julilili42/papers huggingface dataset:
Epipalaeolithic animal tending to Neolithic herding at Abu Hureyra, Syria (12,800–7,800 calBP): Deciphering dung spherulites
2022-09-14

Excavations at Abu Hureyra, Syria, during the 1970s exposed a long sequence of occupation spanning the transition from hunting-and-gathering to agriculture. Dung spherulites preserved within curated flotation samples from Epipalaeolithic (ca. 13,300–11,400 calBP) and Neolithic (ca. 10,600–7,800 calBP) occupations are examined here alongside archaeological, archaeobotanical, and zooarchaeological data to consider animal management, fuel selection, and various uses of dung. Spherulites were present throughout the entire sequence in varying concentrations. Using a new method to quantify spherulites, exclusion criteria were developed to eliminate samples possibly contaminated with modern dung, strengthening observations of ancient human behavior. Darkened spherulites within an Epipalaeolithic 1B firepit (12,800–12,300 calBP) indicate burning between 500–700°C, documenting early use of dung fuel by hunter-gatherers as a supplement to wood, coeval with a dramatic shift to rectilinear architecture, increasing proportions of wild sheep and aurochsen, reduced emphasis on small game, and elevated dung concentrations immediately outside the 1B dwelling. Combined, these observations suggest that small numbers of live animals (possibly wild sheep) were tended on-site by Epipalaeolithic hunter-gatherers to supplement gazelle hunting, raising the question of whether early experiments in animal management emerged contemporaneously with, or pre-date, cultivation. Dung was used to prepare plaster floors during the Neolithic and continued to be burned as a supplemental fuel, indicating that spherulites were deposited via multiple human- and animal-related pathways. This has important implications for interpretations of archaeobotanical assemblages across the region. Spherulite concentrations dropped abruptly during Neolithic 2B (9,300–8,000 calBP) and 2C (8,000–7,800 calBP), when sheep/goat herding surpassed gazelle hunting, possibly corresponding with movement of animals away from the site as herd sizes increased. As hunter-gatherers at Abu Hureyra began interacting with wild taxa in different ways, they set in motion a remarkable transformation in the ways people interacted with animals, plants, and their environment.
The earliest beetle †Coleopsis archaica (Insecta: Coleoptera) – morphological re-evaluation using Reflectance Transformation Imaging (RTI) and phylogenetic assessment
2022-09-14

The earliest know﻿n fossil beetle † Coleopsis archaica is re-examined using Reflectance Transformation Imaging (RTI). The morphological observations are evaluated with respect to phylogenetic implications and the early evolution of Coleoptera. † Coleopsis archaica belongs to an early Permian branch of beetles, outside a monophyletic unit comprising Coleoptera (in the widest sense) excluding †Tshekardocoleidae. This clade is mainly characterized by a complex of apomorphic features: elytra with epipleura and with a close fit with the posterior body, thus forming a tightly sealed subelytral space. In contrast to this, the elytra of † C. archaica and †Tshekardocoleidae cover the metathorax and abdomen in a loose tent-like manner and posteriorly distinctly surpass the abdominal apex. So far, no synapomorphies of the two taxa from the first half of the Permian have been identified. The very short and transverse pronotum is likely an autapomorphy of † C. archaica . A thorough documentation of the structural features of early beetle fossils should have high priority. RTI is a very promising tool to obtain new and well-founded morphological data, which will allow a thorough phylogenetic evaluation of Permian beetles in future studies. We extended the conventional RTI workflow by focus merging and panoramic stitching, in order to overcome previous limitations. Taxonomic re-arrangements of stem group beetles including † C. archaica were suggested in recent studies by A.G. Kirejtshuk and co-workers. As they are not based on shared derived features they are irrelevant in a phylogenetic and evolutionary context.
Early‐Onset and Severe Complex Hereditary Spastic Paraplegia Caused by De Novo Variants in SPAST
2022-09-14

