julilili42/papers huggingface dataset:
Advances in non-invasive tracking of wave-type electric fish in natural and laboratory settings
2022-06-03

ABSTRACT Recent technological advances greatly improved the possibility to study freely behaving animals in natural conditions. However, many systems still rely on animal-mounted devices, which can already bias behavioral observations. Alternatively, animal behaviors can be detected and tracked in recordings of stationary sensors, e.g. video cameras. While these approaches circumvent the influence of animal-mounted devices, identification of individuals is much more challenging. We take advantage of the individual-specific electric fields electric fish generate by discharging their electric organ (EOD) to record and track their movement and communication behaviors without interfering with the animals themselves. EODs of complete groups of fish can be recorded with electrode arrays submerged in the water and then be tracked for individual fish. Here, we present an improved algorithm for tracking electric signals of wave-type electric fish with unprecedented accuracy. Our algorithm benefits from combining and refining previous approaches of tracking individual specific EOD frequencies (EODf) and spatial electric field properties. In this process, the similarity of signal pairs in extended data windows determines their tracking order, making the algorithm more robust against detection losses and intersections. We quantify the performance of the algorithm and show its application for a data set recorded with a 64-electrode array in a stream in the Llanos, Colombia, where we managed, for the first time, to track Apteronotus leptorhynchus over many days. These technological advances make electric fish a unique model system for a detailed analysis of social and communication behaviors, with strong implications for our research on sensory coding.
Urinary Tract Tumor Organoids Reveal Eminent Differences in Drug Sensitivities When Compared to 2-Dimensional Culture Systems
2022-06-04

Generation of organoids from urinary tract tumor samples was pioneered a few years ago. We generated organoids from two upper tract urothelial carcinomas and from one bladder cancer sample, and confirmed the expression of cytokeratins as urothelial antigens, vimentin as a mesenchymal marker, and fibroblast growth factor receptor 3 by immunohistochemistry. We investigated the dose response curves of two novel components, venetoclax versus S63845, in comparison to the clinical standard cisplatin in organoids in comparison to the corresponding two-dimensional cultures. Normal urothelial cells and tumor lines RT4 and HT1197 served as controls. We report that upper tract urothelial carcinoma cells and bladder cancer cells in two-dimensional cultures yielded clearly different sensitivities towards venetoclax, S63845, and cisplatin. Two-dimensional cultures were more sensitive at low drug concentrations, while organoids yielded higher drug efficacies at higher doses. In some two-dimensional cell viability experiments, colorimetric assays yielded different IC50 toxicity levels when compared to chemiluminescence assays. Organoids exhibited distinct sensitivities towards cisplatin and to a somewhat lesser extent towards venetoclax or S63845, respectively, and significantly different sensitivities towards the three drugs investigated when compared to the corresponding two-dimensional cultures. We conclude that organoids maintained inter-individual sensitivities towards venetoclax, S63845, and cisplatin. The preclinical models and test systems employed may bias the results of cytotoxicity studies.
Carbodiimide Bridged Network Structure of [RE6O(NCN)6] Clusters in the Structure of RE8O(CN2)10Br2, RE = La, Ce, Pr, Nd
2022-06-04

Abstract New rare earth (RE) carbodiimides having the formula RE 8 O(CN 2 ) 10 Br 2 were synthesized by solid-state metathesis reactions. Structure determinations and refinements, based on single-crystal X-ray diffraction data, are performed with the space group P ͞3 c1 . Homologous compounds with RE = La, Ce, Pr, and Nd are assigned isotypically. The refined crystal structure appears most unusual for rare earth carbodiimide compounds. The structure is characterized by the formally neutral [RE 6 O(NCN) 8 ] fragment that is tightly interconnected by carbodiimide ions into a network structure, and contains additional RE 3+ ions in the structure. Crystals of the compounds show characteristic colors of their corresponding RE 3+ ions and behave stable in air. The presence of (CN 2 ) 2− ions was confirmed by infrared spectroscopy. Ce 8 O(CN 2 ) 10 Br 2 is a photoluminescent material that is showing a broad and efficient emission band in the yellow region of the visible spectrum.
H3K27m3 overexpression as a new, BCL2 independent diagnostic tool in follicular and cutaneous follicle center lymphomas
2022-06-04

