bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving correlation of wastewater SARS-CoV-2 gene copy numbers with COVID-19 public health cases using readily available biomarkers
Authors: Hutchison Justin M , Li Zhengxi , Chang Chi-Ning , Hiripitiyage Yasawantha , Wittman Megan , Sturm Belinda S M 
Published: April 2022

Abstract
The COVID-19 (coronavirus disease 2019) pandemic has highlighted the potential role that wastewater-based epidemiology can play in assessing aggregate community health. However, efforts to translate SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) gene copy numbers obtained from wastewater samples into meaningful community health indicators are nascent. In this study, SARS-CoV-2 nucleocapsid (N) genes (N1 and N2) were quantified weekly using reverse transcriptase droplet digital PCR from two municipal wastewater treatment plants for 6 months. Four biomarkers [ammonium, biological oxygen demand (BOD), creatinine and human mitochondrial gene NADH dehydrogenase subunit 5] were quantified and used to normalize SARS-CoV-2 gene copy numbers. These were correlated to daily new case data and 1-, 2- and 3-week cumulative case data. Over the course of the study, the strongest correlations were observed with a 1-day case data lag. However, early measurements were strongly correlated with a 5-day case data lag. This indicates that in the early stages of the pandemic, the wastewater samples may have indicated active COVID-19 cases before clinical indications. Mitochondrial and creatinine normalization methods showed the strongest correlations throughout the study, indicating that human-specific biomarkers were better at normalizing wastewater data than ammonium or BOD. Granger causality tests supported this observation and showed that gene copies in wastewater could be predictive of new cases in a sewershed.
Privacy
Authors: Arguelhes Diego Werneck , Moncau Luiz Fernando Marrey 
Published: April 2022

Abstract
This chapter focuses on the right to privacy as primarily involving the control of information about oneself. Section 2 presents a brief comparative, descriptive analysis of how nineteen Latin American constitutions have enshrined different dimensions of this right to control over information about oneself. Section 3 discusses the protection of personal data and the Habeas Data, a right/remedy that many constitutions in the region have enshrined for the protection of aspects of privacy and personal data, and which is considered to be one of the distinct Latin American contributions to the global constitutional repertoire. Section 4 focuses on the emerging idea of a ‘right to be forgotten’ while Section 5 concludes with broader considerations on some of the trends and commonalities that can be identified in the region.
Safety, Efficacy, and Tolerability of Simultaneous Bilateral Cryolipolysis Using a Rapid Cycling Contoured Cup Applicator for Noninvasive Fat Reduction in the Enlarged Male Breast: A Pilot Study
Authors: Munavalli Girish S. , Martin Elise D. , Macri Angela E. 
Published: April 2022

BACKGROUND
A previous study using a parallel cooling plate cryolipolysis applicator demonstrated the efficacy of cryolipolysis for pseudogynecomastia. Although the procedure was safe and effective, treatment times were prolonged and anesthetic was needed to reduce treatment discomfort.

OBJECTIVE
To evaluate the safety, efficacy, and tolerability of a short cycle, reduced vacuum contoured cup cryolipolysis applicator for the treatment of pseudogynecomastia.

MATERIALS AND METHODS
Twelve male subjects received simultaneous bilateral treatment consisting of a 35-minute cryolipolysis cycle, followed by a short manual massage, and a second 35-minute cycle with 50% treatment area overlap in a single treatment visit. At the 6-week follow-up, a second treatment was performed with up to 2 overlapping cycles per side. Efficacy was assessed after the second treatment using transcutaneous ultrasound, standardized clinical photography, and subject surveys.

RESULTS
Ultrasound analysis showed a mean fat layer reduction of 5.1 ± 2.3 mm (p < .001). Blinded, independent reviewers correctly identified 97% of baseline/treatment photography results. Surveys revealed 100% subject satisfaction with 91% reporting visible fat reduction and 100% stating they would recommend treatment. Transient side effects included mild intratreatment discomfort, paresthesia, and tenderness.

CONCLUSION
A rapid cycling, reduced vacuum cryolipolysis applicator provides rapid, safe, effective, and tolerable treatment of pseudogynecomastia.
Impact of Gestational COVID-19 on Neonatal Outcomes
Authors: Vigil-Vázquez Sara , Carrasco-García Itziar , Hernanz-Lobo Alicia , Manzanares Ángela , Pérez-Pérez Alba , Toledano-Revenga Javier , Muñoz-Chapuli Mar , Mesones-Guerra Lara , Martínez-Lozano Andrea , Pérez-Seoane Beatriz , Márquez-Isidro Elena , Sanz-Asín Olga , Caro-Chinchilla Gloria , Sardá-Sánchez Marta , Solaz-García Álvaro , López-Carnero Juan , Pareja-León Marta , Riaza-Gómez Mónica , Ortiz-Barquero María Concepción , León-Luis Juan Antonio , Fernández-Aceñero María Jesús , Muñoz-Fernández María Ángeles , Catalán-Alonso Pilar , Muñoz-García Patricia , Sánchez-Luna Manuel , Navarro-Gómez María Luisa ,   on behalf of GESNEO-COVID cohort Working Group
Published: April 2022

Background:
The vertical transmission of severe acute respiratory coronavirus-2 (SARS-CoV-2) remains highly debated. Here, we evaluated SARS-CoV-2-transmission in newborns with intrauterine conditions.

