bluuebunny/crossref_metadata_2025_split huggingface dataset:
Racial/Ethnic Disparities in the Observed COVID-19 Case Fatality Rate Among the U.S. Population
Authors: Schumm L. Philip , Giurcanu Mihai C. , Locey Kenneth J. , Ortega Jean Czerlinski , Zhang Zhenyu , Grossman Robert L. 
Published: March 2022

AbstractPurposeDuring the initial 12 months of the pandemic, racial and ethnic disparities in COVID-19 death rates received considerable attention but it has been unclear whether disparities in death rates were due to disparities in case fatality rates (CFRs), incidence rates or both. We examined differences in observed COVID-19 case fatality rates (CFRs) between U.S. Whites, Blacks/African Americans and Latinx during this period.MethodsUsing data from the COVID Tracking Project (CTP) and the CDC’s COVID-19 Case Surveillance Public Use dataset, we calculated CFR ratios comparing minority groups to Whites, both overall and separately by age group. We also used a model of monthly COVID-19 deaths to estimate CFR ratios, adjusting for age, gender, and differences across states and time.ResultsOverall Blacks and Latinx had lower CFRs than Whites. However, when adjusting for age, Blacks and Latinx had higher CFRs than Whites among those younger than 65. CFRs varied substantially across states and time.ConclusionsDisparities in COVID-19 case fatality among U.S. Blacks and Latinx under age 65 were evident during the first year of the pandemic. Understanding racial/ethnic differences in COVID-19 CFRs is challenging due to limitations in available data.
The laminin-keratin link shields the nucleus from mechanical deformation and signalling
Authors: Kechagia Zanetta , Sáez Pablo , Gómez-González Manuel , Zamarbide Martín , Andreu Ion , Koorman Thijs , Beedle Amy E.M. , Derksen Patrick W.B. , Trepat Xavier , Arroyo Marino , Roca-Cusachs Pere 
Published: March 2022

AbstractThe mechanical properties of the extracellular matrix (ECM) dictate tissue behaviour. In epithelial tissues, laminin is both a very abundant ECM component, and a key supporting element. Here we show that laminin hinders the mechanoresponses of breast epithelial cells by shielding the nucleus from mechanical deformation. Coating substrates with laminin-111, unlike fibronectin or collagen I, impairs cell response to substrate rigidity, and YAP nuclear localization. Blocking the laminin-specific integrin β4 increases nuclear YAP ratios in a rigidity dependent manner, without affecting cell forces or focal adhesions. By combining mechanical perturbations and mathematical modelling, we show that β4 integrins establish a mechanical linkage between the substrate and the keratin cytoskeleton, which stiffens the network and shields the nucleus from actomyosin-mediated mechanical deformation. In turn, this affects nuclear YAP mechanoresponses and chromatin methylation. Our results demonstrate a mechanism by which tissues can regulate their sensitivity to mechanical signals.
An amyloidosis-associated polymorphism does not alter LECT2 stability in vitro
Authors: Belonogov Liudmila , Taylor Paris E. , Wong Sherry , Morgan Gareth J. 
Published: March 2022

AbstractAmyloid fibrils formed from leukocyte chemotactic factor 2 (LECT2), a secreted human cytokine, are associated with kidney failure in the disease amyloid LECT2 (ALECT2) amyloidosis. This rare disease was recognized in 2008 and has a variable prevalence worldwide. The mechanisms which lead to ALECT2 fibril deposition are not known and there are no treatments other than kidney transplant. The LECT2 gene harbors a single nucleotide polymorphism that leads to either a valine or isoleucine residue at position 40 of the mature protein. Most of the individuals diagnosed with ALECT2 amyloidosis are homozygous for valine at this position, which led us to hypothesize that the valine-containing variant of LECT2 protein is less stable and more prone to aggregation than the isoleucine-containing variant. Here, we investigate the structure, stability and aggregation of both variants of recombinant LECT2. Both variants have similar structures in solution; unfold in similar concentrations of urea; and aggregate at similar rates under native-like conditions, forming structures that bind to thioflavin T. Chelation of the structural zinc ion destabilizes both variants to a similar extent, and increases the rate at which they aggregate. We do not observe a consistent difference in stability or aggregation between the variants of LECT2, so we suggest that the presence of the valine residue at position 40 does not determine whether an individual is at increased risk of ALECT2 amyloidosis.
Human pre-60S assembly factors link rRNA transcription to pre-rRNA processing
Authors: Buhagiar Amber F. , McCool Mason A. , Bryant Carson J. , Abriola Laura , Surovtseva Yulia V. , Baserga Susan J. 
Published: March 2022

