julilili42/papers huggingface dataset:
Reconstructing formation processes at the Canary Islands indigenous site of Belmaco Cave (La Palma, Spain) through a multiproxy geoarchaeological approach
2023-07-28

Abstract The indigenous populations of La Palma (Canary Islands), who arrived on the island from Northwest Africa ca. 2000 years B.P., were predominantly pastoralists. Yet, many aspects of their subsistence economy such as the procurement, management, and use of wild plant resources remain largely unknown. To explore this, we studied the 600–1100‐year‐old archaeological site of Belmaco Cave, which comprises a stratified sedimentary deposit representative of a fumier . Here, we present a high‐resolution, multiproxy geoarchaeological study combining soil micromorphology, lipid biomarker analysis, X‐ray diffraction, μ‐X‐ray diffraction, μ‐X‐ray fluorescence, Fourier transform infrared spectroscopy, and μ‐Fourier transform infrared spectroscopy, to characterize formation processes and explore plant sources. Recurrent goat/sheep habitation and maintenance activities are represented by interstratified layers of unburned dung, charcoal‐rich sediment, and dung ash. Lipid biomarker data show a herd diet mainly composed of herbaceous plants, which is key to understanding the mobility of indigenous shepherds. Our results also revealed an unusual suite of authigenic minerals including hazenite, aragonite, and sylvite, possibly formed through diagenetic processes involving interaction between ash, dung, urine, volcanogenic components, and bacterial activity, coupled with arid and alkaline conditions. Our study shows the potential of a multiproxy approach to a fumier deposit in a volcanogenic sedimentary context.
Which Patients Do We Need to Test for BRCA1/2 Mutation? Feasibility of Adjuvant Olaparib Treatment in Early Breast Cancer–Real-World Data from Two Large German Breast Centers
2023-07-28

Background: Approximately 6% of women with breast cancer carry pathogenic germline variants in predisposition genes such as BRCA1 and BRCA2. Depending on personal and family cancer history, it is therefore recommended to test for hereditary breast cancer. Moreover, as shown by the phase III OlympiA trial, olaparib significantly improves overall survival in patients with HER2 negative (HER2−) early breast cancer who (1) carry a BRCA1 or BRCA2 germline mutation (gBRCA1/2-positive), (2) have received (neo)adjuvant chemotherapy and (3) are at high clinical risk. The objective of the current analysis was to determine the number of patients with early HER2− breast cancer who are at high clinical risk, according to the inclusion criteria of OlympiA, and to estimate how many of these patients would meet the criteria for hereditary cancer testing in a real-world analysis. Methods: All patients included in this retrospective analysis were treated for early breast cancer (eBC) at the Department of Gynecology and Obstetrics, Ulm University Hospital, Germany, and the Department of Women’s Health at Tuebingen University Hospital, Germany, between January 2018 and December 2020. Patients were identified as high risk, in line with the clinicopathological determiners used in the OlympiA trial. The criteria of the German Consortium for Hereditary Breast and Ovarian Cancer were used to identify patients who qualify for hereditary cancer testing. Results: Of 2384 eligible patients, 1738 patients (72.9%) showed a hormone receptor positive (HR+)/HER2− tumor biology, 345 patients (14.5%) displayed HER2+ breast cancer and 301 patients (12.6%) suffered from HR-/HER2− breast cancer (TNBC). Of 2039 HER2− breast cancer patients, 271 patients (13.3%) were at high clinical risk. This cohort encompassed 130 of the 1738 patients with HR+/HER2− breast cancer (7.5%) and 141 of 301 patients with TNBC (46.8%). A total of 121 of 271 patients (44.6%) with high clinical risk met the criteria for hereditary cancer testing (34 of 130 (26.2%) HR+/HER2− patients and 87 of 141 (61.7%) patients with TNBC). Conclusion: Approximately one in ten patients with HR+/HER2−, and half of the patients with TNBC, meet the high-risk criteria according to OlympiA. Half of these patients do not meet the criteria for hereditary cancer testing and should therefore be tested for the presence of gBRCA1/2 mutations, irrespective of their own or family cancer history. The overall number of patients with early breast cancer benefiting from olaparib needs to be investigated in future studies.
Clinical trio genome sequencing facilitates the interpretation of variants in cancer predisposition genes in paediatric tumour patients
2023-07-28

