bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of the German version of the Protein Screener 55+
Authors: Kiesswetter Eva , Siebentritt Hanna M. , Schoene Daniel , Kob Robert , Freiberger Ellen , Sieber Cornel C. , Visser Marjolein , Wijnhoven Hanneke A. H. , Volkert Dorothee 
Published: January 2023

Abstract
Background/Objectives
The Protein Screener 55 + (Pro55 + ) is a brief food questionnaire to screen older community-dwelling adults for low protein intake. The result is the predicted probability of protein intake <1.0 g/kg adjusted body weight (aBW)/d ranging from 0–1. For purposes of cross-cultural validation, we translated the Pro55+ into German and tested its discriminative accuracy in detecting low protein intake of older community-dwelling people in Germany.

Subjects/Methods
After translation and pilot-testing, the Pro55+ and the reference standard (3-day dietary record) were completed by 144 participants (81.6 ± 3.9 years, 61.8% female). Discriminative properties were tested by receiver operating characteristic curves and by calculating sensitivity and specificity for different cut-offs of predicted probability (>0.3/>0.5/>0.7) using <1.0 or <0.8 g/kg aBW/d to define low protein intake.

Results
Protein intake was <1.0 g/kg aBW/d in 39.6% of the sample and <0.8 g/kg aBW/d in 17.4%. Area under the curve was 62.0% (95%CI 52.6–71.5) and 68.8% (58.1–79.4), respectively. Specificity was 82–90% using probability cut-offs of 0.5 and 0.7 for both protein thresholds. Sensitivity was poor for protein threshold of 1.0 g/kg aBW/d regardless of the used probability cut-offs. For protein threshold of <0.8 g/kg aBW/d, sensitivity was 88.0% (71.8–96.9) using a probability cut-off of 0.09.

Conclusion
The overall discriminative accuracy of the German Pro55+ to identify older community-dwelling people with low protein intake was poor. However, applying different probability cut-offs allows increasing specificity and sensitivity for 0.8 g/kg aBW/d to levels justifying the use for certain purposes e.g. excluding individuals with adequate protein intake. Further validation is needed.
Novel WNT10A variant in a Japanese case of nonsyndromic oligodontia
Authors: Adachi Junya , Aoki Yoshihiko , Izumi Hiroto , Nishiyama Takeshi , Nakayama Atsuo , Sana Masatoshi , Morimoto Kyoko , Kaetsu Atsuo , Shirozu Takamasa , Osumi Eriko , Matsuoka Michiko , Hayakawa Eri , Maeda Nasel , Machida Junichiro , Nagao Toru , Tokita Yoshihito 
Published: January 2023

AbstractCongenital tooth agenesis is one of the most common anomalies in humans. Many genetic factors are involved in tooth development, including MSX1, PAX9, WNT10A, and LRP6. Thus, mutations in these genes can cause congenital tooth agenesis in humans. In this study, we identified a novel nonsense WNT10A variant, NM_025216.3(WNT10A_v001):c.1090A > T, which produces a C-terminal truncated gene product, p.(Lys364*), in a sporadic form of congenital tooth agenesis. The variant was not found in the healthy parents and thus was considered to cause congenital tooth agenesis in the case.
Efficient pure blue hyperfluorescence devices utilizing quadrupolar donor-acceptor-donor type of thermally activated delayed fluorescence sensitizers
Authors: Lee Hyuna , Braveenth Ramanaskanda , Muruganantham Subramanian , Jeon Chae Yeon , Lee Hyun Seung , Kwon Jang Hyuk 
Published: January 2023

AbstractThe hyperfluorescence (HF) system has drawn great attention in display technology. However, the energy loss mechanism by low reverse intersystem crossing rate (kRISC) and the Dexter energy transfer (DET) channel is still challenging. Here, we demonstrate that this can be mitigated by the quadrupolar donor-acceptor-donor (D-A-D) type of thermally activated delayed fluorescence (TADF) sensitizer materials, DBA-DmICz and DBA-DTMCz. Further, the HF device with DBA-DTMCz andν-DABNA exhibited 43.9% of high maximum external quantum efficiency (EQEmax) with the Commission Internationale de l'Éclairage coordinates of (0.12, 0.16). The efficiency values recorded for the device are among the highest reported for HF devices. Such high efficiency is assisted by hindered DET process through i) highkRISC, and ii) shielded lowest unoccupied molecular orbital with the presence of two donors in D-A-D type of skeleton. Our current study provides an effective way of designing TADF sensitizer for future HF technology.
Observation of electronic modes in open cavity resonator
Authors: Jung Hwanchul , Park Dongsung T. , Lee Seokyeong , Kim Uhjin , Yang Chanuk , Kim Jehyun , Umansky V. , Kim Dohun , Sim H.-S. , Chung Yunchul , Choi Hyoungsoon , Choi Hyung Kook 
Published: January 2023