AbstractIn eukaryotes, the nucleolus is the site of ribosome biosynthesis, an essential process in all cells. While human ribosome assembly is largely evolutionarily conserved, many of the regulatory details underlying its control and function have not yet been well-defined. The nucleolar protein RSL24D1 was originally identified as a factor important for ribosome biogenesis, and as an interactor with the PeBoW complex (PES1, BOP1, WDR12) in high-throughput affinity purifications. The PeBoW complex has been shown to be required for pre-28S rRNA processing. In this study, we show that RSL24D1 depletion impairs both pre-ribosomal RNA (pre-rRNA) transcription and mature 28S rRNA production, leading to decreased protein synthesis and p53 stabilization in mammalian cells. Surprisingly, each of the PeBoW complex members is also required for pre-rRNA transcription. We also demonstrate that RSL24D1 is physically complexed with RNA polymerase I, revealing a connection between large ribosomal subunit biogenesis and rDNA transcription. These results uncover the dual role of RSL24D1 and the PeBoW complex in multiple steps of ribosome biogenesis, and provide evidence implicating large subunit biogenesis factors in pre-rRNA transcription control.
Cholesterol in the cargo membrane reduces kinesin-1 binding to microtubules in the presence of tau
Authors: Li Qiaochu , Ferrare James T. , Silver Jonathan , Wilson John O. , Arteaga-Castaneda Luis , Qiu Weihong , Vershinin Michael , King Stephen J. , Neuman Keir C. , Xu Jing 
Published: March 2022

AbstractIntracellular cargos are often membrane-bound and transported by microtubule-based motors in the presence of microtubule-associated proteins (MAPs). Whereas increasing evidence reveals how MAPs impact the interactions between motors and microtubules, critical questions remain about the impact of the cargo membrane on transport. Here we combined in vitro optical trapping with theoretical approaches to determine the effect of a lipid cargo membrane on kinesin-based transport in the presence of MAP tau. Attaching kinesins to a fluid lipid membrane decreases the inhibitory effect of tau in comparison to membrane-free cargos. Adding cholesterol, which reduces kinesin diffusion in the cargo membrane, amplifies the inhibitory effect of tau on kinesin in a dosage-dependent manner. Our findings can be understood in a framework in which kinesin diffusion in the cargo membrane counteracts binding-site occlusion by tau. Our study establishes a direct link between the physical properties of cargo membrane and MAP-based regulation of kinesin-1.
Brain embeddings with shared geometry to artificial contextual embeddings, as a code for representing language in the human brain
Authors: Goldstein Ariel , Dabush Avigail , Aubrey Bobbi , Schain Mariano , Nastase Samuel A. , Zada Zaid , Ham Eric , Hong Zhuoqiao , Feder Amir , Gazula Harshvardhan , Buchnik Eliav , Doyle Werner , Devore Sasha , Dugan Patricia , Friedman Daniel , Brenner Michael , Hassidim Avinatan , Devinsky Orrin , Flinker Adeen , Hasson Uri 
Published: March 2022

