bluuebunny/crossref_metadata_2025_split huggingface dataset:
THE FIRST COMBINED RADIOCARBON AND ARCHAEOLOGICAL DATING OF THE GREAT MIGRATION PERIOD MATERIALS IN NORTHERN ALTAI: THE NECROPOLIS OF KARBAN-I
Authors: Seregin N N , Svyatko S V , Barrett G T , Demin M A , Matrenin S S , Papin D V , Reimer P J 
Published: May 2023

ABSTRACTThe lack of systematic chronologies is a key problem for the archaeological sites of Altai and adjacent territories during the Great Migration Period. Here we present an attempt to establish the chronology of the Bulan-Koby culture objects of the Karban-I necropolis by correlation of accelerator mass spectrometry radiocarbon (AMS 14C) data from human remains with data from archaeological dating methods. This is the first application of such a combined targeted 14C and archaeological approach to the chronology of the Great Migration Period materials of northern Altai, and in particular the Bulan-Koby culture. Systematic analysis of the mutual occurrence of dated types of certain grave goods and 14C dating of a series of samples supports a predominant period of use for the site that spans the 2nd–3rd c. AD, which corresponds to the early Xianbei period. This study demonstrates strong agreement between the indicators obtained by archaeological and radiocarbon methods, suggesting chronological consistency of the necropolis which functioned at the beginning of the Great Migration Period. The very combination of the two techniques will allow more precise and detailed chronologies for other archaeological complexes of Altai and adjacent territories from the first centuries of the 1st mil. AD, which is the basis of historical reconstructions.
Zoonotic helminths of dogs and risk factors associated with polyparasitism in Grenada, West Indies
Authors: Macpherson Maxine L.A. , Zendejas-Heredia Patsy A. , Sylvester Wayne , Gasser Robin B. , Traub Rebecca J. , Colella Vito , Macpherson Calum N.L. 
Published: May 2023

AbstractCanine soil-transmitted helminths (STHs) cause important zoonoses in the tropics, with varying degrees of intensity of infection in humans and dogs. This study aimed to investigate the prevalence and associated risk factors for STHs in community dogs residing in Grenada, West Indies. In May 2021, 232 canine fecal samples were examined for zoonotic helminths by microscopy (following flotation), and genomic DNA from a subset of 211 of these samples were subjected to multiplex qPCR for the detection and specific identification of hookworms, Toxocara spp. and Strongyloides. Microscopic examination revealed that 46.5% (108/232, 95% CI 40–52.9), 9% (21/232, 95% CI 5.35–12.7) and 5.2% (12/232, 95% CI 2.3–8) of the samples contained eggs of Ancylostoma spp., Toxocara spp. and Trichuris vulpis, respectively. Multiplex qPCR revealed that, 42.2% (89/211, 95% CI 35.5–48.8) were positive for at least 1 zoonotic parasite. Of these, 40.8% (86/211, 95% CI 34.1–47.3) of samples tested positive for Ancylostoma spp., 36% (76/211, 95% CI 29.5–42.9) were positive for A. caninum, 13.3% (28/211, 95% CI 9–18.6) for A. ceylanicum, 5.7% for T. canis (12/211, 95% CI 2.97–8.81) and 1% (2/211, 95% CI 0–2.26) for Strongyloides spp. (identified as S. stercoralis and S. papillosus by conventional PCR-based Sanger sequencing). Using a multiple logistic regression model, a low body score and free-roaming behaviour were significant predictors of test-positivity for these parasitic nematodes in dogs (P < 0.05). Further studies of zoonotic STHs in humans should help elucidate the public health relevance of these parasites in Grenada.
Reliquary crosses from Middle Byzantine Aphrodisias: intimacy and archaeology
Authors: Jeffery Hugh G. 
Published: May 2023