Abstract Approximately 15% of follicular lymphomas (FL) lack overexpression of BCL2 and the underlying translocation t(14;18). These cases can be diagnostically challenging, especially regarding follicular hyperplasia (FH). In a subset of FL, mutations in genes encoding for epigenetic modifiers, such as the histone-lysine N-methyltransferase EZH2 (enhancer of zeste homolog 2), were found, which might be used diagnostically. These molecular alterations can lead to an increased tri-methylation of histone H3 at position lysine 27 (H3K27m3) that, in turn, can be visualized immunohistochemically. The aim of this study was to analyze the expression of H3K27m3 in FL, primary cutaneous follicle center lymphomas (PCFCL), and pediatric-type FL (PTFL) in order to investigate its value in the differential diagnosis to FH and other B cell lymphomas and to correlate it to BCL2 expression and the presence of t(14;18). Additionally, the mutational profile of selected cases was considered to address H3K27m3’s potential use as a surrogate parameter for mutations in genes encoding for epigenetic modifiers. Eighty-nine percent of FL and 100% of PCFCL cases overexpressed H3K27m3, independently of BCL2, EZH2, and the presence of mutations. In contrast, 95% of FH and 100% of PTFL cases lacked H3K27m3 overexpression. Other B cell lymphomas considered for differential diagnosis also showed overexpression of H3K27m3 in the majority of cases. In summary, overexpression of H3K27m3 can serve as a new, BCL2 independent marker in the differential diagnosis of FL and PCFCL, but not PTFL, to FH, while being not of help in the differential diagnosis of FL to other B cell lymphomas.
Teclistamab in Relapsed or Refractory Multiple Myeloma
2022-06-05

Teclistamab resulted in a high rate of deep and durable response in patients with triple-class-exposed relapsed or refractory multiple myeloma. Cytopenias and infections were common; toxic effects that were consistent with T-cell redirection were mostly grade 1 or 2. (Funded by Janssen Research and Development; MajesTEC-1 ClinicalTrials.gov numbers, NCT03145181 and NCT04557098.).
bHLH heterodimer complex variations shape meristems in Arabidopsis thaliana by affecting target gene specificity
2022-06-05

ABSTRACT The main regions of cell proliferation in plants are the root and shoot apical meristems during primary growth and the vascular cambia as lateral meristems during secondary thickening. A number of unique regulators have been described in each of these meristems, suggesting that these different meristems might have independently evolved dedicated transcriptional networks to balance cell proliferation. Here, we show that the basic Helix Loop Helix (bHLH) transcription factor complexes formed by TARGET OF MONOPTEROS5 (TMO5), LONESOME HIGHWAY (LHW) and their close homologs are broadly expressed throughout plant development and operate as general regulators of cell proliferation in all meristems. Yet, genetic and expression analyses indicate that these complexes have specific functions in distinct meristems mediated by heterodimer complex variations between members of the TMO5 and LHW subclades. We determine that this is primarily due to their expression domains limiting the possible combinations of heterodimer complexes within a certain meristem, and to a certain extent to the absence of some members in a given meristem. We further demonstrate target gene specificity for heterodimer complexes, suggesting that spatial differences in transcriptional responses through heterodimer diversification allow a common bHLH heterodimer complex module to contribute to the control of cell proliferation in multiple meristems.
Automated real-time EEG sleep spindle detection for brain state-dependent brain stimulation
2022-06-05

