A genome-wide genetic association study reveals SNPs significantly associated with environmental variables and specific leaf area in European beech.

European beech is negatively affected by climate change and a further growth decline is predicted for large parts of its distribution range. Despite the importance of this species, little is known about its genetic adaptation and especially the genetic basis of its physiological traits. Here, we used genotyping by sequencing to identify SNPs in 43 German European beech populations growing under different environmental conditions. In total, 28 of these populations were located along a precipitation and temperature gradient in northern Germany, and single tree-based hydraulic and morphological traits were available. We obtained a set of 13,493 high-quality SNPs that were used for environmental and SNP-trait association analysis. In total, 22 SNPs were identified that were significantly associated with environmental variables or specific leaf area (SLA). Several SNPs were located in genes related to stress response. The majority of the significant SNPs were located in non-coding (intergenic and intronic) regions. These may be in linkage disequilibrium with the causative coding or regulatory regions. Our study gives insights into the genetic basis of abiotic adaptation in European beech, and provides genetic resources that can be used in future studies on this species. Besides clear patterns of local adaptation to environmental conditions of the investigated populations, the analyzed morphological and hydraulic traits explained most of the explainable genetic variation. Thus, they could successfully be altered in tree breeding programs, which may help to increase the adaptation of European beech to changing environmental conditions in the future.

Efficient Tandem Cu-Catalyzed Click Synthesis of Multi-Sugar-Modified Oligonucleotides.

Nucleic acids in the form of siRNA, antisense oligonucleotides or mRNA are currently explored as new promising modalities in the pharmaceutical industry. Particularly, the success of mRNA-vaccines against SARS-CoV-2, along with the successful development of the first sugar-modified siRNA therapeutics has inspired the field. The development of nucleic acid therapeutics requires efficient chemistry to link oligonucleotides to chemical structures that can improve stability, boost cellular uptake, or enable specific targeting. For the siRNA therapeutics currently in use, modification of the 3'-end of the oligonucleotides with triple-N-acetylgalactosamine (GalNAc)3 was shown to be of significance. This modification is currently achieved via a cumbersome multi-step synthesis and subsequent loading onto the solid support material. Here, we report the development of a bifunctional click-reactive linker that allows the modification of oligonucleotides in a tandem click reaction with multiple sugars, regardless of the position within the oligonucleotide, with remarkable efficiency and in a one-pot reaction.

Stationary stable cross-correlation pattern and task specific deviations in unresponsive wakefulness syndrome as well as clinically healthy subjects.

Brain dynamics is highly non-stationary, permanently subject to ever-changing external conditions and continuously monitoring and adjusting internal control mechanisms. Finding stationary structures in this system, as has been done recently, is therefore of great importance for understanding fundamental dynamic trade relationships. Here we analyse electroencephalographic recordings (EEG) of 13 subjects with unresponsive wakefulness syndrome (UWS) during rest and while being influenced by different acoustic stimuli. We compare the results with a control group under the same experimental conditions and with clinically healthy subjects during overnight sleep. The main objective of this study is to investigate whether a stationary correlation pattern is also present in the UWS group, and if so, to what extent this structure resembles the one found in healthy subjects. Furthermore, we extract transient dynamical features via specific deviations from the stationary interrelation pattern. We find that (i) the UWS group is more heterogeneous than the two groups of healthy subjects, (ii) also the EEGs of the UWS group contain a stationary cross-correlation pattern, although it is less pronounced and shows less similarity to that found for healthy subjects and (iii) deviations from the stationary pattern are notably larger for the UWS than for the two groups of healthy subjects. The results suggest that the nervous system of subjects with UWS receive external stimuli but show an overreaching reaction to them, which may disturb opportune information processing.

Immunopeptidomics-based identification of naturally presented non-canonical circRNA-derived peptides.