AbstractThe resemblance between electrons and optical waves has strongly driven the advancement of mesoscopic physics, evidenced by the widespread use of terms such as fermion or electron optics. However, electron waves have yet to be understood in open cavity structures which have provided contemporary optics with rich insight towards non-Hermitian systems and complex interactions between resonance modes. Here, we report the realization of an open cavity resonator in a two-dimensional electronic system. We studied the resonant electron modes within the cavity and resolved the signatures of longitudinal and transverse quantization, showing that the modes are robust despite the cavity being highly coupled to the open background continuum. The transverse modes were investigated by applying a controlled deformation to the cavity, and their spatial distributions were further analyzed using magnetoconductance measurements and numerical simulation. These results lay the groundwork to exploring matter waves in the context of modern optical frameworks.
Milankovitch-paced erosion in the southern Central Andes
Authors: Fisher G. Burch , Luna Lisa V. , Amidon William H. , Burbank Douglas W. , de Boer Bas , Stap Lennert B. , Bookhagen Bodo , Godard Vincent , Oskin Michael E. , Alonso Ricardo N. , Tuenter Erik , Lourens Lucas J. 
Published: January 2023

AbstractIt has long been hypothesized that climate can modify both the pattern and magnitude of erosion in mountainous landscapes, thereby controlling morphology, rates of deformation, and potentially modulating global carbon and nutrient cycles through weathering feedbacks. Although conceptually appealing, geologic evidence for a direct climatic control on erosion has remained ambiguous owing to a lack of high-resolution, long-term terrestrial records and suitable field sites. Here we provide direct terrestrial field evidence for long-term synchrony between erosion rates and Milankovitch-driven, 400-kyr eccentricity cycles using a Plio-Pleistocene cosmogenic radionuclide paleo-erosion rate record from the southern Central Andes. The observed climate-erosion coupling across multiple orbital cycles, when combined with results from the intermediate complexity climate model CLIMBER-2, are consistent with the hypothesis that relatively modest fluctuations in precipitation can cause synchronous and nonlinear responses in erosion rates as landscapes adjust to ever-evolving hydrologic boundary conditions imposed by oscillating climate regimes.
Design and characterization of a protein fold switching network
Authors: Ruan Biao , He Yanan , Chen Yingwei , Choi Eun Jung , Chen Yihong , Motabar Dana , Solomon Tsega , Simmerman Richard , Kauffman Thomas , Gallagher D. Travis , Orban John , Bryan Philip N. 
Published: January 2023

AbstractTo better understand how amino acid sequence encodes protein structure, we engineered mutational pathways that connect three common folds (3α, β−grasp, and α/β−plait). The structures of proteins at high sequence-identity intersections in the pathways (nodes) were determined using NMR spectroscopy and analyzed for stability and function. To generate nodes, the amino acid sequence encoding a smaller fold is embedded in the structure of an ~50% larger fold and a new sequence compatible with two sets of native interactions is designed. This generates protein pairs with a 3α or β−grasp fold in the smaller form but an α/β−plait fold in the larger form. Further, embedding smaller antagonistic folds creates critical states in the larger folds such that single amino acid substitutions can switch both their fold and function. The results help explain the underlying ambiguity in the protein folding code and show that new protein structures can evolve via abrupt fold switching.
Concomitant analyses of intratumoral microbiota and genomic features reveal distinct racial differences in breast cancer
Authors: Parida Sheetal , Siddharth Sumit , Xia Yuqing , Sharma Dipali 
Published: January 2023