Abstract The prevalence of pathogenic and likely pathogenic (P/LP) variants in genes associated with cancer predisposition syndromes (CPS) is estimated to be 8-18% for paediatric cancer patients. In more than half of the carriers, the family history is unsuspicious for CPS. Therefore, broad genetic testing could identify germline predisposition in additional children with cancer resulting in important implications for themselves and their families. We thus evaluated clinical trio genome sequencing (TGS) in a cohort of 72 paediatric patients with solid cancers other than retinoblastoma or CNS-tumours. The most prevalent cancer types were sarcoma ( n = 26), neuroblastoma ( n = 15), and nephroblastoma ( n = 10). Overall, P/LP variants in CPS genes were identified in 18.1% of patients (13/72) and P/LP variants in autosomal-dominant CPS genes in 9.7% (7/72). Genetic evaluation would have been recommended for the majority of patients with P/LP variants according to the Jongmans criteria. Four patients (5.6%, 4/72) carried P/LP variants in autosomal-dominant genes known to be associated with their tumour type. With the immediate information on variant inheritance, TGS facilitated the identification of a de novo P/LP in NF1 , a gonadosomatic mosaic in WT1 and two pathogenic variants in one patient ( DICER1 and PALB2 ). TGS allows a more detailed characterization of structural variants with base-pair resolution of breakpoints which can be relevant for the interpretation of copy number variants. Altogether, TGS allows comprehensive identification of children with a CPS and supports the individualised clinical management of index patients and high-risk relatives.
Screening Smarter, Not Harder: A Comparative Analysis of Machine Learning Screening Algorithms and Heuristic Stopping Criteria for Systematic Reviews in Educational Research
2023-07-28

Systematic reviews and meta-analyses are crucial for advancing research; yet, they are time-consuming and resource-demanding. Although machine learning and natural language processing algorithms may reduce this time and these resources, their performance has not been tested in the field of education and educational psychology, and there is a lack of clear information on when researchers should stop the reviewing process. In this study, we conducted a retrospective screening simulation using 27 systematic reviews in education and educational psychology. We evaluated the recall, work saved over sampling, and the estimated time savings of several active learning screening algorithms and heuristic stopping criteria. The results showed on average a 50% (SD = 20%) reduction in screening workload when using active learning algorithms for abstract screening and an estimated time savings of 1.64 days (SD = 1.78). The learning algorithm Random Forests with Sentence Bidirectional Encoder Representations from Transformers outperformed other algorithms—a finding that emphasizes the importance of incorporating semantic and contextual information during feature extraction and modeling in the screening process. Furthermore, we found that 95% of all relevant abstracts within a given dataset can be retrieved using heuristic stopping rules. Specifically, an approach that stops the screening process after consecutively classifying 7% of irrelevant papers yielded the most significant gains in terms of works savings over sampling (M = 41%, SD = 26%). However, the performance of the heuristic stopping criteria depended on the active learning algorithm used, the length and the proportion of relevant papers in a database. Overall, our study provides empirical evidence on the performance of machine learning screening algorithms for abstract screening in systematic reviews in education and educational psychology.
Effects of Early Clozapine Treatment on Remission Rates in Acute Schizophrenia (The EARLY Trial): Protocol of a Randomized-Controlled Multicentric Trial
2023-07-28