ABSTRACT Background Familial hereditary spastic paraplegia (HSP)‐ SPAST (SPG4) typically presents with a pure HSP phenotype. Objective The aim of this study was to delineate the genotypic and phenotypic spectrum of children with de novo HSP‐ SPAST . Methods This study used a systematic cross‐sectional analysis of clinical and molecular features. Results We report the clinical and molecular spectrum of 40 patients with heterozygous pathogenic de novo variants in SPAST (age range: 2.2–27.7 years). We identified 19 unique variants (16/40 carried the same recurrent variant, p.Arg499His). Symptom onset was in early childhood (median: 11.0 months, interquartile range: 6.0 months) with significant motor and speech delay, followed by progressive ascending spasticity, dystonia, neurogenic bladder dysfunction, gastrointestinal dysmotility, and epilepsy. The mean Spastic Paraplegia Rating Scale score was 32.8 ± 9.7 (standard deviation). Conclusions These results confirm that de novo variants in SPAST lead to a severe and complex form of HSP that differs from classic familial pure HSP‐ SPAST . Clinicians should be aware of this syndrome in the differential diagnosis for cerebral palsy. © 2022 International Parkinson and Movement Disorder Society.
Restoration of native saltmarshes can reverse arthropod assemblages and trophic interactions changed by a plant invasion
2022-09-14

Abstract Plant invasions profoundly impact both natural and managed ecosystems, and removal of the invasive plants addresses only part of the problem of restoring impacted areas. The rehabilitation of diverse communities and their ecosystem functions following removal of invasive plants is an important goal of ecological restoration. Arthropod assemblages and trophic interactions are important indicators of the success of restoration, but they have largely been overlooked in saltmarshes. We determined how arthropod assemblages and trophic interactions changed with the invasion of the exotic plant Spartina alterniflora and with the restoration of the native plant Phragmites australis following Spartina removal in a Chinese saltmarsh. We investigated multiple biotic and abiotic variables to gain insight into the factors underlying the changes in arthropod assemblages and trophic structure. We found that although Spartina invasion had changed arthropod diversity, community structure, feeding‐guild composition, and the diets of arthropod natural enemies in the saltmarsh, these changes could be reversed by the restoration of native Phragmites vegetation following removal of the invader. The variation in arthropod assemblages and trophic structure were critically associated with four biotic and abiotic variables (aboveground biomass, plant density, leaf N, and soil salinity). Our findings demonstrate the positive effects of controlling invasive plants on biodiversity and nutrient cycling and provide a foundation for assessing the efficacy of ecological restoration projects in saltmarshes.
Expert consensus on fertility preservation in patients with breast cancer occurring during pregnancy
2022-09-14

The prevalence of breast cancer currently ranks first among Chinese women with malignant tumors, occurring during premenopausal childbearing age in more than 60% of patients. With the increasing age of women at childbirth, the wide application of assisted reproductive technology (ART) and the rejuvenation of tumor patients, the prevalence of breast cancer occurring during pregnancy (PrBC) is gradually increasing. There are many domestic and foreign expert consensus articles and guidelines on fertility preservation for children and patients of childbearing age with malignant tumors, but there is a lack of expert consensus or guidelines on fertility preservation for patients with PrBC. Considering the uniqueness of PrBC patients, there is an urgent need for a standardized suggestion regarding their fertility preservation. The Committee of Fertility Protection and Preservation of China Association for the Promotion of Health Science and Technology together with the Chinese Society of Gynecological Endocrinology affiliated with the International Society of Gynecological Endocrinology (CSGE-ISGE) organized relevant experts from different disciplines to formulate this consensus to guide fertility preservation of PrBC patients.
Accurate machine learning prediction of sexual orientation based on brain morphology and intrinsic functional connectivity
2022-09-14