AbstractWorn constantly on the chest, reliquary crosses were intimately implicated in the lives of medieval people. Previous studies of such crosses have tended to consider them as tools through which people achieved specific ends, either as prophylactics against disease or as signifiers of hierarchical status. An alternative and complementary interpretation would emphasise intimacy: the prolonged rapport of particular crosses with particular bodies. This paper assembles and publishes 14 reliquary crosses from Aphrodisias in Caria, presented with commentary in an appendix. The body of the article addresses the archaeological contexts in which these crosses were found and explores the funerary use of reliquary crosses across Middle Byzantine Asia Minor from this novel perspective.
An investigation of the seasonal relationships between meteorological factors, water quality, and sporadic cases of Legionnaires’ disease in Washington, DC
Authors: Kirpich Alexander , Shishkin Aleksandr , Lhewa Pema , Yang Chen , von Fricken Michael E. , Norris Michael H. , Weppelmann Thomas A. 
Published: May 2023

Abstract
Since the discovery of Legionnaires’ disease (LD), limited progress has been made in understanding the epidemiology of sporadic cases of LD. Outbreaks have confirmed that air conditioning and potable water systems can be sources of community-acquired LD. However, studying the association between water quality and LD incidence has been challenging due to the heterogeneity of water systems across large geographic areas. Furthermore, although seasonal trends in incidence have been linked to increased rainfall and temperatures, the large geographic units have posed similar difficulties. To address this issue, a retrospective ecological study was conducted in Washington, DC, from 2001 to 2019. The study identified aseasonal pattern of LD incidence, with the majority of cases occurring between June and December, peaking in August, October, and November. Increased temperature was found to be associated with LD incidence. In surface water, higher concentrations of manganese, iron, and strontium were positively associated with LD, while aluminum and orthophosphate showed a negative association. Intreatment plant water, higher concentrations of total organic carbon, aluminum, barium, and chlorine were positively associated with LD, while strontium, zinc, and orthophosphate showed a negative association. The results for orthophosphates and turbidity were inconclusive, indicating the need for further research.
Oceanic Primary Production Estimation Based On Machine Learning
Authors: Ping Bo , Meng Yunshan , Xue Cunjin , Su Fenzhen 
Published: May 2023

AbstractOceanic primary production (OPP) is crucial for ecosystem services and global carbon cycle. However, sensitivity to geographic and environmental characteristics limits the application of semi‐empirical OPP estimate models, such as the vertically generalized productivity model (VGPM) and its modified version, particularly in coastal regions. In addition, the difficulty in collecting necessary parameters also hampers long‐term OPP estimates. Data‐driven machine learning (ML) methods can automatically capture the relationships between the input parameters and the objective; hence, they may become new methods for global OPP estimates. In this study, the effectiveness of ML methods to estimate OPP and the key attributes influencing ML performance in different regions and seasons are discussed. First, the ML models obtain a lower root mean square error than the VGPM and Eppley‐VGPM. In addition, the random forest (RF) model achieves the best performance among the four selected ML models. The enhancement in the accuracy of OPP estimates based on the RF model is more obvious in coastal regions than in the open ocean. In the four seasons, the RF model obtains better estimates of OPP than the Eppley‐VGPM, especially for summer. Moreover, input attributes, including sea surface temperature (SST), photosynthetic active radiation (PAR), and chlorophyll‐a concentration (Chlor‐a), achieve the best performance. The suitable alternative input attributes are SST/Chlor‐a in the coastal regions, and single Chlor‐a, SST/Chlor‐a, and PAR/Chlor‐a in the open ocean. Except for the SST/PAR/Chlor‐a combination, input with Chlor‐a, that is, SST/Chlor‐a and PAR/Chlor‐a, result a relatively acceptable performance in the four seasons.
Financial strain and depression in the U.S.: a scoping review
Authors: Ettman Catherine K. , Fan Alice Y. , Philips Alexander P. , Adam Gaelen P. , Ringlein Grace , Clark Melissa A. , Wilson Ira B. , Vivier Patrick M. , Galea Sandro 
Published: May 2023

