bluuebunny/crossref_metadata_2025_split huggingface dataset:
DISCO+QR: rooting species trees in the presence of GDL and ILS
Authors: Willson James , Tabatabaee Yasamin , Liu Baqiao , Warnow Tandy 
Published: February 2023

Abstract

Motivation
Genes evolve under processes such as gene duplication and loss (GDL), so that gene family trees are multi-copy, as well as incomplete lineage sorting (ILS); both processes produce gene trees that differ from the species tree. The estimation of species trees from sets of gene family trees is challenging, and the estimation of rooted species trees presents additional analytical challenges. Two of the methods developed for this problem are STRIDE, which roots species trees by considering GDL events, and Quintet Rooting (QR), which roots species trees by considering ILS.

Results
We present DISCO+QR, a new approach to rooting species trees that first uses DISCO to address GDL and then uses QR to perform rooting in the presence of ILS. DISCO+QR operates by taking the input gene family trees and decomposing them into single-copy trees using DISCO and then roots the given species tree using the information in the single-copy gene trees using QR. We show that the relative accuracy of STRIDE and DISCO+QR depend on the properties of the dataset (number of species, genes, rate of gene duplication, degree of ILS and gene tree estimation error), and that each provides advantages over the other under some conditions.

Availability and implementation
DISCO and QR are available in github.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
Patpat: a public proteomics dataset search framework
Authors: Liao Weiheng , Zhang Xuelian 
Published: February 2023

AbstractSummaryAs the FAIR (Findable, Accessible, Interoperable, Reusable) principles have become widely accepted in the proteomics field, under the guidance of ProteomeXchange and The Human Proteome Organization Proteomics Standards Initiative, proteomics public databases have been providing Application Programming Interfaces for programmatic access. Based on generating logic from proteomics data, we present Patpat, an extensible framework for searching public datasets, merging results from multiple databases to help researchers find their proteins of interest in the vast mass spectrometry. Patpat’s 2D strategy of combining results from multiple databases allows users to provide only protein identifiers to obtain metadata for relevant datasets, improving the ‘Findable’ of proteomics data.Availability and implementationThe Patpat framework is released under the Apache 2.0 license open source, and the source code is stored on GitHub (https://github.com/henry-leo/Patpat) and is freely available.Supplementary informationSupplementary data are available at Bioinformatics online.
Demographic history and species delimitation of threeZamiaspecies (Zamiaceae) in south-eastern Mexico:Z. katzerianais not a product of hybridization
Authors: Gutiérrez-Ortega José Said , Pérez-Farrera Miguel Angel , Lopez Sergio , Vovides Andrew P 
Published: February 2023

AbstractSpeculations on hybridization among wild cycads are abundant, but empirical evidence of hybridization in cycad evolution is almost non-existent and the evolutionary consequences of hybridization in cycads have not been discussed. Previously, Zamia katzeriana was hypothesized to have a hybrid origin between two sympatric species: Z. splendens and Z. loddigesii. In this study, we aimed to reveal whether such a hypothesis is confirmed. Variation in 12 microsatellite loci, 12 morphological traits and environmental niche of ten populations representing the three species was examined. Gene flow and scenarios of demographic history were tested. Ecological niche models were reconstructed to examine present and past niche availability of the two putative parental species. Correlations between genetic, morphological, environmental and geographical distances were tested. We found that Z. katzeriana diverged from Z. splendens without experiencing admixture with its sympatric congeners. However, gene flow between Z. splendens and Z. loddigesii has occurred in one locality. The niches of the two latter species have overlapped since the Last Glacial Maximum, when admixture probably occurred. However, the admixed populations do not resemble Z. katzeriana. These results confirm that Z. katzeriana did not originate from hybridization between Z. splendens and Z. loddigesii.
The seed coat in the evolutionary context of Bromelioideae (Bromeliaceae): morphoanatomical diversity and ontogeny in the core and tankless lineages
Authors: de Carvalho Jordano D Tavares , Leme Elton M C , Mariath Jorge E de Araujo 
Published: February 2023