Abstract Background Sexual orientation in humans represents a multilevel construct that is grounded in both neurobiological and environmental factors. Objective Here, we bring to bear a machine learning approach to predict sexual orientation from gray matter volumes (GMVs) or resting-state functional connectivity (RSFC) in a cohort of 45 heterosexual and 41 homosexual participants. Methods In both brain assessments, we used penalized logistic regression models and nonparametric permutation. Results We found an average accuracy of 62% (±6.72) for predicting sexual orientation based on GMV and an average predictive accuracy of 92% (±9.89) using RSFC. Regions in the precentral gyrus, precuneus and the prefrontal cortex were significantly informative for distinguishing heterosexual from homosexual participants in both the GMV and RSFC settings. Conclusions These results indicate that, aside from self-reports, RSFC offers neurobiological information valuable for highly accurate prediction of sexual orientation. We demonstrate for the first time that sexual orientation is reflected in specific patterns of RSFC, which enable personalized, brain-based predictions of this highly complex human trait. While these results are preliminary, our neurobiologically based prediction framework illustrates the great value and potential of RSFC for revealing biologically meaningful and generalizable predictive patterns in the human brain.
(DIS)SATISFACTION OF FEMALE AND EARLY-CAREER RESEARCHERS WITH THE ACADEMIC SYSTEM IN PHYSICS
2022-09-14

Modern physics encompasses theoretical and experimental research divided into subfields with specific features. For instance, high energy physics (HEP) attracts significant funding and has distinct organizational structures, i.e., large laboratories and cross-institutional collaborations. Expensive equipment and large experiments create a specific work atmosphere and human relations. While the gender imbalance is characteristic for STEM, early-career researchers are inherently dependent on their supervisors. This raises the question of how satisfied researchers working in physics are and how different subgroups−female and early-career researchers−perceive their work environment. We conducted a survey to measure job satisfaction and satisfaction with the academic system among physicists (N = 122) working in large laboratories, universities, and independent institutes. For this we used Likert-type scales. The scale for measuring the satisfaction with the academic system in physics was constructed by us. It performed statistically well and yielded three factors: experience of research autonomy, opportunities to use one's knowledge, and appreciation of the research by the general public. In our study, we detected that physicists are less satisfied with the academic system than with their work environment. Moreover, female scientists and junior researchers evaluated their jobs more negatively. The results emphasize the need for improving work and research conditions for underprivileged groups in physics. Interestingly, no significant effect was found between different types of academic institutions and general job satisfaction. Finally, participants felt that their work has not been well understood by the public.
The mechanism of macroautophagy: The movie
2022-09-14

This animated movie presents the mechanism of macroautophagy, hereafter autophagy, by showing the molecular features of the formation of autophagosomes, the hallmark organelle of this intracellular catabolic pathway. It is based on our current knowledge and it also illustrates how autophagosomes can recognize and eliminate selected cargoes.
Codiversification of gut microbiota with humans
2022-09-15

The gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. The question is whether such specificity arises from a shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification of host and microbiota, we analyzed paired gut metagenomes and human genomes for 1225 individuals in Europe, Asia, and Africa, including mothers and their children. Between and within countries, a parallel evolutionary history was evident for humans and their gut microbes. Moreover, species displaying the strongest codiversification independently evolved traits characteristic of host dependency, including reduced genomes and oxygen and temperature sensitivity. These findings all point to the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease phenotypes.
Glutamine prevents acute kidney injury by modulating oxidative stress and apoptosis in tubular epithelial cells
2022-09-15