AbstractWhile the association between assets and depression has been established, less is known about the link between financial strain and depression. Given rising financial strain and economic inequity due to the COVID-19 pandemic, understanding the role that financial strain plays in shaping population depression in the United States is particularly salient. We conducted a scoping review of the peer-reviewed literature on financial strain and depression published from inception through January 19, 2023, in Embase, Medline via PubMed, and PsycINFO, PsycArticles, SocINDEX, and EconLit via Ebsco. We searched, reviewed, and synthesized the literature on longitudinal studies on financial strain and depression conducted in the United States. Four thousand and four unique citations were screened for eligibility. Fifty-eight longitudinal, quantitative articles on adults in the United States were included in the review. Eighty-three percent of articles (n = 48) reported a significant, positive association between financial strain and depression. Eight articles reported mixed results, featuring non-significant associations for some sub-groups and significant associations for others, one article was unclear, and one article reported no significant association between financial strain and depression. Five articles featured interventions to reduce depressive symptoms. Effective interventions included coping mechanisms to improve one’s financial situation (e.g., mechanisms to assist in finding employment), to modify cognitive behavior (e.g., reframing mindset), and to engage support (e.g., engaging social and community support). Successful interventions were tailored to participants, were group-based (e.g., they included family members or other job seekers), and occurred over multiple sessions. While depression was defined consistently, financial strain was defined variably. Gaps in the literature included studies featuring Asian populations in the United States and interventions to reduce financial strain. There is a consistent, positive association between financial strain and depression in the United States. More research is needed to identify and test interventions that mitigate the ill effects of financial strain on population’s mental health.
Diagnostic yield and clinical relevance of expanded germline genetic testing for nearly 7000 suspected HBOC patients
Authors: Henkel Jan , Laner Andreas , Locher Melanie , Wohlfrom Tobias , Neitzel Birgit , Becker Kerstin , Neuhann Teresa , Abicht Angela , Steinke-Lange Verena , Holinski-Feder Elke 
Published: May 2023

AbstractHere we report the results of a retrospective germline analysis of 6941 individuals fulfilling the criteria necessary for genetic testing of hereditary breast- and ovarian cancer (HBOC) according to the German S3 or AGO Guidelines. Genetic testing was performed by next-generation sequencing using 123 cancer-associated genes based on the Illumina TruSight® Cancer Sequencing Panel. In 1431 of 6941 cases (20.6%) at least one variant was reported (ACMG/AMP classes 3–5). Of those 56.3% (n = 806) were class 4 or 5 and 43.7% (n = 625) were a class 3 (VUS). We defined a 14 gene HBOC core gene panel and compared this to a national and different internationally recommended gene panels (German Hereditary Breast and Ovarian Cancer Consortium HBOC Consortium, ClinGen expert Panel, Genomics England PanelsApp) in regard of diagnostic yield, revealing a diagnostic range of pathogenic variants (class 4/5) from 7.8 to 11.6% depending on the panel evaluated. With the 14 HBOC core gene panel having a diagnostic yield of pathogenic variants (class 4/5) of 10.8%. Additionally, 66 (1%) pathogenic variants (ACMG/AMP class 4 or 5) were found in genes outside the 14 HBOC core gene set (secondary findings) that would have been missed with the restriction to the analysis of HBOC genes. Furthermore, we evaluated a workflow for a periodic re-evaluation of variants of uncertain clinical significance (VUS) for the improvement of clinical validity of germline genetic testing.
A step-for-step main-group replica of the Fischer carbene synthesis at a borylene carbonyl
Authors: Härterich Marcel , Matler Alexander , Dewhurst Rian D. , Sachs Andreas , Oppel Kai , Stoy Andreas , Braunschweig Holger 
Published: May 2023

AbstractThe Fischer carbene synthesis, involving the conversion of a transition metal (TM)-bound CO ligand to a carbene ligand of the form [=C(OR’)R] (R, R’ = organyl groups), is one of the seminal reactions in the history of organometallic chemistry. Carbonyl complexes of p-block elements, of the form [E(CO)n] (E = main-group fragment), are much less abundant than their TM cousins; this scarcity and the general instability of low-valent p-block species means that replicating the historical reactions of TM carbonyls is often very difficult. Here we present a step-for-step replica of the Fischer carbene synthesis at a borylene carbonyl involving nucleophilic attack at the carbonyl carbon followed by electrophilic quenching at the resultant acylate oxygen atom. These reactions provide borylene acylates and alkoxy-/silyloxy-substituted alkylideneboranes, main-group analogues of the archetypal transition metal acylate and Fischer carbene families, respectively. When either the incoming electrophile or the boron center has a modest steric profile, the electrophile instead attacks at the boron atom, leading to carbene-stabilized acylboranes – boron analogues of the well-known transition metal acyl complexes. These results constitute faithful main-group replicas of a number of historical organometallic processes and pave the way to further advances in the field of main-group metallomimetics.
Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments
Authors: Feng Yuzhou , Yang Tianpei , Zhu John , Li Mabel , Doyle Maria , Ozcoban Volkan , Bass Greg T. , Pizzolla Angela , Cain Lachlan , Weng Sirui , Pasam Anupama , Kocovski Nikolce , Huang Yu-Kuan , Keam Simon P. , Speed Terence P. , Neeson Paul J. , Pearson Richard B. , Sandhu Shahneen , Goode David L. , Trigos Anna S. 
Published: May 2023