Abstract
Seed morphology could provide significant characters for understanding the diversification of some clades in Bromeliaceae subfamily Bromelioideae, but little is known about the anatomical diversity and ontogeny of the seed coat in this diverse subfamily. We analysed the morphoanatomy of the seed coat for 48 species from 25 genera of the major lineages of Bromelioideae, from which we selected four species for ontogenetic analysis. Standard techniques for light microscopy were adapted for the anatomical study of seeds. Thirty-three variable characters were described and compared. Flattened or angular usually exappendiculate, tegmic-endotestal seeds, with secondarily thickened endotesta and undulate or costate tegmen, are common characteristics of the tankless lineages. Long oblongoid–obovoid, appendaged or exappendiculate, exclusively tegmic and mucilaginous seeds are common to core Bromelioideae. Anatomical features of the exotegmen and testa and the number of parenchyma layers in the raphe were more variable and especially useful in delimiting genera and some species. The ontogenetic analysis was essential to propose the primary morphological homology hypotheses for the seed coat characters. Seed coat morphoanatomical features offer a promising source of phylogenetically informative characters for integrative and character evolution approaches for Bromelioideae and possibly other subfamilies of Bromeliaceae.
Prospective Cohort Study of Cryptosporidium Infection and Shedding in Infants and Their Households
Authors: Korpe Poonum , Ni Zhanmo , Kabir Mamun , Alam Masud , Ferdous Tahsin , Ara Rifat , Munday Rebecca M , Haque Rashidul , Duggal Priya 
Published: February 2023

Abstract

Background
Cryptosporidium spp. are responsible for significant diarrheal morbidity and mortality in under-5 children. There is no vaccine; thus, a focus on prevention is paramount. Prior studies suggest that person-to-person spread may be an important pathway for transmission to young children. Here we describe a longitudinal cohort study of 100 families with infants to determine rates of cryptosporidiosis within households during the coronavirus disease 2019 (COVID-19) pandemic.

Methods
Families living in Mirpur, Bangladesh, with 1 infant aged 6–8 months were enrolled and followed with weekly illness survey and stool testing for Cryptosporidium for 8 months.

Results
From December 2020 to August 2021, 100 families were enrolled. Forty-four percent of index children and 35% of siblings had at least 1 Cryptosporidium infection. Shedding of Cryptosporidium occurred for a mean (standard deviation) of 19 (8.3) days in index infants, 16.1 (11.6) days in children 1–5 years, and 16.2 (12.8) days in adults. A longer duration of Cryptosporidium shedding was associated with growth faltering in infants. There was a spike in Cryptosporidium cases in May 2021, which coincided with a spike in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases in the region.

Conclusions
In this intensive, longitudinal study of Cryptosporidium infection in families we found high rates of cryptosporidiosis in infants and children, and prolonged parasite shedding, especially among malnourished children. These data support that transmission within the household is an important route of exposure for young infants and that treatment of nondiarrheal infection to interrupt person-to-person transmission within the home may be essential for preventing cryptosporidiosis in infants.
Guidance on the Use of Convalescent Plasma to Treat Immunocompromised Patients With Coronavirus Disease 2019
Authors: Bloch Evan M , Focosi Daniele , Shoham Shmuel , Senefeld Jonathon , Tobian Aaron A R , Baden Lindsey R , Tiberghien Pierre , Sullivan David J , Cohn Claudia , Dioverti Veronica , Henderson Jeffrey P , So-Osman Cynthia , Juskewitch Justin E , Razonable Raymund R , Franchini Massimo , Goel Ruchika , Grossman Brenda J , Casadevall Arturo , Joyner Michael J , Avery Robin K , Pirofski Liise-anne , Gebo Kelly A 
Published: February 2023