Acute kidney injury (AKI) represents a common complication in critically ill patients that is associated with increased morbidity and mortality. In a murine AKI model induced by ischemia/reperfusion injury (IRI), we show that glutamine significantly decreases kidney damage and improves kidney function. We demonstrate that glutamine causes transcriptomic and proteomic reprogramming in murine renal tubular epithelial cells (TECs), resulting in decreased epithelial apoptosis, decreased neutrophil recruitment, and improved mitochondrial functionality and respiration provoked by an ameliorated oxidative phosphorylation. We identify the proteins glutamine gamma glutamyltransferase 2 (Tgm2) and apoptosis signal-regulating kinase (Ask1) as the major targets of glutamine in apoptotic signaling. Furthermore, the direct modulation of the Tgm2-HSP70 signalosome and reduced Ask1 activation resulted in decreased JNK activation, leading to diminished mitochondrial intrinsic apoptosis in TECs. Glutamine administration attenuated kidney damage in vivo during AKI and TEC viability in vitro under inflammatory or hypoxic conditions.
Linking the phenotype of SNCA Triplication with PET-MRI imaging pattern and alpha-synuclein CSF seeding
2022-09-15

Abstract Lewy-body pathology with aggregation of abnormal conformations of the protein alpha-synuclein (α-Syn) represent the histopathological hallmarks of Parkinson’s disease (PD). Genetic prototypes such as PD due to mutations in the alpha-synuclein gene ( SNCA ) offer the opportunity to evaluate α-Syn-related profiles in patient-derived biomaterial. We identified a family with a SNCA triplication and assessed the index patient for CSF α-Syn seeding capacity and levels of total α-Syn along with other neurodegenerative CSF markers (Aβ 1-42 , total-Tau, phospho-Tau, NFL). As no published CSF data in patients with SNCA triplication are available, we descriptively compared his CSF profiles to those of sporadic PD patients and PD patients with GBA mutations as these are also specifically associated with prominent α-Syn pathology. Additionally, skin biopsies with staining for phospho-α-Syn were done. To assess cerebral glucose metabolism and brain atrophy combined positron emission tomography and magnetic resonance imaging ([ 18 F]FDG-PET/MRI) was performed. Age at onset was 24 years and motor impairment was accompanied by prominent non-motor symptoms with early development of dementia, depression, REM sleep behavior disorder, hyposmia, and dysautonomia. Correspondingly, PET-MRI showed hypometabolism and atrophy in frontal, temporoparietal and occipital regions. CSF levels of total α-Syn were threefold higher and RT-QuIC showed remarkable α-Syn seeding activity in all kinetic categories in the SNCA Triplication patient compared to patients with GBA mutations. Our results are consistent with findings that not only mutant forms but also overexpression of the wild-type α-Syn protein lead to PD and PD dementia and show a striking CSF α-Syn seeding profile, thus substantiating the role of RT-QuIC as a specific in vivo biomarker of α-Syn brain pathology.
Community-level prevalence of epilepsy and of neurocysticercosis among people with epilepsy in the Balaka district of Malawi: A cross-sectional study
2022-09-15

Background Epilepsy and neurocysticercosis (NCC) prevalence estimates in sub-Saharan Africa are still scarce but show important variation due to the population studied and different screening and diagnosis strategies used. The aims of this study were to estimate the prevalence of epileptic seizures and epilepsy in the sampled population, and the proportion of NCC among people with epilepsy (PWE) in a large cross-sectional study in a rural district of southern Malawi. Methods We conducted a community-based door-to-door screening study for epileptic seizures in Balaka, Malawi between October and December 2012. Past epileptic seizures were reported through a 15-item questionnaire answered by at least one person per household generating five major criteria. People who screened positive were further examined by a neurologist to establish diagnosis. Patients diagnosed with epilepsy were examined and offered Taenia solium cyst antigen and antibody serological tests, and a CT scan for the diagnosis of NCC. Results In total, screening information on 69,595 individuals was obtained for lifetime occurrence of epileptic seizures. 3,100 (4.5%) participants screened positive, of whom 1,913 (62%) could be followed-up and underwent further assessment. Lifetime prevalence was 3.0% (95% Bayesian credible interval [CI] 2.8 to 3.1%) and 1.2% (95%BCI 0.9 to 1.6%) for epileptic seizures and epilepsy, respectively. NCC prevalence among PWE was estimated to be 4.4% (95%BCI 0.8 to 8.5%). A diagnosis of epilepsy was ultimately reached for 455 participants. Conclusion The results of this large community-based study contribute to the evaluation and understanding of the burden of epilepsy in the population and of NCC among PWE in sub-Saharan Africa.
Postgraduate medical education in obstetrics and gynaecology: Where are we now and what do we need for the future? A study on postgraduate training in obstetrics and gynaecology in Germany, Austria and Switzerland
2022-09-15