Circular RNAs (circRNAs) are covalently closed non-coding RNAs lacking the 5' cap and the poly-A tail. Nevertheless, it has been demonstrated that certain circRNAs can undergo active translation. Therefore, aberrantly expressed circRNAs in human cancers could be an unexplored source of tumor-specific antigens, potentially mediating anti-tumor T cell responses. This study presents an immunopeptidomics workflow with a specific focus on generating a circRNA-specific protein fasta reference. The main goal of this workflow is to streamline the process of identifying and validating human leukocyte antigen (HLA) bound peptides potentially originating from circRNAs. We increase the analytical stringency of our workflow by retaining peptides identified independently by two mass spectrometry search engines and/or by applying a group-specific FDR for canonical-derived and circRNA-derived peptides. A subset of circRNA-derived peptides specifically encoded by the region spanning the back-splice junction (BSJ) are validated with targeted MS, and with direct Sanger sequencing of the respective source transcripts. Our workflow identifies 54 unique BSJ-spanning circRNA-derived peptides in the immunopeptidome of melanoma and lung cancer samples. Our approach enlarges the catalog of source proteins that can be explored for immunotherapy.

Impact of thrombosis location on walking capacity: a cohort study of patients with acute deep vein thrombosis.

Background: Data on walking impairment during the acute phase of deep vein thrombosis (DVT) are limited. Objectives: This study aimed to assess the degree of walking impairment in patients with acute DVT, with a particular focus on the relation to the DVT's anatomical location. Methods: Patients with sonographically confirmed DVT were eligible for inclusion in this cohort study. Pain-free walking distance (PWD) and maximum walking distance (MWD) were determined using standardized treadmill ergometer tests and analyzed in relation to DVT location. The impact of previous DVT on walking capacity was evaluated in an exploratory analysis. Results: The study included 64 patients (31% women; median age, 55 years). The median (IQR) time from diagnosis to exercise test was 3 (1-5) days. Patients with suprainguinal DVT demonstrated significantly shorter median (IQR) MWD than those with infrainguinal DVT (130 (61-202) m vs 565 (128-750) m; P < .01), while PWD did not significantly differ (PWD: 20 (0-30) m vs 40 (0-222) m; P = .14). The proportion of patients who had to terminate treadmill tests prematurely was higher in patients with suprainguinal DVT (91.7% vs 57.7%; P = .04). PWD and MWD seemed to be similar in patients with and without a history of DVT. Premature test termination and suprainguinal DVT location were associated with reduced quality of life, as measured by the EuroQoL Group 5-Dimension 5-Level questionnaire and visual analog scale. Conclusion: Suprainguinal DVT was linked to a more pronounced walking impairment compared with infrainguinal DVT. Limited walking capacity was associated with a reduced quality of life.

Capillaroscopic differences between primary Raynaud phenomenon and healthy controls indicate potential microangiopathic involvement in benign vasospasms.

BACKGROUND: For primary Raynaud phenomenon (PRP), an otherwise unexplained vasospastic disposition is assumed. To test the hypothesis of an additional involvement of distinct ultrastructural microvascular alterations, we compared the nailfold capillary pattern of patients with PRP and healthy controls. METHODS: A total of 120 patients with PRP (with a median duration of vasospastic symptoms of 60 [IQR: 3-120] months) were compared against 125 controls. In both groups, nailfold capillaroscopy was performed to record the presence of dilatations, capillary edema, tortuous capillaries, ramifications, hemorrhages, and reduced capillary density and to determine a semiquantitative rating score. Further, the capacity of finger skin rewarming was investigated by performing infrared thermography in combination with cold provocation. RESULTS: Unspecific morphologic alterations were found in both, PRP, such as controls, whereby the risk for PRP was four times as high in the presence of capillary dilations (CI: 2.3-7.6) and five times as high if capillary density was reduced (CI: 1.9-13.5). Capillary density correlated with thermoregulatory capacity in both hands in the PRP group, but not in controls. In addition, a negative correlation between the microangiopathy score and the percentage degree of rewarming in both hands was found for patients with PRP only. CONCLUSION: We found specific differences within the microvascular architecture between patients with PRP and controls. As a conclusion, PRP may not be an entirely benign vasospastic phenomenon, but might be associated with subtle microcirculatory vasculopathy. In addition, we suggest that the implementation of a scoring system might serve as guidance in the diagnostic process at least of patients with long-standing PRP.

