julilili42/papers huggingface dataset:
Cerebral glucose hypometabolism and hypoperfusion of cingulate gyrus: an imaging biomarker of autoimmune encephalitis with psychiatric symptoms
2023-11-09

Abstract Background About 60% of autoimmune encephalitis (AE) patients present psychiatric symptoms, but the underlying mechanism remains unknown. This study examined the role of the cingulate cortex in such patients to identify predictive poor psychiatric factors. Methods In this study, 49 AE patients and 39 healthy controls were enrolled. AE patients were further divided into two groups based on the presence/absence of psychiatric symptoms. The ratio of the standardized uptake value (SUVR) and relative cerebral blood flow (rCBF) in different regions of the cingulate cortex were calculated through positron emission tomography–computed tomography (PET/CT) and arterial spin labeling (ASL) MRI, and the results were compared among the three groups. In addition, we followed-up on the psychiatric outcomes and identified the risk factors for poor psychiatric prognosis, focusing on the cingulate cortex. Results More than half of the AE patients (27/49) exhibited psychiatric symptoms. Agitation and thought blocking were typical psychiatric phenotypes, except for anti-glutamic acid decarboxylase 65 (GAD65) encephalitis, which mainly presented with catatonia and a depressed mood. AE patients with psychiatric symptoms experienced reduced metabolism and perfusion of the anterior cingulate cortex (ACC), midcingulate cortex (MCC), and posterior cingulate cortex (PCC). The SUVR of ACC can be used as an independent risk factor of poor psychiatric outcomes, which had an area under the ROC curve (AUC) of 0.865. Conclusion Impaired cingulate cortex function in AE may be the potential mechanism of psychiatric symptoms. Hypometabolism of ACC is an independent prognostic factor predicting an unfavorable psychiatric prognosis in AE.
Neuroanatomical location of brain metastases from solid tumours based on pathology: An analysis of 511 patients with a comparison to the provided clinical history
2023-11-09

Brain metastases are a frequent occurrence in neuropathology practices. The literature on their neuroanatomical location is frequently derived from radiological analyses. This work examines brain metastases through the lens of pathology specimens. All brain surgical pathology reports for cases accessioned 2011–2020 were retrieved from a laboratory. Specimens were classified by neuroanatomical location, diagnosis and diagnostic category with a hierarchical free text string-matching algorithm (HFTSMA) and also subsequently audited. All reports classified as probable metastasis were reviewed by a pathologist. The provided history was compared to the final categorization by a pathologist. The cohort had 4,625 cases. The HFTSMA identified 854 cases (including metastases from a definite primary, metastases from primary not known and improperly classified cases). 514/854 cases had one definite primary site per algorithm and on report review 538/854 cases were confirmed as such. The 538 cases originated from 511 patients. Primaries from breast, gynecologic tract, and gastrointestinal tract not otherwise specified were most frequently found in the cerebellum. Kidney metastases were most frequently found in the occipital lobe. Lung, metastatic melanoma and colorectal primaries were most commonly found in the frontal lobe. The provided clinical history predicted the primary in 206 cases (40.3%), was discordant in 17 cases (3.3%) and non-contributory in 280 cases (54.8%). The observed distribution of the metastatic tumours in the brain is dependent on the primary site. In the majority (54.8%) of cases, the provided clinical history was non-contributory; this suggests surgeon-pathologist communication may have the potential for optimization.
Effects of different volumes of ovariectomy on fertility and offspring development of rats
2023-11-09