Abstract Sleep spindles are a hallmark electroencephalographic (EEG) feature of non-rapid eye movement (NREM) sleep and believed to be instrumental for sleep-dependent memory reactivation and consolidation. However, direct proof of their causal relevance is hard to obtain, and our understanding of their immediate neurophysiological consequences is limited. To investigate their causal role, spindles need to be targeted in real-time with sensory or non-invasive brain stimulation techniques. While fully automated offline detection algorithms are well established, spindle detection in real time is highly challenging due to their spontaneous and transient nature. Here, we present the real-time spindle detector (RTSD), a robust multi-channel EEG signal processing algorithm that enables the automated triggering of stimulation during sleep spindles in a phase-specific manner. We validated the RTSD method by streaming pre-recorded sleep EEG datasets to a real-time computer system running a Simulink® Real-TimeTM implementation of the algorithm. Sleep spindles were detected with high levels of sensitivity (∼83%) and precision (∼78%) and an F1-score of ∼0.81 in reference to state-of-the-art offline algorithms (which reached similar levels when compared to each other), for both naps and full nights, and largely independent of sleep scoring information. Detected spindles were comparable in frequency, duration, amplitude, and symmetry, and showed the typical time-frequency characteristics as well as a centroparietal topography. Spindles were detected close to their center and reliably at the predefined target phase. The RTSD algorithm therefore empowers researchers to target spindles during human sleep and apply the stimulation method and experimental paradigm of their choice.
Protein profiling of breast carcinomas reveals expression of immune-suppressive factors and signatures relevant to patient outcome
2022-06-05

Abstract Background In cancerous tissue, a complex interplay of tumour cells with different cell types from the tumour microenvironment is causing modulations in signalling processes. By directly assessing expression of a multitude of proteins and protein variants, extensive information on signalling pathways, their activation status and the effect of the immunological landscape can be obtained providing viable information for treatment response. Methods Protein extracted from archived breast cancer tissue from patients without adjuvant therapy was subjected to high-throughput Western blotting using the DigiWest technology. Expression of 150 proteins and protein variants covering cell cycle control, apoptosis, Jak/Stat, MAPK-, Pi3K/Akt-, Wnt-, and, autophagic signalling as well as general tumour markers was monitored in a cohort of 84 patient samples. The degree of immune cell infiltration was investigated and set against treatment outcome by integrating patient specific follow-up data. Results Characterization of the tumour microenvironment by monitoring CD8α, CD11c, CD16 and CD68 expression revealed a strong correlation of event-free patient survival with immune cell infiltration. Furthermore, the presence of tumour infiltrating lymphocytes was linked to a pronounced activation of the Jak/Stat signalling pathway and apoptotic processes. Elevated phosphorylation of peroxisome proliferator-activated receptor gamma (PPARγ, pS112) in non-immune infiltrated tumour tissue suggests a novel immune evasion mechanism in breast cancer characterized by increased PPARγ activation. Conclusion Multiplexed immune cell marker assessment and protein profiling of tumour tissue provides functional signalling data facilitating breast cancer patient stratification.
Dataset (III) related to publication: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist
2022-06-05

&lt;p&gt;MD simulation data related to the publication Rashidian et al.: Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist.&nbsp;&lt;a href="https://doi.org/10.1016/j.csbj.2022.06.020"&gt;https://doi.org/10.1016/j.csbj.2022.06.020&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files)&lt;/p&gt; &lt;p&gt;dataset I: systems SRL+Co,&nbsp;C-100 and BAY-1797&lt;/p&gt; &lt;p&gt;dataset I: each file contains all branched replicas and the&nbsp;main&nbsp;replica.&lt;/p&gt; &lt;p&gt;dataset1:&nbsp;&nbsp;C_100_Replica1&nbsp;contains four branched replicas and the main replica.&nbsp;The two of four branched replicas which stem&nbsp;from the middle of the main replica named:&nbsp;b_c_D1_r1_2285 (corresponding name in the SI data is R1_a) and b_c_D1_2285_r1_2 (corresponding name in the SI data is R1_b).&lt;/p&gt; &lt;p&gt;dataset1: C_100_Replica2&ndash;5 , each file contains one main replica and the two branches.&lt;/p&gt; &lt;p&gt;dataset I: system&nbsp;SRL+Co ;each file contains one main replica&lt;/p&gt; &lt;p&gt;dataset I:&nbsp;system BAY-1797;&nbsp;each file contains one main replica&lt;/p&gt; &lt;p&gt;dataset II:system SRL ;&nbsp;each file contains one main replica.&lt;/p&gt; &lt;p&gt;dataset III:system C-100+Co (compound 100 in presence of SRC-1 coactivator)&nbsp;;&nbsp;each file contains one main replica.&lt;/p&gt;
Signatures of glial activity can be detected in the CSF proteome
2022-06-06

