julilili42/papers huggingface dataset:
The morphological consequences of segmentation anomalies in the human sacrum
2021-12-29

Abstract Objectives Despite the high frequency of segmentation anomalies in the human sacrum, their evolutionary and clinical implications remain controversial. Specifically, inconsistencies involving the classification and counting methods obscure accurate assessment of lumbosacral transitional vertebrae. Therefore, we aim to establish more reliable morphological and morphometric methods for differentiating between sacralizations and lumbarizations in clinical and paleontological contexts. Materials and Methods Using clinical CT data from 145 individuals aged 14–47 years, vertebral counts and the spatial relationship between the sacrum and adjoining bony structures were assessed, while the morphological variation of the sacrum was assessed using geometric morphometrics based on varied landmark configurations. Results The prevalence of lumbosacral and sacrococcygeal segmentation anomalies was 40%. Lumbarizations and sacralizations were reliably distinguishable based on the spatial relationship between the iliac crest and the upward or downward trajectory of the linea terminalis on the sacrum. Different craniocaudal orientations of the alae relative to the corpus of the first sacral vertebra were also reflected in the geometric morphometric analyses. The fusion of the coccyx (32%) was frequently coupled with lumbarizations, suggesting that the six‐element sacra more often incorporate the coccyx rather than the fifth lumbar vertebra. Conclusions Our approach allowed the consistent identification of segmentation anomalies even in isolated sacra. Additionally, our outcomes either suggest that homeotic border shifts often affect multiple spinal regions in a unidirectional way, or that sacrum length is highly conserved perhaps due to functional constraints. Our results elucidate the potential clinical, biomechanical, and evolutionary significance of lumbosacral transitional vertebrae.
Interfaces between Different Iron Phthalocyanines and Au(111): Influence of the Fluorination on Structure and Interfacial Interactions
2021-12-29

The interface properties of iron phthalocyanine (FePc) as well as partially fluorinated and perfluorinated iron phthalocyanine (FePcF4 and FePcF16) have been studied and compared. Well-ordered monolayers have been prepared and investigated with scanning tunneling microscopy (STM). X-ray photoelectron spectroscopy (XPS) and ultraviolet photoelectron spectroscopy (UPS) have been used to study the electronic structure of FePcFx in the monolayer in comparison with FePcFx in thin films. While the fluorination changes the structural ordering as well the total interface dipole, local interactions of the central iron atom and the Au(111) surface remain unchanged. The interplay of substrate–molecule and intermolecular interactions is discussed.
High‐resolution neural network‐driven mapping of multiple diffusion metrics leveraging asymmetries in the balanced steady‐state free precession frequency profile
2021-12-29

We propose to utilize the rich information content about microstructural tissue properties entangled in asymmetric balanced steady‐state free precession (bSSFP) profiles to estimate multiple diffusion metrics simultaneously by neural network (NN) parameter quantification. A 12‐point bSSFP phase‐cycling scheme with high‐resolution whole‐brain coverage is employed at 3 and 9.4 T for NN input. Low‐resolution target diffusion data are derived based on diffusion‐weighted spin‐echo echo‐planar‐imaging (SE‐EPI) scans, that is, mean, axial, and radial diffusivity (MD, AD, and RD), fractional anisotropy (FA), as well as the spherical coordinates (azimuth Φ and inclination Θ) of the principal diffusion eigenvector. A feedforward NN is trained with incorporated probabilistic uncertainty estimation. The NN predictions yielded highly reliable results in white matter (WM) and gray matter structures for MD. The quantification of FA, AD, and RD was overall in good agreement with the reference but the dependence of these parameters on WM anisotropy was somewhat biased (e.g. in corpus callosum). The inclination Θ was well predicted for anisotropic WM structures, while the azimuth Φ was overall poorly predicted. The findings were highly consistent across both field strengths. Application of the optimized NN to high‐resolution input data provided whole‐brain maps with rich structural details. In conclusion, the proposed NN‐driven approach showed potential to provide distortion‐free high‐resolution whole‐brain maps of multiple diffusion metrics at high to ultrahigh field strengths in clinically relevant scan times.
Increased persuadability and credulity in people with corpus callosum dysgenesis
2021-12-29