Objective The purpose of this study was to explore the effect of removal of different volumes of ovarian tissue on fertility and offspring development of SD rats. Methods SD rats were randomly divided into 6 groups according to different volumes of ovariectomy: Sham group (n=6), non-ovariectomized; 25%-OVX group (n=6), with half of the left ovary excised; 50%-OVX group (n=5), with the left ovary excised; 75%-OVX group (n=5), with the left ovary and half of the right ovary excised; 87.5%-OVX group (n=6), with the left ovary and three quarters of the right ovary excised; 100%-OVX group (n=6), with bilateral ovaries excised. These female rats (F0) were mated with healthy male rats one and four months after the surgery, and the offspring of F0 rats were named F1 1mon and F1 4mon , respectively. The number of days from mating to delivery and number of live cubs were recorded. At postnatal day 21 (P21), the body weight, length and anogenital distance (AGD) of the cubs were measured. Results There were no differences in the number of live cubs between 25%-OVX, 50%-OVX and sham groups. Rats in the 87.5%-OVX group did not give birth at 1 month and 4 months after the operation. When compared with the sham group, the body weight and length of F1 1mon at P21 were increased in 25%-OVX group and 50%-OVX group. However, after the second delivery, we controlled each mother’s lactation to no more than eight pups. As a result, there were no differences in the body weight, length and AGD of F1 4mon compared with sham group. Conclusion Removal of less than 50% of the ovaries did not affect the fertility of rats and offspring development of rats.
Identification of impactful imaging biomarker: Clinical applications for breast and prostate carcinoma
2023-11-09

Background Imaging biomarkers are quantitative parameters from imaging modalities, which are collected noninvasively, allow conclusions about physiological and pathophysiological processes, and may consist of single (monoparametric) or multiple parameters (bi- or multiparametric). Method This review aims to present the state of the art for the quantification of multimodal and multiparametric imaging biomarkers. Here, the use of biomarkers using artificial intelligence will be addressed and the clinical application of imaging biomarkers in breast and prostate cancers will be explained. For the preparation of the review article, an extensive literature search was performed based on Pubmed, Web of Science and Google Scholar. The results were evaluated and discussed for consistency and generality. Results and Conclusion Different imaging biomarkers (multiparametric) are quantified based on the use of complementary imaging modalities (multimodal) from radiology, nuclear medicine, or hybrid imaging. From these techniques, parameters are determined at the morphological (e. g., size), functional (e. g., vascularization or diffusion), metabolic (e. g., glucose metabolism), or molecular (e. g., expression of prostate specific membrane antigen, PSMA) level. The integration and weighting of imaging biomarkers are increasingly being performed with artificial intelligence, using machine learning algorithms. In this way, the clinical application of imaging biomarkers is increasing, as illustrated by the diagnosis of breast and prostate cancers. Key Points Citation Format
Revisiting Audio Observations to Collect Qualitative Data During the COVID-19 Pandemic
2023-11-09

With its physical distancing rules, the COVID-19 pandemic regulations urged researchers working in a qualitative paradigm to find pandemic-ready approaches to data collection. While many researchers turned to modern videoconferencing software, we explored an alternative route, and revisited audio observations. Audio observations replace the researcher as observer with audio recorders. Audio observations were pioneered in the 1960s, and continued to attract interest into the 1980s. Connecting with the methods literature from this earlier phase of interest, we evaluate a study design that combines audio observations with an interactive task that we applied to study active parental mediation of harmful media content. Drawing on a re-coding of data from two waves of data collection, we report on participants’ awareness of the observation episodes, issues with the recording quality, and the situational control during the observation episodes. We conclude that, although truly not a panacea, the combination of audio observations with interactive tasks not only helps to confront the challenges of physical distancing but also constitutes a serious alternative to more established qualitative data gathering approaches—even beyond pandemic restrictions. Thus, this article contributes to the extension of the methods repertoire in qualitative research.
The Hidden Oases: Unveiling Trophic Dynamics in Namib's Fog Plant Ecosystem
2023-11-09

<title>Abstract</title> The Namib Desert is a hyperarid coastal desert where fog is a major moisture source. We hypothesized that the fog-harvesting grass Stipagrostis sabulicola establishes an important ecological niche in the extreme Namib Sand Sea ecosystem, referred to as "Fog-Plant-Oases (FPO)". Using a combination of extraction methods, we collected and described the above- and belowground FPO invertebrate communities and inferred their trophic feedings based on stable carbon and nitrogen isotope values. Our findings revealed a complex trophic structure and a unique food web, all of which revolve around a single fog plant as the primary producer. We demonstrated that S. sabulicola serves as the primary energy source for the aboveground food web, encompassing a diverse range of trophic levels. Nevertheless, the distinctive stable isotope values of bacterial- and fungal-feeding nematodes indicated the separation of the aboveground niche, which is primarily sustained by S. sabulicola, from the belowground niche, where wind-blown sediments serve as the main energy source. These findings further accentuate the role of S. sabulicola not only as a primary producer but also as a source of moisture and habitat provider for belowground invertebrates. Huei Ying Gan, Karin Hohberg, and Clément Schneider contributed equally to this work.
Machine learning of a density functional for anisotropic patchy particles
2023-11-09