Significance Single-cell transcriptomics has revealed specific glial activation states associated with the pathogenesis of neurodegenerative diseases, such as Alzheimer’s and Parkinson’s disease (AD and PD). What is still needed are clinically relevant biomarkers for deciphering such glial states in AD and PD patients. To this end, we applied proteome analysis in cerebrospinal fluid (CSF) of mouse models of AD and PD pathology. This allowed us to identify a panel of glial CSF proteins that largely match the transcriptomic changes. The identified proteins can also be quantified in human CSF and show changes in AD patients, supporting their relevance as biomarker candidates to stage glial activation in patients with neurodegenerative diseases.
Artificial Intelligence-Based Prediction of Oroantral Communication after Tooth Extraction Utilizing Preoperative Panoramic Radiography
2022-06-06

Oroantral communication (OAC) is a common complication after tooth extraction of upper molars. Profound preoperative panoramic radiography analysis might potentially help predict OAC following tooth extraction. In this exploratory study, we evaluated n = 300 consecutive cases (100 OAC and 200 controls) and trained five machine learning algorithms (VGG16, InceptionV3, MobileNetV2, EfficientNet, and ResNet50) to predict OAC versus non-OAC (binary classification task) from the input images. Further, four oral and maxillofacial experts evaluated the respective panoramic radiography and determined performance metrics (accuracy, area under the curve (AUC), precision, recall, F1-score, and receiver operating characteristics curve) of all diagnostic approaches. Cohen’s kappa was used to evaluate the agreement between expert evaluations. The deep learning algorithms reached high specificity (highest specificity 100% for InceptionV3) but low sensitivity (highest sensitivity 42.86% for MobileNetV2). The AUCs from VGG16, InceptionV3, MobileNetV2, EfficientNet, and ResNet50 were 0.53, 0.60, 0.67, 0.51, and 0.56, respectively. Expert 1–4 reached an AUC of 0.550, 0.629, 0.500, and 0.579, respectively. The specificity of the expert evaluations ranged from 51.74% to 95.02%, whereas sensitivity ranged from 14.14% to 59.60%. Cohen’s kappa revealed a poor agreement for the oral and maxillofacial expert evaluations (Cohen’s kappa: 0.1285). Overall, present data indicate that OAC cannot be sufficiently predicted from preoperative panoramic radiography. The false-negative rate, i.e., the rate of positive cases (OAC) missed by the deep learning algorithms, ranged from 57.14% to 95.24%. Surgeons should not solely rely on panoramic radiography when evaluating the probability of OAC occurrence. Clinical testing of OAC is warranted after each upper-molar tooth extraction.
Selective autophagy: adding precision in plant immunity
2022-06-06

Abstract Plant immunity is antagonized by pathogenic effectors during interactions with bacteria, viruses or oomycetes. These effectors target core plant processes to promote infection. One such core plant process is autophagy, a conserved proteolytic pathway involved in ensuring cellular homeostasis. It involves the formation of autophagosomes around proteins destined for autophagic degradation. Many cellular components from organelles, aggregates, inactive or misfolded proteins have been found to be degraded via autophagy. Increasing evidence points to a high degree of specificity during the targeting of these components, strengthening the idea of selective autophagy. Selective autophagy receptors bridge the gap between target proteins and the forming autophagosome. To achieve this, the receptors are able to recognize specifically their target proteins in a ubiquitin-dependent or -independent manner, and to bind to ATG8 via canonical or non-canonical ATG8-interacting motifs. Some receptors have also been shown to require oligomerization to achieve their function in autophagic degradation. We summarize the recent advances in the role of selective autophagy in plant immunity and highlight NBR1 as a key player. However, not many selective autophagy receptors, especially those functioning in immunity, have been characterized in plants. We propose an in silico approach to identify novel receptors, by screening the Arabidopsis proteome for proteins containing features theoretically needed for a selective autophagy receptor. To corroborate these data, the transcript levels of these proteins during immune response are also investigated using public databases. We further highlight the novel perspectives and applications introduced by immunity-related selective autophagy studies, demonstrating its importance in research.
Genome sequencing and transcriptome profiling in twins discordant for Mayer-Rokitansky-Küster-Hauser syndrome
2022-06-06