Abstract
Coronavirus disease 2019 (COVID-19) convalescent plasma (CCP) is a safe and effective treatment for COVID-19 in immunocompromised (IC) patients. IC patients have a higher risk of persistent infection, severe disease, and death from COVID-19. Despite the continued clinical use of CCP to treat IC patients, the optimal dose, frequency/schedule, and duration of CCP treatment has yet to be determined, and related best practices guidelines are lacking. A group of individuals with expertise spanning infectious diseases, virology and transfusion medicine was assembled to render an expert opinion statement pertaining to the use of CCP for IC patients. For optimal effect, CCP should be recently and locally collected to match circulating variant. CCP should be considered for the treatment of IC patients with acute and protracted COVID-19; dosage depends on clinical setting (acute vs protracted COVID-19). CCP containing high-titer severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies, retains activity against circulating SARS-CoV-2 variants, which have otherwise rendered monoclonal antibodies ineffective.
Evaluation of Face Validity and Acceptability of the Care Partner Hospital Assessment Tool
Authors: Fields Beth , Carbery Madelyn , Schulz Richard , Rodakowski Juleen , Terhorst Lauren , Still Catherine 
Published: February 2023

AbstractBackground and ObjectivesCare partners of hospitalized older adults report their caregiving needs are not being addressed. The Care Partner Hospital Assessment Tool (CHAT) is a feasible and appropriate tool for practitioners’ use with care partners in the hospital setting. This article explores the face validity and acceptability of the CHAT among care partners of hospitalized older adults.Research Design and MethodsA qualitative descriptive study was used to identify common themes among care partners’ responses from semistructured interviews. The CHAT was administered to care partners of older adults admitted to a medical–surgical unit in an academic medical center in Madison, WI, from October 2021 to January 2022. A semistructured, follow-up interview was completed by the same care partners after discharge. Interviews were transcribed and coded for themes to capture overall impressions of the CHAT. Care partners addressed the usefulness, comfort, content, and complexity of the CHAT.ResultsTwelve care partners participated in the study. Care partners reported that the CHAT was easy to understand and complete, was judged to be useful to both the care partner and older adult, and helped identify care partner needs. Care partners suggested ways to improve the tool including administration, additional content areas to include, and modes of delivery.Discussion and ImplicationsThe results establish the face validity of the CHAT and support the acceptability of the tool for use with care partners of hospitalized older adults.
Positive Aging and Death or Dying: A Scoping Review
Authors: Otto Robin Brown , Fields Noelle L , Bennett Michael , Anderson Keith A 
Published: February 2023

Abstract

Background and Objectives
This scoping review aims to examine the extent and the manner in which research that utilizes successful, active, productive, and healthy aging framework(s) includes death or dying.

Research Design and Methods
An examination of peer-reviewed academic journal articles was conducted following Joanna Briggs Institute’s methodological standards for scoping reviews and conforming to Arskey and O’Malley’s 5-stage framework. The initial search resulted in 1,759 articles for review, and following the rigorous screening, 35 studies were included for the final review. A qualitative thematic analysis was used to identify how research utilizes the concepts of death and dying in the context of 4 positive aging models.

Results
The core themes identified include (a) the absence of death and dying dimensions in positive aging models; (b) older adults’ outlooks on death and dying while aging well; (c) religious and spiritual dimensions of aging well; (d) negative consequences of positive aging models without death and dying dimensions; and (e) the future of death and dying in positive aging models.

Discussion and Implications
The review delivers a critique by researchers on the noticeable absence of death and dying processes within the framework of successful, active, productive, and healthy aging models. These findings represent a rich opportunity for future research on these concepts.
Friendships and Emotional Well-Being in the Context of Race and Age
Authors: Ng Yee To , Fingerman Karen L , Birditt Kira S 
Published: February 2023

Abstract

Background and Objectives
Research suggests that friendships are associated with better emotional outcomes. Still, little is known about the implications of daily friend encounters on emotional well-being in the context of race and age. Guided by the integrative conceptual framework for friendship research, this study considers racism and cultural beliefs associated with racial groups and different social and emotional goals associated with age and investigates whether the frequency of friend encounters and the link between friend encounters and emotional well-being in everyday life would vary by race and age.