AbstractContextual embeddings, derived from deep language models (DLMs), provide a continuous vectorial representation of language. This embedding space differs fundamentally from the symbolic representations posited by traditional psycholinguistics. Do language areas in the human brain, similar to DLMs, rely on a continuous embedding space to represent language? To test this hypothesis, we densely recorded the neural activity in the Inferior Frontal Gyrus (IFG, also known as Broca’s area) of three participants using dense intracranial arrays while they listened to a 30-minute podcast. From these fine-grained spatiotemporal neural recordings, we derived for each patient a continuous vectorial representation for each word (i.e., a brain embedding). Using stringent, zero-shot mapping, we demonstrated that brain embeddings in the IFG and the DLM contextual embedding space have strikingly similar geometry. This shared geometry allows us to precisely triangulate the position of unseen words in both the brain embedding space (zero-shot encoding) and the DLM contextual embedding space (zero-shot decoding). The continuous brain embedding space provides an alternative computational framework for how natural language is represented in cortical language areas.
Arbuscular mycorrhizal fungal composition across US citrus orchards, management strategies, and disease severity spectrum
Authors: Xi MengYuan , Deyett Elizabeth , Ginnan Nichole , Ashworth Vanessa E.T.M. , Dang Tyler , Bodaghi Sohrab , Vidalakis Georgios , Roper M. Caroline , Glassman Sydney I. , Rolshausen Philippe E. 
Published: March 2022

SummaryArbuscular mycorrhizal fungi (AMF) remain understudied in perennial cropping systems. Citrus is a globally grown fruit tree and under threat by the pandemic Huanglongbing (HLB) disease. Here, we assessed in what capacity geographical location, management strategies and disease affect AMF citrus root communities. Root samples were collected from 88 trees in ten orchards located in the two major citrus producing states in the US. Orchards were selected based on conventional or organic practices in California and based on HLB symptom severity in Florida. We used AMF-specific amplicon sequencing primers to capture community composition and diversity. Taxa names were assigned based on a phylogenetic analysis that comprised a backbone of AMF references sequences from Mycobank and virtual taxa from the MaarjAM database. AMF were detected in 78% of citrus root samples with taxa belonging to six known (Dominikia, Funneliformis, Glomus, Rhizophagus, Sclerocystis, Septoglomus) and unknown Glomeraceae genera. Geographical location affected AMF community composition but not richness, whereas management practice and disease influenced both richness and composition. Our approach indicated that perennial agroecosystems share a set of AMF generalist and specialist taxa. Some taxa could improve environmental fitness and be exploited for agricultural purposes.
Classifying interactions in a synthetic bacterial community is hindered by inhibitory growth medium
Authors: Santos Andrea R. Dos , Martino Rita Di , Testa Samuele , Mitri Sara 
Published: March 2022

AbstractPredicting the fate of a microbial community and its member species relies on understanding the nature of their interactions. However, designing simple assays that distinguish between interaction types can be challenging. Here, we performed spent media assays based on the predictions of a mathematical model to decipher the interactions between four bacterial species: Agrobacterium tumefaciens (At), Comamonas testosteroni (Ct), Microbacterium saperdae (Ms) and Ochrobactrum anthropi (Oa). While most experimental results matched model predictions, the behavior of Ct did not: its lag phase was reduced in the pure spent media of At and Ms, but prolonged again when we replenished with our growth medium. Further experiments showed that the growth medium actually delayed the growth of Ct, leading us to suspect that At and Ms could alleviate this inhibitory effect. There was, however, no evidence supporting such “cross-detoxification” and instead, we identified metabolites secreted by At and Ms that were then consumed or “crossfed” by Ct, shortening its lag phase. Our results highlight that even simple, defined growth media can have inhibitory effects on some species and that such negative effects need to be included in our models. Based on this, we present new guidelines to correctly distinguish between different interaction types, such as cross-detoxification and cross-feeding.
Differential Effects of Koisio Technology-Modulated Solutions on the Growth of Lung Fibroblast Cell Cultures and Lung Cancer Cell Cultures
Authors: Zhang Mingchao , Men Yinghui , Zhu Qi , Ying Weihai 
Published: March 2022