Abstract Objective Mayer-Rokitansky-Küster-Hauser syndrome (MRKH) is a rare congenital disease manifesting with aplasia or severe hypoplasia of uterine structures. Even though extensive studies have been performed, for the majority of cases the etiology remains unclear. In this study, we sought to identify genetic causes in discordant monozygotic (MZ) twins using genome sequencing of blood of both twins as well as uterine tissue of the affected twin. In addition, we profiled the endometrial transcriptome of affected twins to compare perturbations with those of sporadic MRKH cases. Results First, analyzing the data under the assumption that a variant solely identified in the affected twin or affected tissue could cause the phenotype, we identified a mosaic variant in ACTR3B with a high allele frequency in affected tissue, a low allele frequency in blood of the affected twin and almost absent in the blood of the unaffected twin. Since ACTR3B has not been reported for genitourinary anomalies before, clinical relevance of the variant needs to be clarified. Second, examining the data for candidate genes previously implied in MRKH, we detected a pathogenic variant in GREB1L in one twin pair and their unaffected mother showing a reduced phenotypic penetrance. Furthermore, two variants of unknown clinical significance in PAX8 and WNT9B were identified. Analysis for copy number and structural variants revealed no discordant variants in the twins or variants in candidate genes or regions. Third, we conducted transcriptome analysis of affected tissue and observed widespread perturbations largely similar to those in sporadic MRKH cases. These shared transcriptional changes were enriched for terms associated with estrogen and its receptors pointing at a key role of estrogen in MRKH pathology. Conclusion Our study on genome sequencing of blood and uterine tissue of discordant twins is the most extensive study performed on twins discordant for MRKH so far. Nevertheless, no clear pathogenic differences in the twins or between blood and tissue samples were detected. This points towards a more complex etiology of MRKH less dependent on genetic differences and more determined by epigenetic changes or environmental factors. Our transcriptome data showed a clear overlap with gene expression data of sporadic MRKH cases, indicating that the etiology for MRKH in discordant twins and sporadic cases is largely similar.
Faster Grasping of High-Calorie Food Objects in Virtual Reality
2022-06-06

Abstract Purpose : Theoretical models and behavioral studies indicate faster approach behavior for high-calorie food (approach bias) among healthy participants. A previous study with Virtual Reality (VR) and online motion-capture quantified this approach bias towards food and non-food cues in a controlled VR environment with hand movements. The aim of this study was to test the specificity of a manual approach bias for high-calorie food in grasp movements compared to low-calorie food and neutral objects of different complexity, namely, simple balls and geometrically more complex office tools. Methods : In a VR setting, healthy participants repeatedly grasped or pushed high-calorie food, low-calorie food, balls and office tools in randomized order with 30 item repetitions. All objects were rated for valence and arousal. Results : High-calorie food was less attractive and more arousing in subjective ratings than low-calorie food and neutral objects. Movement onset was faster for high-calorie food in push-trials, but overall push responses were comparable. In contrast, responses to high-calorie food relative to low-calorie food and to control objects were faster in grasp trials for later stages of interaction (grasp and collect). Non-parametric tests confirmed an approach bias for high-calorie food. Conclusion : A behavioral bias for food was specific to high-calorie food objects. More systematic variations of object fidelity and in clinical populations are outstanding. The utility of VR in assessing approach behavior is confirmed in this study by exploring manual interactions in a controlled environment. Level of evidence: Basic science