Anisotropic patchy particles have become an archetypical statistical model system for associating fluids. Here we formulate an approach to the Kern-Frenkel model via classical density functional theory to describe the positionally and orientationally resolved equilibrium density distributions in flat wall geometries. The density functional is split into a reference part for the orientationally averaged density and an orientational part in mean-field approximation. To bring the orientational part into a kernel form suitable for machine learning techniques, an expansion into orientational invariants and the proper incorporation of single-particle symmetries is formulated. The mean-field kernel is constructed via machine learning on the basis of hard wall simulation data. Results are compared to the well-known random-phase approximation which strongly underestimates the orientational correlations close to the wall. Successes and shortcomings of the mean-field treatment of the orientational part are highlighted and perspectives are given for attaining a full density functional via machine learning.
The relevance of structural variability in the time-domain for computational reflection anisotropy spectroscopy at solid-liquid interfaces
2023-11-09

In electrochemistry, reactions and charge-transfer are to a large extent determined by the atomistic structure of the solid-liquid interface. Yet due to the presence of the liquid electrolyte, many surface-science methods cannot be applied here. Hence, the exact microscopic structure that is present under operating conditions often remains unknown. Reflection anisotropy spectroscopy (RAS) is one of the few techniques that allow for an in operando investigation of the structure of solid-liquid interfaces. However, an interpretation of RAS data on the atomistic scale can only be obtained by comparison to computational spectroscopy. While the number of computational RAS studies related to electrochemical systems is currently still limited, those studies so far have not taken into account the dynamic nature of the solid-liquid interface. In this work, we investigate the temporal evolution of the spectroscopic response of the Au(110) missing row reconstruction in contact with water by combining ab initio molecular dynamics with computational spectroscopy. Our results show significant changes in the time evolution of the RA spectra, in particular providing an explanation for the typically observed differences in intensity when comparing theory and experiment. Moreover, these findings point to the importance of structural surface/interface variability while at the same time emphasising the potential of RAS for probing these dynamic interfaces.
Mind the (spectral) gap: how the temporal resolution of wind data affects multi-decadal wind power forecasts
2023-11-10

Abstract To forecast wind power generation in the scale of years to decades, outputs from climate models are often used. However, one major limitation of the data projected by these models is their coarse temporal resolution—usually not finer than three hours and sometimes as coarse as one month. Due to the non-linear relationship between wind speed and wind power, and the long forecast horizon considered, small changes in wind speed can result in big changes in projected wind power generation. Our study indicates that the distribution of observed 10 min wind speed data is relatively well preserved using three- or six-hourly instantaneous values. In contrast, daily or monthly values, as well as any averages, including three-hourly averages, are almost never capable of preserving the distribution of the underlying higher resolution data. Assuming that climate models behave in a similar manner to observations, our results indicate that output at three-hourly or six-hourly temporal resolution is high enough for multi-decadal wind power generation forecasting. In contrast, wind speed projections of lower temporal resolution, or averages over any time range, should be handled with care.
Mesenchymal stem cells and their extracellular vesicles in urological cancers: Prostate, bladder, and kidney
2023-11-10

Abstract Mesenchymal stem cells (MSCs) are recognized for their remarkable ability to differentiate into multiple cell types. They are also known to possess properties that can fight cancer, leading to attempts to modify MSCs for use in anticancer treatments. However, MSCs have also been found to participate in pathways that promote tumor growth. Many studies have been conducted to explore the potential of MSCs for clinical applications, but the results have been inconclusive, possibly due to the diverse nature of MSC populations. Furthermore, the conflicting roles of MSCs in inhibiting tumors and promoting tumor growth hinder their adaptation to anticancer therapies. Antitumorigenic and protumorigenic properties of MSCs in urological cancers such as bladder, prostate, and renal are not as well established, and data comparing them are still limited. MSCs hold significant promise as a vehicle for delivering anticancer agents and suicide genes to tumors. Presently, numerous studies have concentrated on the products derived from MSCs, such as extracellular vesicles (EVs), as a form of cell‐free therapy. This work aimed to review and discuss the current knowledge of MSCs and their EVs in urological cancer therapy.
Evidence Of The Earliest Freshwater Decapod Fossil From Southeast Asia (Crustacea: Decapoda: Brachyura)
2023-11-10