Research Design and Methods
Black (n = 80; Mage = 53.62) and White American adults (n = 89, Mage = 52.01) from the Stress and Well-being in Everyday Life study provided background and social network information, followed by ecological momentary assessment surveys in which they reported their social encounters and mood every 3 hours for 4 consecutive days.

Results
Multilevel linear models revealed no significant differences by race or age in the frequency of friend encounters. At times when individuals were with friends, their positive mood was elevated compared to when they were not (within-person association). Yet, this association was observed only among White adults and among Black individuals who were aged 41 or younger.

Discussion and Implications
This work contributes to the conceptual framework for friendship research by considering how individuals’ race and age are linked to friendship patterns. Findings highlight the importance of everyday contact with friends for enhancing momentary emotional well-being, particularly among White individuals and younger Black adults.
Pornography and religiosity: prediction and process
Authors: Wright Paul J , Tokunaga Robert , Perry Samuel L , Rains Stephen 
Published: February 2023

AbstractSexual behavior and religious practice are fundamental social dynamics of longstanding interest to communication scholars. Drawing insights from the Reinforcing Spirals Model (RSM) and Sexual Script Acquisition, Activation, Application Model (3AM), this study examined whether (a) religiosity operated primarily as a predictor of later pornography consumption, which in turn predicted heightened sexual permissiveness, or (b) earlier pornography consumption predicted lower religiosity, which in turn predicted increased sexual permissiveness. Analyses of four subsamples from nationally representative three-wave panel data yielded some evidence for both pathways, but support for the latter pathway was more robust. These findings underscore the potential influence of media on attitudes through changes in ostensibly more stable characteristics such as religiosity, in addition to the direct attitudinal effects typically theorized in communication research. They also suggest several areas where the explanatory and predictive power of the RSM and/or 3AM might be enhanced through increased clarity, nuance, and scope.
Integrating an algorithmic and health systems thinking approach to improve the uptake of government antenatal nutrition services in Vidisha, Madhya Pradesh (India), 2018 to 2021
Authors: Sethi Vani , Mishra Archana , Ahirwar K S , Singh A P , Pawar Sameer , Awasthy Pushpa , Tiwari Ankita , Saini Avi , Patel Narendra , Kumar Abhishek , Choedan Tashi , Shekhar Mansi , Joe William 
Published: February 2023

AbstractIn 2018, the Government of Madhya Pradesh initiated the feasibility testing of integrating an algorithmic approach (assess, give, counsel, treat) to strengthen antenatal nutrition services in routine government-funded programmes coupled with a health system thinking approach to strengthen the health service delivery platform. Implementation phases included (1) an evidence review and stakeholder consultations (April 2018) and (2) a health systems strengthening preparedness phase (May–December 2018), including pilot testing in Vidisha district (January–December 2019) covering ∼54 100 pregnant women with 237 antenatal contact points through 241 government auxiliary nurse midwives/staff nurses. During 2020–21, feasibility testing was expanded to an additional 7 districts. We used programme registers of the Auxiliary Nurse Midwives Registers (2019–21) and National Family Health Survey data for 2016 and 2021 to show changes in the Vidisha district and 7 expansion districts. We compare the performance of Vidisha district with Ashok Nagar district, where no such intervention occurred. Comparing 2016 and 2021 data, the Vidisha district showed improvements in receipt of antenatal care in the first trimester (29 to 85%) and in four antenatal visits (17 to 54%). Using the difference-in-difference approach, a 42% net increase in first-trimester antenatal check-ups in Vidisha as compared to Ashok Nagar is observed. There was also an improvement in the maternal nutrition budget of the state from USD 8.5 million to USD 17.8 million during this period. The Vidisha initiative offers several lessons in time-effective workflow to deliver all constituents of nutrition services at various antenatal contact points through and via routine government health systems. Continued execution of the algorithm for screening, with longitudinal data on the management of all nutrition risks, will be critical to show its long-term impact on maternal morbidities and birth outcomes.
Parental perspectives on the quality of life of children with cochlear implants in Armenia
Authors: Danielian Marie , Danielian Arman , Harutunyan Lilit , Ishiyama Akira , Akaragian Salpy 
Published: February 2023