AbstractCell growth is a crucial biological property of cells, which plays key roles in several major biological processes including organ development, tissue repair and cancer development. It is of both scientific and medical significance to discover new strategies to modulate cell growth. Koisio technology is a novel technology that modulates the properties of water solely by physical approaches without additions of any external substances. In our current study we obtained the following findings regarding the effects of Koisio technology-modulated solutions on cell growth: First, compared with the lung fibroblast (L929) cell cultures cultured in normal media, the L929 cells cultured in Koisio technology-modulated media grew at approximately 20% higher speed; second, compared with the lung cancer cell cultures (LLC cells) cultured in normal media, the LLC cells cultured in Koisio technology-modulated media grew at approximately 9% lower speed; and third, compared with the telomere lengths of the L929 cells cultured in normal media, the L929 cells cultured in Koisio technology-modulated media had approximately 14% longer telomere length. Collectively, our study has provided the first evidence indicating that Koisio technology-modulated solutions affect differentially the growth of lung fibroblast cell cultures and that of lung cancer cell cultures. The capacity of the Koisio technology-modulated solutions to promote the growth of lung fibroblast cell cultures may result at least partially from its capacity to protect the telomere length.
LITOS - a versatile LED illumination tool for optogenetic stimulation
Authors: Höhener Thomas Christoph , Landolt Alex , Dessauges Coralie , Gagliardi Paolo Armando , Pertz Olivier 
Published: March 2022

AbstractOptogenetics has become a key tool to manipulate biological processes with high spatio-temporal resolution. Recently, a number of commercial and open-source multi-well illumination devices have been developed to provide throughput in optogenetics experiments. However, available commercial devices remain expensive and lack flexibility, while open-source solutions require programming knowledge and/or include complex assembly processes. We present a LED Illumination Tool for Optogenetic Stimulation (LITOS) based on an assembled printed circuit board controlling a commercially available 32×64 LED matrix as illumination source. LITOS can be quickly assembled without any soldering, and includes an easy-to-use interface, accessible via a website hosted on the device itself. Complex light stimulation patterns can easily be programmed without coding expertise. LITOS can be used with different formats of multi-well plates, petri dishes, and flasks. We validated LITOS by measuring the activity of the MAPK/ERK signaling pathway in response to different dynamic light stimulation regimes using FGFR1 and Raf optogenetic actuators. LITOS can uniformly stimulate all the cells in a well and allows for flexible temporal stimulation schemes. LITOS’s ease of use aims at democratizing optogenetics in any laboratory.
Stereochemistry of transient protein-protein interactions in a signaling hub: exploring G3BP1-mediated regulation of CFTR deubiquitination
Authors: Sheehan Colin T. , Madden Dean R. 
Published: March 2022

AbstractIntrinsically disordered proteins (IDPs) can coordinate often transient or weak interactions with multiple proteins to mediate complex signals within large, reversible protein networks. Among these, the IDP hub protein G3BP1 forms protein complexes with Caprin1 and USP10, and the resulting control of USP10 activity plays an important role in a pathogenic virulence system that targets CFTR endocytic recycling. However, while the identities of protein interactors are known for many of these IDP hub proteins, the relationship between pairwise affinities and the extent of protein recruitment and activity is not well understood. Here we describe in vitro analysis of the G3BP1 affinities, and show that substitution of G3BP1 residues F15 or F33 to tryptophan reduces affinity for both the USP10 and Caprin1 motif peptides. These same mutations significantly reduce formation of complexes by the full-length proteins. The crystal structure of G3BP1 TripleW (F15W/F33W/F124W) mutant reveals a clear reorientation of the side chain of W33, creating a steric clash with the USP10 and Caprin1 peptides. An amino-acid scan of the USP10 and Caprin1 motif peptides reveals similarities and differences in the ability to substitute residues in the core motifs as well as specific mutations with the potential to create higher affinity peptides. Taken together, these data show that small changes in 1:1 binding affinity can have significant effects on the composition of cellular interaction hubs. These specific protein mutations can be harnessed to manipulate complex protein networks, informing future investigations into roles of these networks in cellular processes.
Prediction of long-term service life of an organic coating based on short-term exposure results
Authors: Xu Yuqing , Song Guang-Ling , Zheng Dajiang 
Published: March 2022

Purpose
This study aims to provide a model to predict the service life of a thick organic coating.