AbstractRacial disparities are most accentuated among Black women as their lifetime risk of breast cancer incidence is lower than white and Asian women but their breast cancer related mortality is the highest among all races. Black women are more likely to develop triple-negative breast cancer at a younger age and harbor more aggressive tumors. In addition to tumor-centric alterations, tumor growth is also influenced by multiple other tumor microenvironment-related features, including resident immune cells and microbiota. Hence, in this study, we conduct concurrent genomic and metagenomic analyses, and uncover distinctive intratumoral microbial community compositions and tumor immune microenvironment-related traits in breast tumors from Asian, Black and white women. Interestingly, unique racially associated genomic nodes are found in the breast tumors from Asian, Black and white women. Examination of the cellular heterogeneity show differential enrichment of 11 out of 64 immune and stroma cell types in the breast tumors from different racial groups. In terms of microbial diversity, significant differences are revealed in alpha and beta-diversity measures. Intriguingly, potential race-specific microbial biomarkers of breast cancer are identified which significantly correlate with genes involved with tumor aggressiveness, angiogenesis, tumor cell migration and metastasis as well as oncogenic pathways-GLI and Notch. Investigating the metabolic features of intratumoral microbes, we find a significant differential enrichment of environmental information processing pathways, oncogenic pathways, and lipid metabolism pathways. Concomitantly investigating tumor-centric, tumor immune microenvironment-related and microbial alterations, our study provides a comprehensive understanding of racial disparities in breast cancer and warrants further exploration.
Photoswitching neutral homoaromatic hydrocarbons
Authors: Tran Ngoc Trung , Grabicki Niklas , Irran Elisabeth , Dumele Oliver , Teichert Johannes F. 
Published: January 2023

AbstractHomoaromatic compounds possess an interruptedπsystem but display aromatic properties due to through-space or through-bond interactions. Stable neutral homoaromatic hydrocarbons have remained rare and are typically unstable. Here we present the preparation of a class of stable neutral homoaromatic molecules, supported by experimental evidence (ring current observed by NMR spectroscopy and equalization of bond lengths by X-ray structure analysis) and computational analysis via nucleus-independent chemical shifts (NICS) and anisotropy of the induced current density (ACID). We also show that one homoaromatic hydrocarbon is a photoswitch through a reversible photochemical [1, 11] sigmatropic rearrangement. Our computational analysis suggests that, upon photoswitching, the nature of the homoaromatic state changes in its perimeter from a more pronounced local 6πhomoaromatic state to a global 10πhomoaromatic state. These demonstrations of stable and accessible homoaromatic neutral hydrocarbons and their photoswitching behaviour provide new understanding and insights into the study of homoconjugative interactions in organic molecules, and for the design of new responsive molecular materials.
Urban scaling laws arise from within-city inequalities
Authors: Arvidsson Martin , Lovsjö Niclas , Keuschnigg Marc 
Published: January 2023

AbstractTheories of urban scaling have demonstrated remarkable predictive accuracy at aggregate levels. However, they have overlooked the stark inequalities that exist within cities. Human networking and productivity exhibit heavy-tailed distributions, with some individuals contributing disproportionately to city totals. Here we use micro-level data from Europe and the United States on interconnectivity, productivity and innovation in cities. We find that the tails of within-city distributions and their growth by city size account for 36–80% of previously reported scaling effects, and 56–87% of the variance in scaling between indicators of varying economic complexity. Providing explanatory depth to these findings, we identify a mechanism—city size-dependent cumulative advantage—that constitutes an important channel through which differences in the size of tails emerge. Our findings demonstrate that urban scaling is in large part a story about inequality in cities, implying that the causal processes underlying the heavier tails in larger cities must be considered in explanations of urban scaling. This result also shows that agglomeration effects benefit urban elites the most, with the majority of city dwellers partially excluded from the socio-economic benefits of growing cities.
A universal deep-learning model for zinc finger design enables transcription factor reprogramming
Authors: Ichikawa David M. , Abdin Osama , Alerasool Nader , Kogenaru Manjunatha , Mueller April L. , Wen Han , Giganti David O. , Goldberg Gregory W. , Adams Samantha , Spencer Jeffrey M. , Razavi Rozita , Nim Satra , Zheng Hong , Gionco Courtney , Clark Finnegan T. , Strokach Alexey , Hughes Timothy R. , Lionnet Timothee , Taipale Mikko , Kim Philip M. , Noyes Marcus B. 
Published: January 2023