Abstract

Objectives
The aim of this project is to assess the quality of life (QOL) of children living with cochlear implants (CIs) in Armenia using the ‘Children with Cochlear Implants: Parental Perspectives’ (CCIPP) questionnaire.

Design
A group of children received CIs after an international medical mission trip. Parents of 39 children who received CIs (30 male and 9 female, age range between 1 and 7 years, mean 6.31 years post-implantation, and mean age at time of implantation 2.92 years old) completed the CCIPP questionnaire. The questionnaire had 107 items, which were scored using a 5-point Likert scale.

Results
General functioning, communication, and support of the child domains (mean 4.13, 4.01, and 4.00, respectively) achieved the highest ratings. Effects of implantation (mean 2.97) and education (mean 3.24) received less positive ratings. Communication, general functioning, social relationship, and well-being and happiness had the most positive correlations with other domains (P &lt; 0.05). Significant but weak correlations were observed between communication and age of implantation (rs = −0.352, P &lt; 0.05), general functioning and number of spoken languages (rs = 0.372, P &lt; 0.05), and supporting the child and number of spoken languages (rs = 0.376, P &lt; 0.05).

Conclusion
The parents positively rated most domains indicating that the QOL of the child at ≥3 years post-implantation is improved and that parents view the implant as having a positive impact on their child’s life. Future studies should investigate and implement solutions to enhance parents’ satisfaction with education and effects of implantation domains by improving resource allocation to schools and providing better preoperative counseling to parents, respectively. Importantly, this project demonstrates that an international medical aid trip model can be an effective means of providing cochlear implantation to resource-limited countries.
The drifting subpulse and nulling of PSR B0820 + 02 observed with FAST
Authors: Zhi Qijun , Xu Xin , Shang Lunhua , Bai Juntao , Dang Shijun , Lu Jiguang , Dai Shi , Zhao Rushuang , Wen Zhigang , Qiao Guojun , Dong Aijun 
Published: February 2023

ABSTRACT
PSR B0820 + 02 is known to exhibit the subpulse drifting phenomenon, which carries vital information about the pulsar radiation process. In this work, we studied the subpulse drifting of PSR B0820 + 02 at a central frequency of 1250 MHz using the Five-hundred-meter Aperture Spherical radio Telescope (FAST). Thanks to the superior sensitivity of FAST, we found that PSR B0820 + 02 shows four distinct subpulse drifting modes (A, B, C, and D), the last three of which have not been reported before. The drifting periodicities of these four modes are found to be 4.3P1, 6.4P1, 8.2P1, and 10.3P1 (P1 is the pulse period), respectively. No null pulse is found in our FAST observation. By comparing the energy distribution of single pulses of all four modes, we found that mode A has the highest energy and mode D has the lowest energy. Finally, we interpreted the drift modes in terms of the carousel model, and showed that if B0820 + 02’s different drift modes are due to aliasing effects, the carousel rotation period of P4 lies in the range 29P1–33P1. The new subpulse drifting phenomena of PSR B0820 + 02 reported here provide a unique opportunity for understanding the mechanism and radiation geometry of pulsar radio radiation.
The tRNA identity landscape for aminoacylation and beyond
Authors: Giegé Richard , Eriani Gilbert 
Published: February 2023

AbstracttRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.