AbstractSpatial proteomics technologies have revealed an underappreciated link between the location of cells in tissue microenvironments and the underlying biology and clinical features, but there is significant lag in the development of downstream analysis methods and benchmarking tools. Here we present SPIAT (spatial image analysis of tissues), a spatial-platform agnostic toolkit with a suite of spatial analysis algorithms, and spaSim (spatial simulator), a simulator of tissue spatial data. SPIAT includes multiple colocalization, neighborhood and spatial heterogeneity metrics to characterize the spatial patterns of cells. Ten spatial metrics of SPIAT are benchmarked using simulated data generated with spaSim. We show how SPIAT can uncover cancer immune subtypes correlated with prognosis in cancer and characterize cell dysfunction in diabetes. Our results suggest SPIAT and spaSim as useful tools for quantifying spatial patterns, identifying and validating correlates of clinical outcomes and supporting method development.
Structural basis for breadth development in the HIV-1 V3-glycan targeting DH270 antibody clonal lineage
Authors: Henderson Rory , Zhou Ye , Stalls Victoria , Wiehe Kevin , Saunders Kevin O. , Wagh Kshitij , Anasti Kara , Barr Maggie , Parks Robert , Alam S. Munir , Korber Bette , Haynes Barton F. , Bartesaghi Alberto , Acharya Priyamvada 
Published: May 2023

AbstractAntibody affinity maturation enables adaptive immune responses to a wide range of pathogens. In some individuals broadly neutralizing antibodies develop to recognize rapidly mutating pathogens with extensive sequence diversity. Vaccine design for pathogens such as HIV-1 and influenza has therefore focused on recapitulating the natural affinity maturation process. Here, we determine structures of antibodies in complex with HIV-1 Envelope for all observed members and ancestral states of the broadly neutralizing HIV-1 V3-glycan targeting DH270 antibody clonal B cell lineage. These structures track the development of neutralization breadth from the unmutated common ancestor and define affinity maturation at high spatial resolution. By elucidating contacts mediated by key mutations at different stages of antibody development we identified sites on the epitope-paratope interface that are the focus of affinity optimization. Thus, our results identify bottlenecks on the path to natural affinity maturation and reveal solutions for these that will inform immunogen design aimed at eliciting a broadly neutralizing immune response by vaccination.
A general model to predict small molecule substrates of enzymes based on machine and deep learning
Authors: Kroll Alexander , Ranjan Sahasra , Engqvist Martin K. M. , Lercher Martin J. 
Published: May 2023

AbstractFor most proteins annotated as enzymes, it is unknown which primary and/or secondary reactions they catalyze. Experimental characterizations of potential substrates are time-consuming and costly. Machine learning predictions could provide an efficient alternative, but are hampered by a lack of information regarding enzyme non-substrates, as available training data comprises mainly positive examples. Here, we present ESP, a general machine-learning model for the prediction of enzyme-substrate pairs with an accuracy of over 91% on independent and diverse test data. ESP can be applied successfully across widely different enzymes and a broad range of metabolites included in the training data, outperforming models designed for individual, well-studied enzyme families. ESP represents enzymes through a modified transformer model, and is trained on data augmented with randomly sampled small molecules assigned as non-substrates. By facilitating easy in silico testing of potential substrates, the ESP web server may support both basic and applied science.
The NELF pausing checkpoint mediates the functional divergence of Cdk9
Authors: DeBerardine Michael , Booth Gregory T. , Versluis Philip P. , Lis John T. 
Published: May 2023