Objective: In this study, we aim to assess the current situation of postgraduate medical education in obstetrics and gynaecology in Germany, Austria and Switzerland. In addition, we aim to determine transferable advantages amongst the countries. Study design: We performed a survey through a digital questionnaire with a total of 40 questions. The survey was advertised via communication channels of the German, Austrian and Swiss gynaecological societies; the participants were enrolled anonymously. Results: A total of 422 trainees took part in the survey. Differences within the three countries where found regarding the workload and the training of sub-specialties. Generally, the participants described to spend the majority of their daily working hours on documentation. Concerning assessment of current training regulations, more than half of trainees stated that they were actually faced with notable difficulties to fulfil the required obligatory numbers of self-performed interventions being documented. When asked for their intrinsic feeling of safety, around two-third of trainees felt “confident to very confident” during standard interventions. These numbers were up to 12% higher in the group of trainees who experienced simulation training during their education. Conclusion: With the help of this survey, weak points can be identified such as workload and implementation of current training regulations. Projects and ideas as EBCOG PACT, EPAs, the reduction of bureaucracy through digitization and deepening skills through simulation make a valuable contribution to compensate for these deficits and to adapt to future requirements.
Subradiant edge states in an atom chain with waveguide-mediated hopping
2022-09-15

We analyze the topological and dynamical properties of a system formed by two chains of identical emitters coupled to a waveguide, whose guided modes induce all-to-all excitation hopping. We find that, in the single excitation limit, the bulk topological properties of the Hamiltonian that describes the coherent dynamics of the system are identical to the ones of a one-dimensional Su-Schrieffer-Heeger (SSH) model. However, due to the long-range character of the exchange interactions, we find weakening of the bulk-boundary correspondence. This is illustrated by the variation of the localization length and mass gap of the edge states encountered as we vary the lattice constant and offset between the chains. Most interestingly, we analytically identify parameter regimes where edge states arise which are fully localized to the boundaries of the chain, independently of the system size. These edge states are shown to be not only robust against positional disorder of the atoms in the chain, but also subradiant, i.e., dynamically stable even in the presence of inevitable dissipation processes, establishing the capacity of waveguide QED systems for the realization of symmetry protected topological phases.
Reply to Oren et al., “New Phylum Names Harmonize Prokaryotic Nomenclature”
2022-09-15

We thank Oren et al., 2022 (1) for providing the International Committee on Systematics of Prokaryotes (ICSP) Executive Board's response to the recent opinion piece “Harmonizing Prokaryotic Nomenclature: Fixing the Fuss over Phylum Name Flipping” (2). &#13;\\n&#13;\\nHerein, we (a group of concerned microbiologists) offer several additional comments on the naming of prokaryotic phyla. Our concerns arise from the perception that the ICSP Executive Board is not directly addressing the plight of microbiologists around the world concerning the long-lasting confusion that the proposed phylum name changes will create throughout the scientific literature. Instead of selectively pointing out certain ICSP rules, we would have appreciated opening a door for a more inclusive discussion about the process of naming phyla. As previously stated (2), we are in favor of the International Code of Nomenclature of Prokaryotes (ICNP) rules for the recognition of the rank of “phylum” and the usage of “-ota” as the suffix for naming phyla. However, we feel that the drastic name changes of six phyla at the prefix level will create significant dissonance and confusion between the old and new names when considering past and future publications.