Klaus, Sebastian, Böhme, Madelaine, Schneider, Simon, Prieto, Jérôme (2011): Evidence Of The Earliest Freshwater Decapod Fossil From Southeast Asia (Crustacea: Decapoda: Brachyura). Raffles Bulletin of Zoology 59 (1): 47-51, DOI: http://doi.org/10.5281/zenodo.10106786
Metabolic rewiring compensates for the loss of glutamate and aspartate biosynthesis inBacillus subtilis
2023-11-10

Summary Glutamate serves as the major cellular amino group donor. In Bacillus subtilis , glutamate is synthesized by the combined action of the glutamine synthetase and the glutamate synthase (GOGAT). The glutamate dehydrogenases are devoted to glutamate degradation in vivo . To keep the cellular glutamate concentration high, the genes and the encoded enzymes involved in glutamate biosynthesis and degradation need to be tightly regulated depending on the available carbon and nitrogen sources. Serendipitously, we found that the inactivation of the ansR and citG genes encoding the repressor of the ansAB genes and the fumarase, respectively, enables the GOGAT-deficient B. subtilis mutant to synthesize glutamate via a non-canonical fumarate-based ammonium assimilation pathway. We also show that the de-repression of the ansAB genes is sufficient to restore aspartate prototrophy of an aspB aspartate transaminase mutant. Moreover, with excess nitrogen, B. subtilis mutants lacking fumarase activity show a growth defect that can be relieved by aspB overexpression, by reducing arginine uptake and by decreasing the metabolic flux through the TCA cycle. It will be interesting to investigate whether the B. subtilis strain using the alternative glutamate biosynthesis route can evolve in such a way that it robustly grows during nitrogen limitation and excess.
DLG1 functions upstream of SDCCAG3 and IFT20 to control ciliary targeting of polycystin-2
2023-11-10

Summary Polarized vesicular trafficking directs specific receptors and ion channels to cilia, but the underlying mechanisms are poorly understood. Here we describe a role for DLG1, a core component of the Scribble polarity complex, in regulating ciliary protein trafficking in kidney epithelial cells. Conditional knockout of Dlg1 in mouse kidney caused ciliary elongation and cystogenesis, and cell-based proximity labelling proteomics and fluorescence microscopy showed alterations in the ciliary proteome upon loss of DLG1. Specifically, the retromer-associated protein SDCCAG3, IFT20 and polycystin-2 (PC2) were reduced in cilia of DLG1 deficient cells compared to control cells. This phenotype was recapitulated in vivo and rescuable by re-expression of wildtype DLG1, but not a Congenital Anomalies of the Kidney and Urinary Tract (CAKUT)-associated DLG1 variant, p.T489R. Finally, biochemical approaches and Alpha Fold modelling suggested that SDCCAG3 and IFT20 form a complex that associates, at least indirectly, with DLG1. Our work identifies a key role for DLG1 in regulating ciliary protein composition and suggests that ciliary dysfunction of the p.T489R DLG1 variant may contribute to CAKUT.
Nuthatch (Sitta europaea) responses towards simulated territorial intrusion (STI) vary in strength during the non-breeding season — a matter of temperature and photoperiod?
2023-11-10

Abstract Many bird species defend their territories against conspecifics during the breeding season. Although some temperate species have been observed to defend territories outside of the breeding season, such cases are rarely noted in the literature, and it remains largely unknown which environmental factors influence such behaviour. In this study, we investigated non-breeding territorial behaviour in the Eurasian nuthatch ( Sitta europaea ). Territorial responses were elicited with a simulated territory intrusion (playbacks of calls combined with a wooden model of nuthatch) in autumn, winter and spring. Territorial responses did not differ between autumn and winter but differed between the autumn/winter and spring; they declined until about mid-December (winter) and increased after that into the spring. We found an increase in territorial responses with increasing photoperiod (day length) in autumn and with decreasing ambient temperature during spring. Our study provides novel evidence about non-breeding territorial behaviour in temperate birds and indicates that this behaviour is influenced by environmental factors.
Elevated Plasma Complement Factors inCRB1-associated Inherited Retinal Dystrophies
2023-11-10

