical Abstract
Outcomes of haploidentical transplants with PT-CY vs 10/10 MUD transplants with ATG in Germany
2024-10-05

Abstract Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is the best curative treatment modality for many malignant hematologic disorders. In the absence of a matched related donor, matched unrelated donors (MUDs) and haploidentical donors are the most important stem cell sources. In this registry-based retrospective study, we compared the outcomes of allo-HSCTs from 10/10 MUDs with antithymocyte globulin (ATG)–based regimens (n = 7050) vs haploidentical transplants (Haplo-Tx) using posttransplant cyclophosphamide (PT-CY Haplo; n = 487) in adult patients with hematologic malignancies between 2010 and 2020. Cox proportional hazard-and competing risks regression models were formed to compare the outcomes. Overall survival (OS), Disease-free survival (DFS), and graft-versus-host disease (GVHD)–free and relapse-free survival (GRFS) were superior for 10/10 MUDs (OS [hazard ratio (HR), 1.27; 95% confidence interval (CI), 1.10-1.47; P = .001]; DFS [HR, 1.17; CI, 1.02-1.34; P = .022]; GRFS [HR, 1.34; CI, 1.19-1.50; P &amp;lt; .001]). The risk of acute GVHD (aGVHD) grade 2 to 4, aGVHD grade 3 to 4, and chronic GVHD (cGVHD) was higher in the PT-CY Haplo group than the 10/10 MUD group (aGVHD grade 2-4 [HR, 1.46; CI, 1.25-1.71; P &amp;lt; .001]; aGVHD grade 3-4 [HR, 1.74; CI, 1.37- 2.20; P &amp;lt; .001]; cGVHD [HR, 1.30; CI, 1.11-1.51; P = .001]). A lower incidence of relapse was observed in the PT-CY Haplo group (relapse: HR, 0.83; CI, 0.69-0.99; P = .038). Unrelated 10/10 matched transplantation with ATG leads to lower GVHD rates and improved survival rates compared with PT-CY Haplo transplantation in Germany.