bluuebunny/crossref_metadata_2025_split huggingface dataset:
ZetaDesign: an end-to-end deep learning method for protein sequence design and side-chain packing
Authors: Yan Junyu , Li Shuai , Zhang Ying , Hao Aimin , Zhao Qinping 
Published: July 2023

Abstract
Computational protein design has been demonstrated to be the most powerful tool in the last few years among protein designing and repacking tasks. In practice, these two tasks are strongly related but often treated separately. Besides, state-of-the-art deep-learning-based methods cannot provide interpretability from an energy perspective, affecting the accuracy of the design. Here we propose a new systematic approach, including both a posterior probability and a joint probability parts, to solve the two essential questions once for all. This approach takes the physicochemical property of amino acids into consideration and uses the joint probability model to ensure the convergence between structure and amino acid type. Our results demonstrated that this method could generate feasible, high-confidence sequences with low-energy side conformations. The designed sequences can fold into target structures with high confidence and maintain relatively stable biochemical properties. The side chain conformation has a significantly lower energy landscape without delegating to a rotamer library or performing the expensive conformational searches. Overall, we propose an end-to-end method that combines the advantages of both deep learning and energy-based methods. The design results of this model demonstrate high efficiency, and precision, as well as a low energy state and good interpretability.
Public art and social media: street art tourism, sociocultural agency and cultural production in contemporary Lisbon
Authors: Garrido Castellano Carlos , Raposo Otávio 
Published: July 2023

Abstract
This essay engages with Guias do Mocho [Mocho’s Tourist Guides], a bottom-up cultural tourism initiative emerging in Quinta do Mocho, a ‘peripheral’ neighbourhood of Lisbon, as a way of problematizing the relationship between public and street art and social media aesthetics. Scholarship on digital creative industries and street art tourism tends to emphasize the complicities of this kind of cultural experience with neoliberal understandings of the urban space. By examining an example of bottom-up, localized guided tours that operates through social media in the context of peripheral areas of Lisbon, we argue that public art and social media should be seen as part of a more complicated correlation, one in which the affects and effects of creative, site-specific projects are actively developed and expanded in unforeseen ways. Our research demonstrates that public art and social media are mutually developing a renewed economy of attention and system of valorization. The critical examination of both elements is compulsory when measuring the impact of art-driven processes of community development.
Atrial fibrillation in embolic stroke of undetermined source: role of advanced imaging of left atrial function
Authors: Chousou Panagiota Anna , Chattopadhyay Rahul , Ring Liam , Khadjooi Kayvan , Warburton Elizabeth A , Mukherjee Trisha , Bhalraam U , Tsampasian Vasiliki , Potter John , Perperoglou Aris , Pugh Peter John , Vassiliou Vassilios S 
Published: July 2023

Abstract

Aims
Atrial fibrillation (AF) is detected in over 30% of patients following an embolic stroke of undetermined source (ESUS) when monitored with an implantable loop recorder (ILR). Identifying AF in ESUS survivors has significant therapeutic implications, and AF risk is essential to guide screening with long-term monitoring. The present study aimed to establish the role of left atrial (LA) function in subsequent AF identification and develop a risk model for AF in ESUS.

Methods and results
We conducted a single-centre retrospective case–control study including all patients with ESUS referred to our institution for ILR implantation from December 2009 to September 2019. We recorded clinical variables at baseline and analysed transthoracic echocardiograms in sinus rhythm. Univariate and multivariable analyses were performed to inform variables associated with AF. Lasso regression analysis was used to develop a risk prediction model for AF. The risk model was internally validated using bootstrapping. Three hundred and twenty-three patients with ESUS underwent ILR implantation. In the ESUS population, 293 had a stroke, whereas 30 had suffered a transient ischaemic attack as adjudicated by a senior stroke physician. Atrial fibrillation of any duration was detected in 47.1%. The mean follow-up was 710 days. Following lasso regression with backwards elimination, we combined increasing lateral PA (the time interval from the beginning of the P wave on the surface electrocardiogram to the beginning of the A′ wave on pulsed wave tissue Doppler of the lateral mitral annulus) [odds ratio (OR) 1.011], increasing Age (OR 1.035), higher Diastolic blood pressure (OR 1.027), and abnormal LA reservoir Strain (OR 0.973) into a new PADS score. The probability of identifying AF can be estimated using the formula. Model discrimination was good [area under the curve (AUC) 0.72]. The PADS score was internally validated using bootstrapping with 1000 samples of 150 patients showing consistent results with an AUC of 0.73.