Fourier phase index for extracting signatures of determinism and nonlinear features in time series.

Detecting determinism and nonlinear properties from empirical time series is highly nontrivial. Traditionally, nonlinear time series analysis is based on an error-prone phase space reconstruction that is only applicable for stationary, largely noise-free data from a low-dimensional system and requires the nontrivial adjustment of various parameters. We present a data-driven index based on Fourier phases that detects determinism at a well-defined significance level, without using Fourier transform surrogate data. It extracts nonlinear features, is robust to noise, provides time-frequency resolution by a double running window approach, and potentially distinguishes regular and chaotic dynamics. We test this method on data derived from dynamical models as well as on real-world data, namely, intracranial recordings of an epileptic patient and a series of density related variations of sediments of a paleolake in Tlaxcala, Mexico.

Can Clinical Assessment of Postural Control Explain Locomotive Body Function, Mobility, Self-Care and Participation in Children with Cerebral Palsy?

Trunk control may influence self-care, mobility, and participation, as well as how children living with cerebral palsy (CP) move around. Mobility and Gross Motor performance are described over environmental factors, while locomotion can be understood as the intrinsic ontogenetic automatic postural function of the central nervous system, and could be the underlying element explaining the relationship between these factors. Our goal is to study the correlation among Trunk Control Measurement Scale (TCMS) and Pediatric Evaluation of Disability Inventory (PEDI) domains, as well as Locomotor Stages (LS). METHODS: A feasibility observational analysis was designed including 25 children with CP who were assessed with these scales. RESULTS: The strong correlation confirms higher levels of trunk control in children with better self-care, mobility and participation capacities. Strong correlations indicate also that higher LS show better levels of PEDI and TCMS domains. CONCLUSIONS: Our results suggest that more mature LS require higher levels of trunk control, benefitting self-care, mobility and social functions.

Femoral vessel complications after transfemoral TAVR-A contemporary sonography-based assessment of 480 patients with third-generation transcatheter valves.

BACKGROUND: Postinterventional sonographic assessment of the femoral artery after transfemoral transcatheter aortic valve replacement (TF-TAVR) has the potential to identify several pathologies. We investigated the incidence and risk factors of femoral vessel complications in a modern TAVR collective using postinterventional sonography. METHODS: Between September 2017 and March 2022, 480 patients underwent TF-TAVR with postinterventional femoral sonography at a single center. Clinical outcomes and adverse events were analyzed after the Valve Academic Research Consortium 3 (VARC-3) criteria. RESULTS: In this cohort (51.2% male; age 80 ± 7.5 years, median EuroSCORE II 3.7) 74.8% (n = 359) were implanted with a self-expandable and 25.2% (n = 121) with a balloon-expandable valve. The main access (valve-delivery) was located right in 91.4% (n = 438), and the primary closure system was Proglide in 95% (n = 456). Vascular complications (VC) were observed in 29.16% (n = 140) of patients; 23.3% (n = 112) presented with minor- and 5.8% (n = 28) with major VC. Postinterventional femoral artery stenosis on the main access was observed in 9.8% (n = 47). Multivariable logistic regression analysis revealed female sex (p = .03, odds ratio [OR] 2.32, 95% confidence interval [CI] 1.09-4.89) and the number of used endovascular closure devices (p = .014, OR 0.11, 95%CI 0.02-0.64) as predictive factors for femoral artery stenosis. CONCLUSIONS: The incidence of postinterventional femoral artery stenosis following TF-TAVR was higher than expected with a number of used closure devices and female sex being independent risk factors. Considering the continuous advance of TAVR in low-risk patients with preserved physical activity, emphasis should be directed at the correct diagnosis and follow-up of these complications.

Driveline infections in left ventricular assist devices-Incidence, epidemiology, and staging proposal.