Abstract Background Quick symptomatic remission after the onset of psychotic symptoms is critical in schizophrenia treatment, determining the subsequent disease course and recovery. In this context, only every second patient with acute schizophrenia achieves symptomatic remission within three months of initiating antipsychotic treatment. The potential indication extension of clozapine—the most effective antipsychotic—to be introduced at an earlier stage (before treatment-resistance) is supported by several lines of evidence, but respective clinical trials are lacking. Methods Two hundred-twenty patients with acute non-treatment-resistant schizophrenia will be randomized in this double-blind, 8-week parallel-group multicentric trial to either clozapine or olanzapine. The primary endpoint is the number of patients in symptomatic remission at the end of week 8 according to international consensus criteria (‘Andreasen criteria’). Secondary endpoints and other assessments comprise a comprehensive safety assessment (i. e., myocarditis screening), changes in psychopathology, global functioning, cognition, affective symptoms and quality of life, and patients’ and relatives’ views on treatment. Discussion This multicentre trial aims to examine whether clozapine is more effective than a highly effective second-generation antipsychotics (SGAs), olanzapine, in acute schizophrenia patients who do not meet the criteria for treatment-naïve or treatment-resistant schizophrenia. Increasing the likelihood to achieve symptomatic remission in acute schizophrenia can improve the overall outcome, reduce disease-associated burden and potentially prevent mid- and long-term disease chronicity.
Development of a PNGase Rc column for online deglycosylation of complex glycoproteins during HDX-MS
2023-07-28

ABSTRACT Protein glycosylation is one of the most common PTMs and many cell surface receptors, extracellular proteins and biopharmaceuticals are glycosylated. However, HDX-MS analysis of such important glycoproteins has so far been limited by difficulties in determining the HDX of the protein segments that contain glycans. We have developed a column containing immobilized PNGase Rc (from Rudaea cellulosilytica ) that can readily be implemented into a conventional HDX-MS setup to allow improved analysis of glycoproteins. We show that HDX-MS with the PNGase Rc column enables efficient online removal of N-linked glycans and the determination of the HDX of glycosylated regions in several complex glycoproteins. Additionally, we use the PNGase Rc column to perform a comprehensive HDX-MS mapping of the binding epitope of a mAb to c-Met, a complex glycoprotein drug target. Importantly, the column retains high activity in the presence of common quench-buffer additives like TCEP and urea and performed consistent across 114 days of extensive use. Overall, our work shows that HDX-MS with the integrated PNGase Rc column can enable fast and efficient online deglycosylation at harsh quench conditions to provide comprehensive analysis of complex glycoproteins.
A Water-Stable Boronate Ester Cage
2023-07-28

The reversible condensation of catechols and boronic acids to boronate esters is a paradigm reaction in dynamic covalent chemistry. However, facile backwards hydrolysis is detrimental for stability and has so far prevented applications for boronate-based materials. Here, we introduce cubic boronate ester cages 6 derived from hexahydroxy tribenzotriquinacenes and phenylene diboronic acids with ortho-t-butyl substituents. Due to steric shielding, dynamic exchange at the Lewis acidic boron sites is only feasible under acid or base catalysis but fully prevented at neutral conditions. For the first time, boronate ester cages 6 tolerate substantial amounts of water or alcohols both in solution and solid state. The unprecedented applicability of these materials under ambient and aqueous conditions is showcased by efficient encapsulation and on-demand release of β-carotene dyes and heterogeneous water oxidation catalysis after encapsulation of ruthenium catalysts.
Large-scale universality in quantum reaction-diffusion from Keldysh field theory
2023-07-28