Abstract Objective To determine the profile of inflammation-related proteins and complement system factors in serum of CRB1 -associated inherited retinal dystrophies ( CRB1 -IRDs). Design A case-control study. Subjects, Participants, and/or Controls A cohort of 30 Dutch CRB1 -IRD patients and 29 Dutch healthy controls (HC) (Cohort I), and a second cohort of 123 CRB1 -IRD patients from 14 countries and 1292 controls (Cohort II) were used in this study. Methods Quantitative 370-plex targeted proteomics in blood plasma and genotyping of the single nucleotide variant (SNV) rs7535263 in the CFH gene. Main Outcome Measures Plasma concentrations of inflammation-related proteins and the genotype of the SNV rs7535263. Results CRB1 -IRD patients showed increased plasma levels of complement system and coagulation cascade proteins compared to healthy controls. Complement Factor I [CFI], Serpin Family D1 [SERPIND1], and Complement Factor H [CFH] were significantly elevated (q&lt;0.05, adjusted for age and sex), which correlated (Pearson’s correlation coefficient &gt;0.6) with higher levels of plasma Complement Component 3 [C3] (q = 0.064). The most enriched pathway in patients was the “Complement cascade” (R-HSA-166658, Padj = P = 3.03 × 10 -15 ). An analysis of the genotype of CFH variant rs7535263, which is in close physical proximity to the CRB1 gene and is associated with other retinal conditions by influencing plasma complement levels, revealed significantly skewed allele distribution specifically in Dutch patients (A allele of rs7535263, odds ratio (OR) [95%CI = 2.85 [1.35-6.02], P = 6.19 × 10 -3 ), but not in a global case-control cohort ( P = 0.12). However, CRB1 missense variants that are common in patients display strong linkage disequilibrium (LD) with rs7535263 in CFH in the UK Biobank (D’ = 0.97 for p.(Cys948Tyr); D’ = 1.0 for p.(Arg764Cys)), indicating that genetic linkage may influence plasma complement factor levels in CRB1 -IRD patients. After accounting for the CFH genotype in the proteomic analyses, we also detected significantly elevated plasma levels of Complement Factor H Related 2 [CFHR2] in CRB1 -IRD patients (q = 0.04). Conclusions CRB1 -IRDs are characterized by changes in plasma levels of complement factors and proteins of the innate immune system, which is influenced by common functional variants in the CFH-CFHR locus. This indicates that innate immunity is implicated in CRB1 -IRDs.
Clinical course and follow-up of pediatric patients with COVID-19 vaccine-associated myocarditis compared to non–vaccine-associated myocarditis within the prospective multicenter registry—“MYKKE”
2023-11-11

Course of COVID-19 vaccine-associated myocarditis in pediatric patients seems to be mild and differs from non-vaccine-associated myocarditis. Due to a considerable number of residual symptoms and diagnostic abnormalities at follow-up, further studies are needed to define its long-term implications.
FLASHQuant: a fast algorithm for proteoform quantification in top-down proteomics
2023-11-11

ABSTRACT Liquid chromatography-mass spectrometry (LC-MS) based top-down proteomics (TDP) is an essential method for the analysis of intact proteoforms. The accurate quantification of individual proteoforms is a crucial step in identifying proteome-wide alterations in different biological conditions. Label-free quantification (LFQ) is the most common method for proteoform quantification as it requires no additional costly labeling. In TDP, due to frequent co-elution and complex signal structures, overlapping signals deriving from multiple proteoforms complicate accurate quantification. Here, we introduce FLASHQuant for MS1-level LFQ analysis in TDP, which is capable of automatically resolving and quantifying co-eluting proteoforms. FLASHQuant performs highly accurate and reproducible quantification in short runtimes of just a few minutes per LC-MS run. To validate the proteoforms reported by FLASHQuant, we evaluated them with identified proteoforms confirmed by tandem mass spectrometry, which showed high match rates. FLASHQuant is publicly available as platform-independent open-source software at https://openms.org/flashquant/ .