BACKGROUND: Driveline infections (DLI) are a serious complication in patients with left ventricular assist devices (LVAD). Apart from the differentiation between superficial and deep DLI, there is no consensus on the classification of the severity of DLI. Little is known about risk factors and typical bacteria causing DLI in centrifugal-flow LVADs. METHODS: In this single-center study with 245 patients, DLI were classified by their local appearance using a modification of a score suggested by the Sharp Memorial group. The driveline exit site was inspected routinely every 6 months. RESULTS: Severe DLI were detected in 34 patients (15%) after 6 months and in 24 patients (22%) after 24 months. The proportion of patients with DLI increased significantly during the follow-up (p = 0.0096). The most common bacteria in local smears were Corynebacterium, coagulase-negative Staphylococcus, and Staphylococcus aureus. Fifty-nine patients were hospitalized more than once for DLI. In these patients, S. aureus was the most common bacterium. It was also the most common bacterium in blood cultures. Higher BMI, no partnership, and a HeartMate 3 device were identified as risk factors for DLI in a multivariable cause-specific Cox regression. CONCLUSION: This study is a standardized analysis of DLI in a large cohort with centrifugal-flow LVADs.

Markers of oxidative stress during post-COVID-19 fatigue: a hypothesis-generating, exploratory pilot study on hospital employees.

Introduction: Post-COVID-19 fatigue is common after recovery from COVID-19. Excess formation of reactive oxygen species (ROS) leading to oxidative stress-related mitochondrial dysfunction is referred to as a cause of these chronic fatigue-like symptoms. The present observational pilot study aimed to investigate a possible relationship between the course of ROS formation, subsequent oxidative stress, and post-COVID-19 fatigue. Method: A total of 21 post-COVID-19 employees of the General Hospital Nuremberg suffering from fatigue-like symptoms were studied during their first consultation (T1: on average 3 months after recovery from COVID-19), which comprised an educational talk on post-COVID-19 symptomatology and individualized outpatient strategies to resume normal activity, and 8 weeks thereafter (T2). Fatigue severity was quantified using the Chalder Fatigue Scale together with a health survey (Patient Health Questionnaire) and self-report on wellbeing (12-Item Short-Form Health Survey). We measured whole blood superoxide anion (O2•-) production rate (electron spin resonance, as a surrogate for ROS production) and oxidative stress-induced DNA strand breaks (single cell gel electrophoresis: "tail moment" in the "comet assay"). Results: Data are presented as mean ± SD or median (interquartile range) depending on the data distribution. Differences between T1 and T2 were tested using a paired Wilcoxon rank sign or t-test. Fatigue intensity decreased from 24 ± 5 at T1 to 18 ± 8 at T2 (p < 0.05), which coincided with reduced O2•- formation (from 239 ± 55 to 195 ± 59 nmol/s; p < 0.05) and attenuated DNA damage [tail moment from 0.67 (0.36-1.28) to 0.32 (0.23-0.71); p = 0.05]. Discussion: Our pilot study shows that post-COVID-19 fatigue coincides with (i) enhanced O2•- formation and oxidative stress, which are (ii) reduced with attenuation of fatigue symptoms.

Evidence mapping on how to perform an optimal surgical repair of large hiatal hernias.

BACKGROUND: Symptomatic and large hiatal hernia (HH) is a common disorder requiring surgical management. However, there is a lack of systematic, evidence-based recommendations summarizing recent reviews on surgical treatment of symptomatic HH. Therefore, this systematic review aimed to create evidence mapping on the key technical issues of HH repair based on the highest available evidence. METHODS: A systematic review identified studies on eight key issues of large symptomatic HH repair. The literature was screened for the highest level of evidence (LE from level 1 to 5) according to the Oxford Center for evidence-based medicine's scale. For each topic, only studies of the highest available level of evidence were considered. RESULTS: Out of the 28.783 studies matching the keyword algorithm, 47 were considered. The following recommendations could be deduced: minimally invasive surgery is the recommended approach (LE 1a); a complete hernia sac dissection should be considered (LE 3b); extensive division of short gastric vessels cannot be recommended; however, limited dissection of the most upper vessels may be helpful for a floppy fundoplication (LE 1a); vagus nerve should be preserved (LE 3b); a dorso-ventral cruroplasty is recommended (LE 1b); routine fundoplication should be considered to prevent postoperative gastroesophageal reflux (LE 2b); posterior partial fundoplication should be favored over other forms of fundoplication (LE 1a); mesh augmentation is indicated in large HH with paraesophageal involvement (LE 1a). CONCLUSION: The current evidence mapping is a reasonable instrument based on the best evidence available to guide surgeons in determining optimal symptomatic and large HH repair.