Methods:
This was a prospective, observational and multicentric study involving 13 Spanish hospitals included in the GEStational and NEOnatal-COVID cohort. Pregnant women with microbiologically confirmed SARS-CoV-2 infection during any trimester of pregnancy or delivery and their newborns were included from March to November 2020. Demographic, clinical and microbiological data were also obtained. Viral loads were analyzed in different maternal and newborn biological samples (placenta, breast milk and maternal blood; urine, meconium and newborn blood).

Results:
A total of 177 newborns exposed to SARS-CoV-2 were included. Newborns were tested by reverse transcriptase-polymerase chain reaction using nasopharyngeal swabs within the first 24–48 hours of life and at 14 days of life. In total 5.1% were considered to have SARS-CoV-2 infection in the neonatal period, with 1.7% considered intrauterine and 3.4% intrapartum or early postnatal transmission cases. There were no differences in the demographic and clinical characteristics of the pregnant women and their newborns’ susceptibility to infections in their perinatal history or background.

Conclusions:
Intrauterine transmission of SARS-CoV-2 is possible, although rare, with early postnatal transmission occurring more frequently. Most infected newborns remained asymptomatic or had mild symptoms that evolved well during follow-up. We did not find any maternal characteristics predisposing infants to neonatal infection. All infected newborn mothers had acute infection at delivery.
Although there was no presence of SARS-CoV2 in cord blood or breast milk samples, SARS-CoV-2 viral load was detected in urine and meconium samples from infected newborns.
Forensic Mental Health Care Staff Experiences of Providing Palliative Care
Authors: Matthew Wendy , Collier Aileen , McKenna Brian 
Published: April 2022

ABSTRACT

Background
There is a steady increase in the number of people dying within the walls of forensic institutions across the world. This escalation is, to a large extent, because of an aging population. There is a need to explore how palliative care can be delivered in these settings where, historically, security has been the main focus.

Objective
The aims of this study were to explore staff experiences of providing palliative care in a forensic mental health unit and to establish the subjective significance of those experiences.

Method
A qualitative, descriptive, case study approach was used. This study examined staff perspectives of provision of palliative care to a long-term service user who had been diagnosed with a life-limiting illness and who subsequently died. Interviews were analyzed using codebook thematic analysis.

Results
There were nine in-depth interviews with staff who were involved in the service user's care. Analysis resulted in five main themes: intrinsic dignity, “It was out of our depth,” “It's just the way these places are,” “Hospital was the practical place,” and specialist services.

Conclusion
If equitable access to palliative care is a human right, then it is essential that individuals in secure care with mental illness are able to access palliative care services that are responsive to their needs. Forensic mental health services need to be proactively prepared for the inevitability that people will die in their care.
Climate Change and Physiatry: A Call to Proportional and Prospective Action
Authors: Taylor Anita Lowe , Perret Danielle , Morice Karen , Zafonte Ross , Skelton Felicia , Rivers Evan , Alexander Marcalee 
Published: April 2022

Abstract
Through increased temperature-related illness, exposure to wildfire smoke and air pollutants, and more frequent and intense natural disasters, climate change is disproportionately affecting the health of people with disabilities. While the evidence behind the health effects of climate change is growing, there remain critical research gaps in the physiatric literature that must be addressed. Increased education throughout the medical-education continuum is also needed to prepare physiatrists to address the climate-related health effects impacting their patient populations. Physiatrists and their member organizations should advocate for policies that address climate change with a focus on the unique needs of their patient population and the inclusion of people with disabilities in the policy making process.
The maintenance of self-incompatibility and the genetic architecture of inbreeding depression
Authors: Schoen Daniel J. , Baldwin Sarah J. 
Published: March 2022