Abstract Corpus callosum dysgenesis is one of the most common congenital neurological malformations. Despite being a clear and identifiable structural alteration of the brain’s white matter connectivity, the impact of corpus callosum dysgenesis on cognition and behaviour has remained unclear. Here we build upon past clinical observations in the literature to define the clinical phenotype of corpus callosum dysgenesis better using unadjusted and adjusted group differences compared with a neurotypical sample on a range of social and cognitive measures that have been previously reported to be impacted by a corpus callosum dysgenesis diagnosis. Those with a diagnosis of corpus callosum dysgenesis ( n = 22) demonstrated significantly higher persuadability, credulity, and insensitivity to social trickery than neurotypical ( n = 86) participants, after controlling for age, sex, education, autistic-like traits, social intelligence, and general cognition. To explore this further, machine learning, utilising a set neurotypical sample for training the normative covariance structure of our psychometric variables, was used to test whether these dimensions possessed the capability to discriminate between a test-set of neurotypical and corpus callosum dysgenesis participants. We found that participants with a diagnosis of corpus callosum dysgenesis were best classed within dimension space along the same axis as persuadability, credulity, and insensitivity to social trickery after controlling for age and sex, with Leave-One-Out-Cross-Validation across 250 training-set permutations providing a mean accuracy of 71.7%. These results have wide- reaching implications for a) the characterisation of corpus callosum dysgenesis, and b) the role of the corpus callosum in social inference.
Global maps of soil temperature
2021-12-30

Abstract Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1‐km 2 resolution for 0–5 and 5–15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1‐km 2 pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse‐grained air temperature estimates from ERA5‐Land (an atmospheric reanalysis by the European Centre for Medium‐Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (−0.7 ± 2.3°C). The observed substantial and biome‐specific offsets emphasize that the projected impacts of climate and climate change on near‐surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil‐related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications.
Bioavailability and Cardiometabolic Effects of Xanthohumol: Evidence from Animal and Human Studies
2021-12-30

Abstract Xanthohumol is the main prenylflavonoid in hops and has been associated with a wide range of health benefits, due to its anti‐inflammatory, anti‐oxidative, and cancer‐preventive properties. Increasing evidence suggests that xanthohumol positively affects biomarkers associated with metabolic syndrome and cardiovascular diseases (CVDs). This review summarizes the effects of xanthohumol supplementation on body weight, lipid and glucose metabolism, systemic inflammation, and redox status. In addition, it provides insights into the pharmacokinetics of xanthohumol intake. Animal studies show that xanthohumol exerts beneficial effects on body weight, lipid profile, glucose metabolism, and other biochemical parameters associated with metabolic syndrome and CVDs. Although in vitro studies are increasingly elucidating the responsible mechanisms, the overall in vivo results are currently inconsistent and quantitatively insufficient. Pharmacokinetic and safety studies confirm that intake of xanthohumol is safe and well tolerated in both animals and humans. However, little is known about the metabolism of xanthohumol in the human body, and even less about its effects on body weight and CVD risk factors. There is an urgent need for studies investigating whether the effects of xanthohumol on body weight and cardiometabolic parameters observe in animal studies are reproducible in humans, and what dosage, formulation, and intervention period are required.
Temporal Analysis of Protein Ubiquitylation and Phosphorylation During Parkin-Dependent Mitophagy
2021-12-30