Design/methodology/approach
A series of thin coating films are rapidly tested under the same exposure condition as the thick coating in its service condition by means of electrochemical impedance spectroscopy, scanning electron microscopy, energy dispersive spectroscopy and X-ray diffraction.

Findings
The validity of the model is successfully verified. The long-term protectiveness or service life of a thick organic coating can be rapidly predicted.

Originality/value
The prediction model does not require long-term experiments or any test that may alter the degradation mechanism of the thick coating.
Effectiveness of interventions to convert the energy consumption of an educational building to zero energy
Authors: Zaferanchi Mahdiyeh , Sozer Hatice 
Published: March 2022

PurposeThe amount of energy consumption of buildings has obtained international concern so the concept of zero energy building becomes a target for building designers. There are various definitions and evaluation methods for efficient buildings. However, detailed research about the critical parameters that have a major effect through the operational time to reduce the energy consumption is not emphasized as this paper represents. The main aim of this study is to identify the effect of applicable interventions on energy consumption parameters with their sensitivity to each other to reach zero energy building. Relatedly, the cost of energy reduction is also determined.Design/methodology/approachEnergy consumption parameters were defined as area lightings, space heating, space cooling, ventilation fans, pumps, auxiliary equipment and related miscellaneous equipment. The effect of each applied intervention on energy consumption was classified as high, medium, low, very low, no effect and negative effect by utilizing a sensitivity analysis. The base case's energy model is created by utilizing energy performance software such as e-Quest. Accordingly, energy performance improvement scenarios are developed by applying interventions such as lamp replacements, sensors, heat pumps and photovoltaic panels’ integration. Furthermore, sensitivity analyses of each intervention were developed for consumed energy and its cost.FindingsResults indicated the electric consumption is more effective than gas consumption on primary energy and energy cost. Solar systems decline primary energy by 78.53%, lighting systems by 13.47% and heat pump by 5.48% in this building; therefore, integrating mentioned strategies could rise the improvement rate to 100%, in other words, zero amount of energy is using from the grid that means saving $ 5,750.39 in one year.Research limitations/implicationsThe study can be applied to similar buildings. It is worthwhile to investigate suggested methods in diverse buildings with different functions and climates in future works.Practical implicationsThis study aims to investigate of energy consumption of an educational building in the Mediterranean climate to convert an existing building into a zero energy building by saving energy and renewable sources. Subsequent purposes are analyzing the effect of each strategy on energy consumption and cost.Originality/valueThe novelty of this study is filling gaps in sensitivity analysis of energy consumption parameters by not only identifying their effect on overall energy consumption but also identifying their effect on each other. Some interventions may have a positive effect on overall consumption while having a negative effect on each other. Identifying this critical effect in detail not only further improves the energy performance, but also may affect the decision-making of the interventions.
United Kingdom general elections and the impact on house prices
Authors: Aha Bismark , Higgins David , Lee Timothy 
Published: March 2022

Purpose
The paper considers if house price movements in the United Kingdom (UK) can be linked to the political cycle as governments realise homeowners represent a large portion of the voter base and their voting decisions could be influenced by the magnitude and direction of house price changes. Specifically, this paper aims to investigate whether house prices behave differently before and after elections and under different political regimes.

Design/methodology/approach
The paper analyses quarterly house price data from 1960 to 2018 together with data on UK parliamentary elections for the same period. Descriptive statistics and significance tests are used to analyse the impact of the political cycle on house price movements in the UK.

Findings
While there is no evidence that house prices in the UK performed significantly differently under different political parties, the authors observed that house prices performed much better in the last year before an election compared to the first year after an election. On average, house prices increased by 5.3% per annum in the last year before an election compared to 1.3% per annum in the first year following an election.

Research limitations/implications
The study highlights significant variations in the performance of UK house prices around election times.

Practical implications
It is imperative that the political cycle is given adequate consideration when making residential property investment decisions.

Social implications
House buyers and investors in the residential property market could include the election timings as part of their decision-making process.

Originality/value
This paper represents a unique systematic examination of the influence of the political cycle on residential houses prices in the UK.