Conclusion
The novel PADS score can identify the risk of AF on prolonged monitoring with ILR following ESUS and should be considered a dedicated risk stratification tool for decision-making regarding the screening strategy for AF in stroke.
Where the wild things are: genetic associations of environmental adaptation in the Oryza rufipogon species complex
Authors: Wang Diane R , Kantar Michael B , Murugaiyan Varunseelan , Neyhart Jeffrey 
Published: July 2023

Abstract
Crop wild relatives host unique adaptation strategies that enable them to thrive across a wide range of habitats. As pressures from a changing climate mount, a more complete understanding of the genetic variation that underlies this adaptation could enable broader utilization of wild materials for crop improvement. Here, we carry out environmental association analyses (EAA) in the Oryza rufipogon species complex (ORSC), the wild progenitor of cultivated Asian rice, to identify genomic regions associated with environmental adaptation characterized by variation in bioclimatic and soil variables. We further examine regions for colocalizations with phenotypic associations within the same collection. EAA results indicate that significant regions tend to associate with single environmental variables, although 2 significant loci on chromosomes 3 and 5 are detected as common across multiple variable types (i.e. precipitation, temperature, and/or soil). Distributions of allele frequencies at significant loci across subpopulations of cultivated Oryza sativa indicate that, in some cases, adaptive variation may already be present among cultivars, although evaluation in cultivated populations is needed to empirically test this. This work has implications for the potential utility of wild genetic resources in pre-breeding efforts for rice improvement.
Lepidopteran Synteny Units reveal deep chromosomal conservation in butterflies and moths
Authors: Traut Walther , Sahara Ken , ffrench-Constant Richard H 
Published: July 2023

Abstract
DNA is compacted into individual particles or chromosomes that form the basic units of inheritance. However, different animals and plants have widely different numbers of chromosomes. This means that we cannot readily tell which chromosomes are related to which. Here, we describe a simple technique that looks at the similarity of genes on each chromosome and thus gives us a true picture of their homology or similarity through evolutionary time. We use this new system to look at the chromosomes of butterflies and moths or Lepidoptera. We term the associated synteny units, Lepidopteran Synteny Units (LSUs). Using a sample of butterfly and moth genomes from across evolutionary time, we show that LSUs form a simple and reliable method of tracing chromosomal homology back through time. Surprisingly, this technique reveals that butterfly and moth chromosomes show conserved blocks dating back to their sister group the Trichoptera. As Lepidoptera have holocentric chromosomes, it will be interesting to see if similar levels of synteny are shown in groups of animals with monocentric chromosomes. The ability to define homology via LSU analysis makes it considerably easier to approach many questions in chromosomal evolution.
Nursing Home Resident Preferences for Daily Care and Activities: A Latent Class Analysis of National Data
Authors: Duan Yinfei , Ng Weiwen , Bowblis John R , Akosionu Odichinma , Shippee Tetyana P 
Published: July 2023

Abstract

Background and Objectives
Uncovering subgroups of nursing home residents sharing similar preference patterns is useful for developing systematic approaches to person-centered care. This study aimed to (i) identify preference patterns among long-stay residents, and (ii) examine the associations of preference patterns with resident and facility characteristics.

Research Design and Methods
This study was a national cross-sectional analysis of Minimum Data Set assessments in 2016. Using resident-rated importance for 16 preference items in the Preference Assessment Tool as indicators, we conducted latent class analysis to identify preference patterns and examined their associations with resident and facility characteristics.

Results
We identified 4 preference patterns. The high salience group (43.5% of the sample) was the most likely to rate all preferences as important, whereas the low salience group (8.7%) was the least likely. The socially engaged (27.2%) and the socially independent groups (20.6%) featured high importance ratings on social/recreational activities and maintaining privacy/autonomy, respectively. The high salience group reported more favorable physical and sensory function than the other 3 groups and lived in facilities with higher staffing of activity staff. The low salience and socially independent groups reported a higher prevalence of depressive symptoms, whereas the low salience or socially engaged groups reported a higher prevalence of cognitive impairment. Preference patterns also varied by race/ethnicity and gender.