Mitophagy, the selective degradation of mitochondria by autophagy, affects defective mitochondria following damage or stress. At the onset of mitophagy, parkin ubiquitylates proteins on the mitochondrial outer membrane. While the role of parkin at the onset of mitophagy is well understood, less is known about its activity during later stages in the process. Here, we used HeLa cells expressing catalytically active or inactive parkin to perform temporal analysis of the proteome, ubiquitylome, and phosphoproteome during 18 h after induction of mitophagy by mitochondrial uncoupler carbonyl cyanide m-chlorophenyl hydrazine. Abundance profiles of proteins downregulated in parkin-dependent manner revealed a stepwise and "outside-in" directed degradation of mitochondrial subcompartments. While ubiquitylation of mitochondrial outer membrane proteins was enriched among early parkin-dependent targets, numerous mitochondrial inner membrane, matrix, and cytosolic proteins were also found ubiquitylated at later stages of mitophagy. Phosphoproteome analysis revealed a possible crosstalk between phosphorylation and ubiquitylation during mitophagy on key parkin targets, such as voltage-dependent anion channel 2.
Paraquat sorption- and organic matter-induced modifications of soil spectral induced polarization (SIP) signals
2021-12-30

SUMMARY Quantifying the capacity of soils to immobilize sorbing contaminants of concern relies on batch sorption experiments, typically performed at skewed solid-to-liquid ratios. The geophysical method spectral induced polarization (SIP) provides a powerful non-invasive monitoring alternative that can capture changes in soil electrical properties driven by contaminant sorption, yielding an approach whereby immobilization can be monitored in situ. Here, we present SIP signals obtained from a series of columns packed with a water saturated natural sandy-loam soil, with and without solid organic matter (SOM) amendment, contaminated with increasing concentrations of the herbicide paraquat. Our results highlight that soil polarization drops proportional to increasing amounts of sorbed paraquat in the SOM-free soil, exhibiting a Langmuir-type leveling-off behaviour. The addition of 8 percent-SOM yielded an increase in both the real ( ) and imaginary ( ) conductivity of the uncontaminated treatment, driven by the contribution of charged sites in the SOM. Further, SOM modified the dependence between and sorbed paraquat, likely driven by continued polarization within the polydisperse SOM with continued paraquat addition. However, the time constant ( ), derived using the Cole–Cole model, shed light on a saturation-type dependence governed by a drop in ion mobility with increasing sorption. Thus, aiding the interpretation of sorption-driven SIP signals.
Cultural similarities and specificities of finger counting and montring: evidence from Amazon Tsimane’ people
2021-12-30

Numerical Cognition might be embodied, that is, grounded in bodily actions. This claim is supported by the observation that, potentially due to our shared biology, finger counting is prevalent among a variety of cultures. Differences in finger counting are apparent even within Western cultures. Relatively few indigenous cultures have been systematically analyzed in terms of traditional finger counting and montring (i.e., communicating numbers with fingers) routines. Even fewer studies used the same protocols across cultures, allowing for a systematic comparison of indigenous and Western finger counting routines. We analyze the finger counting and montring routines of Tsimane’ (N = 121), an indiginous people living in the Bolivian Amazon rainforest, depending on handedness, education level, and exposure to mainstream, industrialised Bolivian culture. Tsimane' routines are compared with those of German and British participants. Tsimane’ reveal a greater variation in finger counting and montring routines, which seems to be modified by their education level. We outline a framework on how different factors such as handedness and reading direction might affect cross-cultural and within-cultural variation in finger counting.
Corporate Wealth Over Public Health? Assessing the Resilience of Developing Countries' COVID-19 Responses Against Investment Claims and the Implications for Future Public Health Crises
2021-12-30