AbstractPromoter-proximal pausing by RNA Pol II is a rate-determining step in gene transcription that is hypothesized to be a prominent point at which regulatory factors act. The pausing factor NELF is known to induce and stabilize pausing, but not all kinds of pausing are NELF-mediated. Here, we find that NELF-depleted Drosophila melanogaster cells functionally recapitulate the NELF-independent pausing we previously observed in fission yeast (which lack NELF). Critically, only NELF-mediated pausing establishes a strict requirement for Cdk9 kinase activity for the release of paused Pol II into productive elongation. Upon inhibition of Cdk9, cells with NELF efficiently shutdown gene transcription, while in NELF-depleted cells, defective, non-productive transcription continues unabated. By introducing a strict checkpoint for Cdk9, the evolution of NELF was likely critical to enable increased regulation of Cdk9 in higher eukaryotes, as Cdk9 availability can be restricted to limit gene transcription without inducing wasteful, non-productive transcription.
Deep learning to estimate lithium-ion battery state of health without additional degradation experiments
Authors: Lu Jiahuan , Xiong Rui , Tian Jinpeng , Wang Chenxu , Sun Fengchun 
Published: May 2023

AbstractState of health is a critical state which evaluates the degradation level of batteries. However, it cannot be measured directly but requires estimation. While accurate state of health estimation has progressed markedly, the time- and resource-consuming degradation experiments to generate target battery labels hinder the development of state of health estimation methods. In this article, we design a deep-learning framework to enable the estimation of battery state of health in the absence of target battery labels. This framework integrates a swarm of deep neural networks equipped with domain adaptation to produce accurate estimation. We employ 65 commercial batteries from 5 different manufacturers to generate 71,588 samples for cross-validation. The validation results indicate that the proposed framework can ensure absolute errors of less than 3% for 89.4% of samples (less than 5% for 98.9% of samples), with a maximum absolute error of less than 8.87% in the absence of target labels. This work emphasizes the power of deep learning in precluding degradation experiments and highlights the promise of rapid development of battery management algorithms for new-generation batteries using only previous experimental data.
Computational study on the catalytic control of endo/exo Diels-Alder reactions by cavity quantum vacuum fluctuations
Authors: Pavošević Fabijan , Smith Robert L. , Rubio Angel 
Published: May 2023

AbstractAchieving control over chemical reaction’s rate and stereoselectivity realizes one of the Holy Grails in chemistry that can revolutionize chemical and pharmaceutical industries. Strong light-matter interaction in optical or nanoplasmonic cavities might provide the knob to reach such control. In this work, we demonstrate the catalytic and selectivity control of an optical cavity for two selected Diels-Alder cycloaddition reactions using the quantum electrodynamics coupled cluster (QED-CC) method. Herein, we find that by changing the molecular orientation with respect to the polarization of the cavity mode the reactions can be significantly inhibited or selectively enhanced to produce major endo or exo products on demand. This work highlights the potential of utilizing quantum vacuum fluctuations of an optical cavity to modulate the rate of Diels-Alder cycloaddition reactions and to achieve stereoselectivity in a practical and non-intrusive way. We expect that the present findings will be applicable to a larger set of relevant reactions, including the click chemical reactions.
Turn air-captured CO2 with methanol into amino acid and pyruvate in an ATP/NAD(P)H-free chemoenzymatic system
Authors: Liu Jianming , Zhang Han , Xu Yingying , Meng Hao , Zeng An-Ping 
Published: May 2023

AbstractThe use of gaseous and air-captured CO2 for technical biosynthesis is highly desired, but elusive so far due to several obstacles including high energy (ATP, NADPH) demand, low thermodynamic driving force and limited biosynthesis rate. Here, we present an ATP and NAD(P)H-free chemoenzymatic system for amino acid and pyruvate biosynthesis by coupling methanol with CO2. It relies on a re-engineered glycine cleavage system with the NAD(P)H-dependent L protein replaced by biocompatible chemical reduction of protein H with dithiothreitol. The latter provides a higher thermodynamic driving force, determines the reaction direction, and avoids protein polymerization of the rate-limiting enzyme carboxylase. Engineering of H protein to effectively release the lipoamide arm from a protected state further enhanced the system performance, achieving the synthesis of glycine, serine and pyruvate at g/L level from methanol and air-captured CO2. This work opens up the door for biosynthesis of amino acids and derived products from air.