AbstractCys2His2 zinc finger (ZF) domains engineered to bind specific target sequences in the genome provide an effective strategy for programmable regulation of gene expression, with many potential therapeutic applications. However, the structurally intricate engagement of ZF domains with DNA has made their design challenging. Here we describe the screening of 49 billion protein–DNA interactions and the development of a deep-learning model, ZFDesign, that solves ZF design for any genomic target. ZFDesign is a modern machine learning method that models global and target-specific differences induced by a range of library environments and specifically takes into account compatibility of neighboring fingers using a novel hierarchical transformer architecture. We demonstrate the versatility of designed ZFs as nucleases as well as activators and repressors by seamless reprogramming of human transcription factors. These factors could be used to upregulate an allele of haploinsufficiency, downregulate a gain-of-function mutation or test the consequence of regulation of a single gene as opposed to the many genes that a transcription factor would normally influence.
APOBEC mutagenesis is a common process in normal human small intestine
Authors: Wang Yichen , Robinson Philip S. , Coorens Tim H. H. , Moore Luiza , Lee-Six Henry , Noorani Ayesha , Sanders Mathijs A. , Jung Hyunchul , Katainen Riku , Heuschkel Robert , Brunton-Sim Roxanne , Weston Robyn , Read Debbie , Nobbs Beverley , Fitzgerald Rebecca C. , Saeb-Parsy Kourosh , Martincorena Iñigo , Campbell Peter J. , Rushbrook Simon , Zilbauer Matthias , Buczacki Simon James Alexander , Stratton Michael R. 
Published: January 2023

AbstractAPOBEC mutational signatures SBS2 and SBS13 are common in many human cancer types. However, there is an incomplete understanding of its stimulus, when it occurs in the progression from normal to cancer cell and the APOBEC enzymes responsible. Here we whole-genome sequenced 342 microdissected normal epithelial crypts from the small intestines of 39 individuals and found that SBS2/SBS13 mutations were present in 17% of crypts, more frequent than most other normal tissues. Crypts with SBS2/SBS13 often had immediate crypt neighbors without SBS2/SBS13, suggesting that the underlying cause of SBS2/SBS13 is cell-intrinsic. APOBEC mutagenesis occurred in an episodic manner throughout the human lifespan, including in young children. APOBEC1 mRNA levels were very high in the small intestine epithelium, but low in the large intestine epithelium and other tissues. The results suggest that the high levels of SBS2/SBS13 in the small intestine are collateral damage from APOBEC1 fulfilling its physiological function of editing APOB mRNA.
EGOC inhibits TOROID polymerization by structurally activating TORC1
Authors: Prouteau Manoël , Bourgoint Clélia , Felix Jan , Bonadei Lenny , Sadian Yashar , Gabus Caroline , Savvides Savvas N. , Gutsche Irina , Desfosses Ambroise , Loewith Robbie 
Published: January 2023

AbstractTarget of rapamycin complex 1 (TORC1) is a protein kinase controlling cell homeostasis and growth in response to nutrients and stresses. In Saccharomyces cerevisiae, glucose depletion triggers a redistribution of TORC1 from a dispersed localization over the vacuole surface into a large, inactive condensate called TOROID (TORC1 organized in inhibited domains). However, the mechanisms governing this transition have been unclear. Here, we show that acute depletion and repletion of EGO complex (EGOC) activity is sufficient to control TOROID distribution, independently of other nutrient-signaling pathways. The 3.9-Å-resolution structure of TORC1 from TOROID cryo-EM data together with interrogation of key interactions in vivo provide structural insights into TORC1-TORC1′ and TORC1-EGOC interaction interfaces. These data support a model in which glucose-dependent activation of EGOC triggers binding to TORC1 at an interface required for TOROID assembly, preventing TORC1 polymerization and promoting release of active TORC1.
Feature-rich multiplex lexical networks reveal mental strategies of early language learning
Authors: Citraro Salvatore , Vitevitch Michael S. , Stella Massimo , Rossetti Giulio 
Published: January 2023