In the wake of the Covid-19 pandemic, states around the world swiftly enacted a multitude of far-reaching emergency responses to contain the viruses’ spread and to cope with the economic repercussions of the ensuing crisis. However, these measures detrimentally impacted the operating conditions of many businesses or, at the least, decreased their profitability. As this inevitably affected foreign investments, investors could be tempted to invoke “Investor State Dispute Settlement” (“ISDS”) clauses in International Investment Agreements (IIAs) to initiate proceedings before arbitral tribunals and seek compensation for loss of profit caused by states’ Covid-19 responses. Due to the specific circumstances in most developing countries, they were hit particularly hard by the crisis and are especially vulnerable to the threat of investment claims. It is therefore important to enable developing countries to realistically anticipate the risk of investment arbitration by assessing the chances of success of foreign investment claims against those policies that were most frequently adopted by them amidst the crisis. Against this background, this paper assesses how likely developing countries’ Covid-19 responses breached substantive standards of investor treatment under typical IIAs and which defense strategies states may invoke to justify their regulatory action. Based on this analysis, this paper concludes by formulating policy recommendations on how developing countries may enhance the resilience of their emergency responses against foreign investors amidst future public health crises.
Palaeomagnetic indication for India–Asia collision at 12°N and maximum 810 km Greater India extent in the western suture zone
2021-12-31

SUMMARY Knowing the pre-collisional extent of the northern Indian Plate margin (‘Greater India’) is vital to understanding the tectonic evolution of the India–Asia collision and the formation of the Himalayan–Tibetan orogen. However, suitable geological units for palaeomagnetic investigations along the Himalayan belt are limited, which makes it difficult to reconstruct Greater India during the pre-collisional period in Late Cretaceous to Palaeogene. Often the palaeomagnetic results from the Zongpu Formation at Gamba in southern Tibet (∼88.5°E) were used for estimates of Greater India, but their validity was recently questioned. As a contribution to closing the data gap, we performed a palaeomagnetic study of the Palaeocene/Lower Eocene Dibling limestone (DL) in the western Tethyan Himalaya of Zanskar (34.0°N/76.6°E). The results from 27 sites revealed a well grouping (k = 71.7) syntectonic magnetization with best grouping at 52 per cent unfolding. The remagnetization of the DL was acquired shortly after ∼54 Ma, at the latest at ∼49 Ma, and is probably carried by fine-grained magnetite formed during the early orogenic phase. Assuming proportional tilting of the fold limbs, the corresponding palaeolatitude of 11.8 ± 2.4°N suggests a maximum Greater India extent of 810 ± 420 km and a first continental contact with the southern Eurasian margin at ∼12°N in the western part of the suture zone. The tectonostratigraphic equivalence of the DL with the Zongpu Formation at Gamba and a great similarity in their magnetic properties supports a secondary origin of the Gamba results. Through understanding the mechanism of remagnetization in the DL, an early orogenic remanence acquisition is also indicated for the Zongpu Formation, and thus the Gamba results deserve further credit for Greater India reconstructions. However, we note a large inconsistency of the available Late Cretaceous and Palaeogene palaeolatitude data from the Tethyan Himalaya by up to ∼20°, corresponding to differences of up to ∼2000 km in the size of Greater India. These discrepancies require further palaeomagnetic work in the Tethyan Himalaya, and in particular we recommend comparative studies at same locations and of same units.
Beyond Bogoliubov dynamics
2021-12-31

We consider a system of N interacting bosons in the mean-field scaling regime and construct corrections to the Bogoliubov dynamics that approximate the true N-body dynamics in norm to arbitrary precision. The N-independent corrections are given in terms of the solutions of the Bogoliubov and Hartree equations and satisfy a generalized form of Wick's theorem. We determine the n-point correlation functions of the excitations around the condensate, as well as the reduced densities of the N-body system, to arbitrary accuracy, given only the knowledge of the two-point functions of a quasi-free state and the solution of the Hartree equation. In this way, the complex problem of computing all n-point correlation functions for an interacting N-body system is essentially reduced to the problem of solving the Hartree equation and the PDEs for the Bogoliubov two-point functions.
Urinary Tract Infections in Kidney Transplant Recipients—Is There a Need for Antibiotic Stewardship?
2021-12-31