Discussion and Implications
Our study advanced the understanding of within-individual variations in preferences, and the role of individual and environmental factors in shaping preferences. The findings provided implications for providing person-centered care in NHs.
CsBZIP40 confers resistance against citrus bacterial canker by repressing CsWRKY43-CsPrx53/CsSOD13 cascade mediated ROS scavenging
Authors: Li Qiang , Qin Xiujuan , Zhang Miao , Yu Qiyuan , Jia Ruirui , Fan Jie , Huang Xin , Fu Jia , Zhang Chenxi , Xian Baohang , Yang Wen , Long Qin , Peng Aihong , Yao Lixiao , Chen Shanchun , He Yongrui 
Published: July 2023

Abstract
As the bacterial etiologic agent causing citrus bacterial canker (CBC), Xanthomonas citri subsp. citri (Xcc) seriously impacts citrus plantation and fruit production globally. In an earlier study, we demonstrated that CsBZIP40 can positively impact CBC resistance in the sweet orange (Citrus sinensis). However, the mechanistic basis for the protective benefits conferred by CsBZIP40 is yet to be delineated. Here, we show that CsBZIP40 positively regulates CBC resistance and reactive oxygen species (ROS) homeostasis in transgenic sweet orange overexpressing CsBZIP40. CsBZIP40 directly binds to the TGA-box of the CsWRKY43 promoter to repress its transcriptional activity. CsWRKY43 overexpression induces CBC susceptibility in transgenic sweet oranges. In contrast, its inhibition produces strong resistance to CBC. CsWRKY43 directly binds to the W-boxes of the CsPrx53 and CsSOD13 promoters to positively regulate the activities of these antioxidant enzymes, resulting in the negative regulation of ROS homeostasis and CBC resistance in sweet orange plants. CsPrx53/CsSOD13 knockdown enhances ROS accumulation and CBC resistance. Overall, our results outline a regulatory pathway through which CsBZIP40 transcriptionally represses CsWRKY43-CsPrx53/CsSOD13 cascade-mediated ROS scavenging in a manner conducive to CBC resistance. These mechanisms underscore the potential importance of CsBZIP40, CsWRKY43, CsPrx53, and CsSOD13, providing promising strategies for the prevention of CBC.
Migration Deals Seen through the Lens of the ICESCR
Authors: Pijnenburg Annick 
Published: July 2023

Abstract
Human rights violations in the context of migration deals have received considerable attention, especially when it comes to more frequently explored human rights such as the principle of non-refoulement, the right to life, and the prohibition on torture. However, such deals also have a negative impact on the socio-economic rights of people on the move, who often live in dire conditions and lack access to education, health care, and work. This article therefore seeks to answer the following question: to what extent do European Union Member States have obligations under the International Covenant on Economic, Social and Cultural Rights towards people on the move contained in third countries as a result of migration deals? The analysis shows that EU Member States may have two types of obligations and examines their nature and scope. First, EU Member States have direct obligations when exercising extraterritorial jurisdiction. This is the case when they can take reasonable measures to avoid reasonably foreseeable human rights violations that result from migration deals. Secondly, they may also have global obligations within the framework of international assistance and cooperation. While the nature and scope of these obligations remain unclear, this article explores whether EU Member States have an obligation to provide international assistance and cooperation to third countries that host people on the move as a result of migration deals. It also examines whether EU Member States can comply with their obligations of international assistance and cooperation by cooperating with third countries on migration control. The article uses the examples of European migration deals with Turkey and Libya to illustrate the analysis.
Invasive Non-CandidaFungal Infections in Acute Burns—A 13-Year Review of a Single Institution and Review of the Literature
Authors: Akhavan Arya Andre , Shamoun Feras , Lagziel Tomer , Rostami Sohayla , Cox Carrie A , Cooney Carisa M , Sood Geeta , Scott Hultman Charles , Caffrey Julie A 
Published: July 2023