We consider the quantum reaction-diffusion dynamics in spatial dimensions of a Fermi gas subject to binary annihilation reactions . These systems display collective nonequilibrium long-time behavior, which is signalled by an algebraic decay of the particle density. Building on the Keldysh formalism, we devise a field theoretical approach for the reaction-limited regime, where annihilation reactions are scarce. By means of a perturbative expansion of the dissipative interaction, we derive a description in terms of a large-scale universal kinetic equation. Our approach shows how the time-dependent generalized Gibbs ensemble assumption, which is often employed for treating low-dimensional nonequilibrium systems, emerges from systematic diagrammatics. It also allows to exactly compute -- for arbitrary spatial dimension -- the decay exponent of the particle density. The latter is based on the large-scale description of the quantum dynamics and it differs from the mean-field prediction even in dimension larger than one. We moreover consider spatially inhomogeneous setups involving an external potential. In confined systems the density decay is accelerated towards the mean-field algebraic behavior, while for deconfined scenarios the power-law decay is replaced by a slower non-algebraic decay.
Lesions in a songbird vocal circuit increase variability in song syntax
2023-07-28

Abstract Complex motor skills like speech and dance are composed of ordered sequences of simpler elements, but the neuronal basis for syntactic ordering of individual actions into sequences is poorly understood. Birdsong is a learned vocal behavior composed of syntactically ordered sequences of individual syllables. Activity in song premotor nucleus HVC (proper name) has been linked to the control of syllable sequencing, but sequencing may also be affected by its recurrent inputs. We here test the contribution of one of HVC’s inputs, mMAN ( medial magnocellular nucleus of the anterior nidopallium ), to the variable songs of adult male Bengalese finches ( Lonchura striata domestica ). The syntax of Bengalese song includes several patterns: 1) chunks , where syllables follow stereotypical order 2) branch points , where a given syllable can be followed by two or more different syllables in a probabilistic manner and 3) repeat phrases , where an individual syllable is repeated a variable number of times. We found that after bilateral lesions of mMAN, the acoustic structure of syllables remained largely intact, but sequencing became more variable for each of these patterns, seen by ‘breaks’ in previously stereotyped chunks, increased uncertainty at branch points and increased variability of repeat numbers. This increase in sequencing variability highlights the potential importance of regions projecting to HVC in the ordering of vocal elements. Previous studies on zebra finches found little effect of mMAN lesions on their relatively stereotyped adult song. In contrast, our results suggest that mMAN contributes to sequencing the variable songs of Bengalese finches and highlight the utility of species with more complex song syntax in investigating neuronal control of ordered motor sequences.
Distinctive Features of Hairy Black Holes in Teleparallel Gauss-Bonnet Gravity
2023-07-28

We examine the teleparallel formulation of non-minimally coupled scalar Einstein-Gauss-Bonnet gravity. In the teleparallel formulation, gravity is described by torsion instead of curvature, causing the usual Gauss-Bonnet invariant expressed through curvature to decay into two separate invariants built from torsion. Consequently, the teleparallel formulation permits broader possibilities for non-minimal couplings between spacetime geometry and the scalar field. In our teleparallel theory, there are two different branches of equations in spherical symmetry depending on how one solves the antisymmetric part of the field equations, leading to a real and a complex tetrad. We first show that the real tetrad seems to be incompatible with the regularity of the equations at the event horizon, which is a symptom that scalarized black hole solutions beyond the Riemannian Einstein-Gauss-Bonnet theory might not exist. Therefore, we concentrate our study on the complex tetrad. This leads to the emergence of scalarized black hole solutions, where the torsion acts as the scalar field source. Extending our previous work, we study monomial non-minimal couplings of degrees one and two, which are intensively studied in conventional, curvature-based, scalar Einstein-Gauss-Bonnet gravity. We discover that the inclusion of torsion can potentially alter the stability of the resulting scalarized black holes. Specifically, our findings indicate that for a quadratic coupling, which is entirely unstable in the pure curvature formulation, the solutions induced by torsion may exhibit stability within certain regions of the parameter space. In a limiting case, we were also able to find black holes with a strong scalar field close to the horizon but with a vanishing scalar charge.
Agouti historiography: the problem of widespread lexical forms and deep linguistic history in Central and South America
2023-07-28