(1) Background: Urinary tract infections (UTI) are the most common infections after kidney transplantation. Given the risk of urosepsis and the potential threat to the graft, the threshold for treating UTI and asymptomatic bacteriuria with broad spectrum antibiotics is low. Historically fluoroquinolones were prescription favorites for patients that underwent kidney transplantation (KT). After the recent recommendation to avoid them in these patients, however, alternative treatment strategies need to be investigated (2) Methods: We retrospectively analyzed the charts of 207 consecutive adult kidney transplantations that were performed at the department of General, Visceral and Transplantation Surgery of the University Hospital of Tuebingen between January 2015 and August 2020. All charts were screened for the diagnosis and treatment of asymptomatic bacteriuria (ASB) and urinary tract infections (UTI) and the patients’ clinical characteristics and outcomes were evaluated. (3) Results: Of the 207 patients, 68 patients suffered from urinary tract infections. Patients who developed UTI had worse graft function at discharge (p = 0.024) and at the 12 months follow-up (p &lt; 0.001). The most commonly prescribed antibiotics were Ciprofloxacin and Piperacillin/Tazobactam. To both, bacterial resistance was more common in the study cohort than in the control group. (4) Conclusions: Urinary tract infections appear to be linked to worse graft functions. Thus, prevention and treatment should be accompanied by antibiotic stewardship teams.
Alveolar Echinococcosis—A Challenging Task for the Hepatobiliary Surgeon
2021-12-31

(1) Background: Alveolar echinococcosis (AE) is an ultimately fatal disease, whose only curative treatment is surgery. Due to its late presentation extended liver resections are often necessary. The true benefit of extensive surgery has yet to be established; (2) Methods: We present a single center experience of 33 cases of Echinococcus multilocularis that have been treated at a high-volume hepatobiliary surgery center between 2004 and 2021. (3) Results: Of the 33 patients 24 patients underwent major liver resection (73%). In addition to the liver resection patients frequently underwent complex extrahepatic procedures such as lymphadenectomy (n = 21, 61%), vascular resections and reconstructions (n = 9, 27%) or resections and reconstruction of the extrahepatic bile duct (n = 11, 33%). Seven patients suffered from ≥ grade III complications (21%). Complete resection was achieved in 17 patients. Fourteen patients had R1 resections and two had macroscopic parasitic remnant (R2). Progressive disease was reported in three patients (The two R2 patients and one R1 resected patient). At a median follow-up of 54 months no mortality has occurred in our cohort; (4) Conclusions: Liver resection remains the gold standard for AE. Even in extensive disease the combination of complex resection and perioperative benzimidazoles can achieve favorable long-term outcomes.
Generation of Lasso Peptide-Based ClpP Binders
2021-12-31

The Clp protease system fulfills a plethora of important functions in bacteria. It consists of a tetradecameric ClpP barrel holding the proteolytic centers and two hexameric Clp-ATPase rings, which recognize, unfold, and then feed substrate proteins into the ClpP barrel for proteolytic degradation. Flexible loops carrying conserved tripeptide motifs protrude from the Clp-ATPases and bind into hydrophobic pockets (H-pockets) on ClpP. Here, we set out to engineer microcin J25 (MccJ25), a ribosomally synthesized and post-translationally modified peptide (RiPP) of the lasso peptide subfamily, by introducing the conserved tripeptide motifs into the lasso peptide loop region to mimic the Clp-ATPase loops. We studied the capacity of the resulting lasso peptide variants to bind to ClpP and affect its activity. From the nine variants generated, one in particular (12IGF) was able to activate ClpP from Staphylococcus aureus and Bacillus subtilis. While 12IGF conferred stability to ClpP tetradecamers and stimulated peptide degradation, it did not trigger unregulated protein degradation, in contrast to the H-pocket-binding acyldepsipeptide antibiotics (ADEPs). Interestingly, synergistic interactions between 12IGF and ADEP were observed.