AbstractThe past decade has demonstrated increased burn wound infections with atypical invasive fungal organisms. The range of previously regiospecific organisms has expanded, and plant pathogens are increasingly represented. Our institution sought to examine changes in severe fungal non-Candida infections in our patients, via retrospective review of patients admitted to our burn center from 2008 to 2021. We identified 37 patients with atypical invasive fungal infections. Non-Candida genera included Aspergillus (23), Fusarium (8), Mucor (6), and 13 cases of 11 different species, including the second-ever human case of Petriella setifera. Three fungi were resistant to at least one antifungal. Concomitant infections included Candida (19), Staphylococcus and Streptococcus (14), Enterococcus and Enterobacter (13), Pseudomonas (9), and 14 additional genera. Complete data was available for 18 patients, who had a median of 3.0 (IQR 8.5, range 0–15) additional bacteria required a median of 1 (IQR 7, range 0–14) systemic antibacterials and 2 (IQR 2.5, range 0–4) systemic antifungals. One case of total-drug-resistant Pseudomonas aeruginosa required bacteriophage treatment. One case of Treponema pallidum was found in infected burn wound tissue. Every patient required Infectious Disease consultation. Eight patients became bacteremic and one developed Candida fermentatifungemia. There were five patient deaths (13.8%), all due to overwhelming polymicrobial infection. Burn patients with atypical invasive fungal infections can have severe concomitant polymicrobial infections and multidrug resistance with fatal results. Early Infectious Disease consultation and aggressive treatment is critical. Further characterization of these patients may provide better understanding of risk factors and ideal treatmentpatterns.
First records of elm zigzag sawfly (Hymenoptera: Argidae) in the United States
Authors: Oten Kelly L F , Day Eric , Dellinger Theresa , Disque Heather Harmon , Barringer Lawrence E , Cancelliere Jessica , Somers Liam , Bertone Matthew A 
Published: July 2023

Abstract
The elm zigzag sawfly (EZS), Aproceros leucopoda Takeuchi, was detected in the United States for the first time in Virginia in 2021. In 2022, it was confirmed in 4 additional states: Pennsylvania, North Carolina, Maryland, and New York. These are the first records of this species in the United States and demonstrate a rapid range expansion of an invasive defoliating pest. Native to Asia, EZS feeds exclusively on Ulmus spp. (elms; Ulmaceae). In the United States, feeding damage ranges in severity from minor to severe. Young instars create a zigzag-shaped pattern in leaves as they feed, while older larvae feed more completely on foliage, leaving only the midvein and sometimes thick lateral veins. This more complete feeding often obscures the signature zigzag defoliation of younger instars. Long-term health impacts to host trees are unknown, though aesthetic damage, growth loss, and branch dieback occur in Europe where it is also invasive. Little is known about management options for this pest, and continued expansion of this species’ range in the United States is expected.
Healthcare Costs of Clostridioides difficile Infection in Commercially Insured Younger Adults
Authors: Sahrmann John M , Olsen Margaret A , Keller Matthew R , Yu Holly , Dubberke Erik R 
Published: July 2023

Abstract
In a US adult population aged &lt;65 years, attributable costs due to Clostridioides difficile infection (CDI) were highest in persons with hospital onset and lowest in those with community-associated CDI treated outside a hospital. The economic burden of CDI in younger adults underscores the need for additional CDI-preventive strategies.
Performance of Blood-Based Nucleocapsid Antigen Tests for Diagnosis of Severe Acute Respiratory Syndrome Coronavirus 2 Infection and Infectious Viral Shedding: A Systematic Review
Authors: Mathur Sujata , So Matthew , Tahir Peggy , Peluso Michael J , Martin Jeffrey N , Kelly J Daniel 
Published: July 2023