Abstract Throughout Central and South America, similar words for salient rodent species, the agoutis ( Dasyprocta spp.), reconstruct to some of the most ancient known languages families in the species’ range, including Chibchan (*’kuri), Cariban (*akuri), Tupian (*akutˀi), and others. Unless these are dismissed as mere chance, this makes for as interesting as problematic evidence for deep linguistic history: what mechanisms account for the striking similarities that must go back far into prehistory? One possibility is that the words are lexical evidence for very old genealogical connections. While this is a possibility worth bearing in mind also in light of current and past suggestions that involve some of the relevant groups, we cannot conclude that this is indeed the case on the basis of the available evidence. Another, and perhaps less costly, hypothesis is very old borrowing involving relevant proto-languages or their ancestors However, is this a plausible scenario? On the basis of a large set of data featuring more than 400 languages from Central and South America, I show that neighboring languages have relatively frequently borrowed agouti-words from one another, involving reflexes of the above forms, but also others. This shows that it is natural to expect borrowing my. In either case, the similarities likely demonstrate very old interactions between the mentioned lineages, something with interesting implications on homeland hypotheses and scenarios of early spread.
Report on scipost_202305_00010v1
2023-07-28

We introduce a new universal framework describing fluctuations and correlations in quantum and classical many-body systems, at the Euler hydrodynamic scale of space and time.The framework adapts the ideas of the conventional macroscopic fluctuation theory (MFT) to systems that support ballistic transport.The resulting "ballistic MFT" (BMFT) is solely based on the Euler hydrodynamics data of the many-body system.Within this framework, mesoscopic observables are classical random variables depending only on the fluctuating conserved densities, and Euler-scale fluctuations are obtained by deterministically transporting thermodynamic fluctuations via the Euler hydrodynamics.Using the BMFT, we show that long-range correlations in space generically develop over time from long-wavelength inhomogeneous initial states in interacting models.This result, which we verify by numerical calculations, challenges the long-held paradigm that at the Euler scale, fluid cells may be considered uncorrelated.We also show that the Gallavotti-Cohen fluctuation theorem for non-equilibrium ballistic transport follows purely from time-reversal invariance of the Euler hydrodynamics.We check the validity of the BMFT by applying it to integrable systems, and in particular the hard-rod gas, with extensive simulations that confirm our analytical results.
Transformation of Iminodi(methylene phosphonate) on Manganese Dioxides – Passivation of the Mineral Surface by (Formed) Mn2+
2023-07-29

Aminopolyphosphonates (APPs) are strong chelating agents with growing use in industrial and household applications. In this study, we investigated the oxidation of the bisphosphonate iminodi(methylene phosphonate) (IDMP) - a major transformation product (TP) of numerous commercially used APPs and a potential precursor for aminomethylphosphonate (AMPA) - on manganese dioxide (MnO<sub>2</sub>). Transformation batch experiments at pH 6 revealed AMPA and phosphate as main TPs, with a phosphorus mass balance of 80 to 92% throughout all experiments. Our results suggest initial cleavage of the C-P bond and formation of the stable intermediate <i>N</i>-formyl-AMPA. Next, C-N bond cleavage leads to the formation of AMPA, which exhibits lower reactivity than IDMP. Reaction rates together with IDMP and Mn<sup>2+</sup> sorption data indicate formation of IDMP-Mn<sup>2+</sup> surface bridging complexes with progressing MnO<sub>2</sub> reduction, leading to the passivation of the mineral surface regarding IDMP oxidation. Compound-specific stable carbon isotope analysis of IDMP in both sorbed and aqueous fractions further supported this hypothesis. Depending on the extent of Mn<sup>2+</sup> surface concentration, the isotope data indicated either sorption of IDMP to the mineral surface or electron transfer from IDMP to Mn<sup>IV</sup> to be the rate-limiting step of the overall reaction. Our study sheds further light on the complex surface processes during MnO<sub>2</sub> redox reactions and reveals abiotic oxidative transformation of APPs by MnO<sub>2</sub> as a potential process contributing to widespread elevated AMPA concentrations in the environment.