Synthesis and Structure Elucidation of Glutamyl-Queuosine.

Queuosine is one of the most complex hypermodified RNA nucleosides found in the Wobble position of tRNAs. In addition to Queuosine itself, several further modified derivatives are known, where the cyclopentene ring structure is additionally modified by a galactosyl-, a mannosyl-, or a glutamyl-residue. While sugar-modified Queuosine derivatives are found in the tRNAs of vertebrates, glutamylated Queuosine (gluQ) is only known in bacteria. The exact structure of gluQ, particularly with respect to how and where the glutamyl side chain is connected to the Queuosine cyclopentene side chain, is unknown. Here we report the first synthesis of gluQ and, using UHPLC-MS-coinjection and NMR studies, we show that the isolated natural gluQ is the α-allyl-connected gluQ compound.

Changes in hospital staff' mental health during the Covid­19 pandemic: Longitudinal results from the international COPE-CORONA study.

This longitudinal study aimed to explore anxiety and depressive symptoms, individual resources, and job demands in a multi-country sample of 612 healthcare workers (HCWs) during the COVID-19 pandemic. Two online surveys were distributed to HCWs in seven countries (Germany, Andorra, Ireland, Spain, Italy, Romania, Iran) during the first (May-October 2020, T1) and the second (February-April 2021, T2) phase of the pandemic, assessing sociodemographic characteristics, contact with COVID-19 patients, anxiety and depressive symptoms, self-compassion, sense of coherence, social support, risk perception, and health and safety at the workplace. HCWs reported a significant increase in depressive and anxiety symptoms. HCWs with high depressive or anxiety symptoms at T1 and T2 reported a history of mental illness and lower self-compassion and sense of coherence over time. Risk perception, self-compassion, sense of coherence, and social support were strong independent predictors of depressive and anxiety symptoms at T2, even after controlling for baseline depressive or anxiety symptoms and sociodemographic variables. These findings pointed out that HCWs during the COVID-19 outbreak experienced a high burden of psychological distress. The mental health and resilience of HCWs should be supported during disease outbreaks by instituting workplace interventions for psychological support.

Machine learning methods and harmonized datasets improve immunogenic neoantigen prediction.

The accurate selection of neoantigens that bind to class I human leukocyte antigen (HLA) and are recognized by autologous T cells is a crucial step in many cancer immunotherapy pipelines. We reprocessed whole-exome sequencing and RNA sequencing (RNA-seq) data from 120 cancer patients from two external large-scale neoantigen immunogenicity screening assays combined with an in-house dataset of 11 patients and identified 46,017 somatic single-nucleotide variant mutations and 1,781,445 neo-peptides, of which 212 mutations and 178 neo-peptides were immunogenic. Beyond features commonly used for neoantigen prioritization, factors such as the location of neo-peptides within protein HLA presentation hotspots, binding promiscuity, and the role of the mutated gene in oncogenicity were predictive for immunogenicity. The classifiers accurately predicted neoantigen immunogenicity across datasets and improved their ranking by up to 30%. Besides insights into machine learning methods for neoantigen ranking, we have provided homogenized datasets valuable for developing and benchmarking companion algorithms for neoantigen-based immunotherapies.

A decrease in the age of respired carbon from the terrestrial biosphere and increase in the asymmetry of its distribution.