AbstractKnowledge in the human mind exhibits a dualistic vector/network nature. Modelling words as vectors is key to natural language processing, whereas networks of word associations can map the nature of semantic memory. We reconcile these paradigms—fragmented across linguistics, psychology and computer science—by introducing FEature-Rich MUltiplex LEXical (FERMULEX) networks. This novel framework merges structural similarities in networks and vector features of words, which can be combined or explored independently. Similarities model heterogenous word associations across semantic/syntactic/phonological aspects of knowledge. Words are enriched with multi-dimensional feature embeddings including frequency, age of acquisition, length and polysemy. These aspects enable unprecedented explorations of cognitive knowledge. Through CHILDES data, we use FERMULEX networks to model normative language acquisition by 1000 toddlers between 18 and 30 months. Similarities and embeddings capture word homophily via conformity, which measures assortative mixing via distance and features. Conformity unearths a language kernel of frequent/polysemous/short nouns and verbs key for basic sentence production, supporting recent evidence of children’s syntactic constructs emerging at 30 months. This kernel is invisible to network core-detection and feature-only clustering: It emerges from the dual vector/network nature of words. Our quantitative analysis reveals two key strategies in early word learning. Modelling word acquisition as random walks on FERMULEX topology, we highlight non-uniform filling of communicative developmental inventories (CDIs). Biased random walkers lead to accurate (75%), precise (55%) and partially well-recalled (34%) predictions of early word learning in CDIs, providing quantitative support to previous empirical findings and developmental theories.
Neuronal chemokine concentration gradients mediate effects of embryonic ethanol exposure on ectopic hypocretin/orexin neurons and behavior in zebrafish
Authors: Collier Adam D. , Yasmin Nushrat , Karatayev Olga , Abdulai Abdul R. , Yu Boyi , Khalizova Nailya , Fam Milisia , Leibowitz Sarah F. 
Published: January 2023

AbstractEmbryonic ethanol exposure in zebrafish and rats, while stimulating hypothalamic hypocretin/orexin (Hcrt) neurons along with alcohol consumption and related behaviors, increases the chemokine receptor Cxcr4 that promotes neuronal migration and may mediate ethanol’s effects on neuronal development. Here we performed a more detailed anatomical analysis in zebrafish of ethanol’s effects on the Cxcl12a/Cxcr4b system throughout the entire brain as it relates to Hcrt neurons developing within the anterior hypothalamus (AH) where they are normally located. We found that ethanol increased these Hcrt neurons only in the anterior part of the AH and induced ectopic Hcrt neurons further anterior in the preoptic area, and these effects along with ethanol-induced behaviors were completely blocked by a Cxcr4 antagonist. Analysis of cxcl12a transcripts and internalized Cxcr4b receptors throughout the brain showed they both exhibited natural posterior-to-anterior concentration gradients, with levels lowest in the posterior AH and highest in the anterior telencephalon. While stimulating their density in all areas and maintaining these gradients, ethanol increased chemokine expression only in the more anterior and ectopic Hcrt neurons, effects blocked by the Cxcr4 antagonist. These findings demonstrate how increased chemokine expression acting along natural gradients mediates ethanol-induced anterior migration of ectopic Hcrt neurons and behavioral disturbances.
Using size-weight relationships to estimate biomass of heavily targeted aquarium corals by Australia’s coral harvest fisheries
Authors: Pacey Kai I. , Caballes Ciemon F. , Pratchett Morgan S. 
Published: January 2023

AbstractCoral reefs are highly threatened environs subject to ongoing unprecedented degradation as a result of anthropogenic activities. Given the existential threat to coral reef ecosystems, extractive industries that make use of coral reef resources, are facing significant public and political pressure to quantify and justify their environmental impact. In Australia, hundreds of thousands of live scleractinian (hard) corals are harvested annually directly from the wild to supply the growing international marine aquarium trade. Many of the most popular and high value aquarium corals are believed to be slow growing, which would make them particularly vulnerable to over-fishing. Corals present a number of unique challenges for fisheries management, not least of which, is the marked variation in the size of corals, which may be harvested in whole or in part. This issue is further compounded because harvest limits are typically weight-based, but there is very limited information on the standing biomass of corals in targeted stocks. Herein, we describe size-weight relationships for some of Australia’s most heavily targeted coral species (Catalaphyllia jardinei, Duncanopsammia axifuga, Euphyllia glabrescens, Homophyllia cf. australis, Micromussa lordhowensis, Trachyphyllia geoffroyi), which allows estimation of standing biomass from transect surveys. This work represents an important first step in the development of ecologically sound management strategies by bridging the gap between catch reporting and stock assessments.