Abstract
Data on the performance of blood-based nucleocapsid antigen tests for diagnosing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and infectious viral shedding are limited. To address this knowledge gap, we conducted a systematic review to assess the performance of blood-based nucleocapsid (N) antigen tests in diagnosing SARS-CoV-2 infection and identifying infectiousness. This review was registered on PROSPERO (registration no. CRD42022339635). We comprehensively searched PubMed, Embase, Web of Science, and the Coronavirus Research Database for relevant studies published through 27 February 2023. Each study's risk of bias was evaluated using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) tool. Our findings indicate that the performance of the N-antigen test is influenced by factors such as assay type, sampling timing, and illness severity. Sensitive assays provide suitable methods for viable screening and laboratory diagnostic tests in different clinical and research settings during the early phase of illness.
Humoral and Cellular Immune Responses of People Living With Human Immunodeficiency Virus After 3 Doses of Messenger RNA BNT162b2 Severe Acute Respiratory Syndrome Coronavirus 2 Vaccine: A Prospective Cohort Study
Authors: Tau Luba , Hagin David , Freund Tal , Halperin Tamar , Adler Amos , Marom Rotem , Ahsanov Svetlana , Matus Natasha , Levi Inbar , Gerber Gal , Lev Shir , Ziv-Baran Tomer , Turner Dan 
Published: July 2023

Abstract

Background
Recent studies have shown good serological and cellular immune responses in people living with human immunodeficiency virus (PLWH) after receipt of 2 doses of messenger RNAA (mRNA) severe acute respiratory syndrome coronavirus 2 vaccine. Data are missing regarding the response after 3 vaccine doses.

Methods
We followed up a group of PLWH who received 3 doses of the mRNA BNT162b2 vaccine and for whom data of humoral immune response after 2 vaccine doses were available. Patients provided a blood sample 4–6 months after the booster dose. The aim of the study was to measure the serological and cellular response after the third dose and to evaluate factors associated with the vaccine response.

Results
Fifty patients have provided a serum sample for serological evaluation after the booster. The anti–receptor-binding domain (RBD) immunoglobulin (Ig) G titers were higher after the booster with a median delta of 3240 arbitrary units/mL. The median CD4+ T-cell count was 660/μL (interquartile range, 515–958/μL) and had no influence on the antibody level. Factors associated with lower delta included higher CD8+ T-cell count (P = .02) and longer time between the third dose and the blood test (P = .01). Higher anti-RBD IgG titer after the second vaccine (P = .03), as well as a longer interval between second and third doses (P = .031) were associated with higher delta. There was no increase in the median number of activated interferon γ+ and tumor necrosis factor α+ CD4+ T cells after the booster (n = 8).

Conclusions
The anti-RBD IgG level after 3 doses of mRNA BNT162b2 vaccine was higher than the level after 2 doses, suggesting additional value of the booster. Cellular response did not further increase after a booster.
Imaging of plant calcium-sensor kinase conformation monitors real time calcium-dependent decoding in planta
Authors: Liese Anja , Eichstädt Bernadette , Lederer Sarah , Schulz Philipp , Oehlschläger Jan , Matschi Susanne , Feijó José A , Schulze Waltraud X , Konrad Kai R , Romeis Tina 
Published: July 2023

Abstract
Changes in cytosolic calcium (Ca2+) concentration are among the earliest reactions to a multitude of stress cues. While a plethora of Ca2+-permeable channels may generate distinct Ca2+ signatures and contribute to response specificities, the mechanisms by which Ca2+ signatures are decoded are poorly understood. Here, we developed a genetically encoded Förster resonance energy transfer (FRET)-based reporter that visualizes the conformational changes in Ca2+-dependent protein kinases (CDPKs/CPKs). We focused on two CDPKs with distinct Ca2+-sensitivities, highly Ca2+-sensitive Arabidopsis (Arabidopsis thaliana) AtCPK21 and rather Ca2+-insensitive AtCPK23, to report conformational changes accompanying kinase activation. In tobacco (Nicotiana tabacum) pollen tubes, which naturally display coordinated spatial and temporal Ca2+ fluctuations, CPK21-FRET, but not CPK23-FRET, reported oscillatory emission ratio changes mirroring cytosolic Ca2+ changes, pointing to the isoform-specific Ca2+-sensitivity and reversibility of the conformational change. In Arabidopsis guard cells, CPK21-FRET-monitored conformational dynamics suggest that CPK21 serves as a decoder of signal-specific Ca2+ signatures in response to abscisic acid and the flagellin peptide flg22. Based on these data, CDPK-FRET is a powerful approach for tackling real-time live-cell Ca2+ decoding in a multitude of plant developmental and stress responses.