We provide here a model-based estimate of the transit time of carbon through the terrestrial biosphere, since the time of carbon uptake through photosynthesis until its release through respiration. We explored the consequences of increasing productivity versus increasing respiration rates on the transit time distribution and found that while higher respiration rates induced by higher temperature increase the transit time because older carbon is respired, increases in productivity cause a decline in transit times because more young carbon is available to supply increased metabolism. The combined effect of increases in temperature and productivity results in a decrease in transit times, with the productivity effect dominating over the respiration effect. By using an ensemble of simulation trajectories from the Carbon Data Model Framework (CARDAMOM), we obtained time-dependent transit time distributions incorporating the twentieth century global change. In these simulations, transit time declined over the twentieth century, suggesting an increased productivity effect that augmented the amount of respired young carbon, but also increasing the release of old carbon from high latitudes. The transit time distribution of carbon becomes more asymmetric over time, with more carbon transiting faster through tropical and temperate regions, and older carbon being respired from high latitude regions. This article is part of the Theo Murphy meeting issue 'Radiocarbon in the Anthropocene'.

Career goals of surgeons in Switzerland.

PURPOSE: Recent studies from the United States and Germany have shown a general decline in the number of surgical residents, as trainees increasingly prioritize a positive work-life balance. The current study sought to evaluate the career goals of surgeons in Switzerland. METHODS: Members of the Swiss College of Surgeons, being surgical consultant or attending regardless of specialty, were surveyed online as to their purported career goals, future employment ideals, aspired leadership positions, and managerial training. RESULTS: A total of 269 questionnaires were analysed. Most participants (93%) were board- certified and 30% of participants were female. With regard to desired specialty, 50% of participants intended to pursue a career in visceral surgery followed by general surgery, traumatology, hand and plastic surgery, vascular surgery and thoracic surgery. Regardless of specialty, 53% of respondents strived for the position of senior physician, while 28% indicated a desire to become chief physician. In terms of work environment, most participants preferred to seek employment at a cantonal hospital, followed by a rural hospital, a university hospital, private practice or a non-clinical setting. About half of respondents favoured the option of part time employment of 80% or less and about a quartile intended to retire before 62 years of age. CONCLUSION: The current study found that surgeons in Switzerland remain highly motivated to pursue leadership positions in their respective fields. Going forward, the challenge will lie in reconciling the needs of the respective departments with the personal ambition, career opportunities, and desired work-life balance of young trainees.

Small volume bone marrow aspirates with high progenitor cell concentrations maximize cell therapy dose manufacture and substantially reduce donor hemoglobin loss.

BACKGROUND: Bone marrow (BM) transplantation is a life-saving therapy for hematological diseases, and the BM harbors also highly useful (progenitor) cell types for novel cell therapies manufacture. Yet, the BM collection technique is not standardized. METHODS: Benchmarking our collection efficiency to BM collections worldwide (N = 1248), we noted a great variability of total nucleated cell (TNC) yields in BM products (HPC-M) with superior performance of our center, where we have implemented a small volume aspirate policy. Thus, we next prospectively aimed to assess the impact of BM collection technique on HPC-M quality. For each BM collection (N = 20 donors), small volume (3 mL) and large volume (10 mL) BM aspirates were sampled at 3 time points and analyzed for cell composition. RESULTS: Compared to large volume aspirates, small volume aspirates concentrated more TNCs, immune cells, platelets, hematopoietic stem/progenitor cells, mesenchymal stromal cells (MSCs), and endothelial progenitors. Inversely, the hemoglobin concentration was higher in large volume aspirates indicating more hemoglobin loss. Manufacturing and dosing scenarios showed that small volume aspirates save up to 42% BM volume and 44% hemoglobin for HPC-M donors. Moreover, MSC production efficiency can be increased by more than 150%. CONCLUSIONS: We propose to consider small volume BM aspiration as standard technique for BM collection.

Schistosomiasis (Schistosoma mansoni)-a rare cause of complex liver cysts.

In this paper, we describe the case of a 40-year-old patient with an expanding and symptomatic complex liver cyst. Despite comprehensive diagnostics, including labs, imaging and biopsy, a clear etiology could not be determined. As a result, a partial liver resection was performed. The histopathological examination revealed evidence of schistosomas. We postulate that the displacement of the portal fields created a pseudocyst and that the resultant ischemia was the root cause of the patient's discomfort. Postoperatively, the patient received an antihelmintic therapy with praziquantel with which she was able to fully recover.