SummaryInbreeding depression plays a fundamental role in evolution. To help detect and characterize viability loci that underlie inbreeding depression, we forced self-pollinated plants from self-incompatible populations of Leavenworthia alabamica to produce families of progeny that were genotyped at hundreds of mapped single nucleotide polymorphism (SNP) loci.Bayesian analysis of segregation data for each SNP was used to explore support for different dominance and selection coefficients at linked viability loci in different genomic regions.There was some support for overdominance (or pseudo-overdominance) at a few viability loci, as well as for recessiveness and underdominance. One recessive viability locus mapped to the genomic region of the novel self-incompatibility locus in Leavenworthia alabamica, but in general there was no support for strongly recessive viability loci of major effect.The results are consistent with earlier findings showing that inbreeding depression is recalcitrant to purging in Leavenworthia alabamica. The results also help account for the maintenance of self-incompatibility in this species and are consistent with expectations from evolutionary genetic theory that recessive, deleterious alleles linked to loci under balancing selection are sheltered from selection.
Development of a Novel Microfluidic Co-culture model to study Organoid Vascularization
Authors: Schulla Lydia S. , Alupoaie E. Diana , De Silva Leanne , Gawlitta Debby , Middendorp Sabine , Coffer Paul J. , Roukens M. Guy 
Published: March 2022

AbstractOrganoids hold great potential for regenerative medicine and biomedical research. While they are able to recapitulate many structural and functional aspects of their in vivo counterparts, they lack a functional vasculature. In this study, we aimed to coculture human small intestinal organoids (hSIO) with a vasculature in a triple co-culture system with endothelial cells (ECs) and fibroblasts in a microfluidic device. Organoids and micro-vessels favour distinct matrix and medium conditions, which were optimized to sustain growth of all cell types. In addition, we found that organoids exhibit poor survival in monoculture in the microfluidic devices. Interestingly, co-culturing hSIO together with ECs and fibroblasts enhances stemness and survival of hSIO. This effect can be further enhanced by adding the GSK-3β inhibitor CHIR99021 to the medium to enhance Wnt signalling. Direct contact of fibroblasts is not required for either vessel formation or for the effect on stem cell maintenance of organoids, as culturing fibroblasts in side-channels yields larger micro-vessels and better organoid survival. Additionally, we observed that the response of cells to different culture media is strongly dependent on the culture set-up as the second setup allows organoids to be cultured in angiogenic medium. Our results suggest that angiocrine signalling by the vasculature affects stem cell maintenance, which should be further investigated. Our co-culture system offers a platform to study angiocrine signalling in the small intestine, which could in the future be used to unravel different mechanisms behind endothelial mediated intestinal homeostasis and (patho) physiology.
A spatial genome aligner for multiplexed DNA-FISH
Authors: Jia Bojing Blair , Jussila Adam , Kern Colin , Zhu Quan , Ren Bing 
Published: March 2022

AbstractMultiplexed fluorescence in situ hybridization (FISH) has emerged as a powerful approach for analyzing 3D genome organization, but it is eminently challenging to derive chromosomal conformations from noisy fluorescence signals. Tracing chromatin is not straightforward as chromosomes lack conserved shapes for reference checking whether an observed fluorescence signal belongs to a chromatin fiber or not. Here we report a spatial genome aligner that parses true chromatin signal from noise by aligning signals to a DNA polymer model. We demonstrate that this spatial genome aligner can efficiently reconstruct chromosome architectures from DNA-FISH data across multiple scales and determine chromosome ploidies de novo in interphase cells. Reprocessing of previous whole-genome chromosome tracing data with this method revealed the spatial aggregation of sister chromatids in S/G2 phase cells in asynchronous mouse embryonic stem cells, and uncovered extranumerary chromosomes that remain tightly paired in post-mitotic neurons of the adult mouse cortex. Our spatial genome aligner may facilitate the adaption of multiplexed DNA-FISH by the community.
NADK upregulation is an essential metabolic adaptation that enables breast cancer metastatic colonization
Authors: Ilter Didem , Schild Tanya , Ward Nathan P. , Drapela Stanislav , Adhikari Emma , Low Vivien , Le-Lau Eric , DeNicola Gina M. , McReynolds Melanie R. , Gomes Ana P. 
Published: March 2022

AbstractMetabolic reprogramming and metabolic plasticity allow cancer cells to fine-tune their metabolism to adapt to the ever-changing environments of the metastatic cascade, for which lipid metabolism and oxidative stress are of particular importance. Continuous production of NADPH, a cornerstone of both lipid and redox homeostasis, is essential for proliferation and cell survival suggesting that cancer cells may require larger pools of NADPH to efficiently metastasize. NADPH is recycled through reduction of NADP+ by several enzymatic systems in cells; however, de novo NADP+ is synthesized only through one known enzymatic reaction, catalysed by NAD+ kinase (NADK). Here, we show that NADK is upregulated in metastatic breast cancer cells enabling de novo production of NADP(H) and the expansion of the NADP(H) pools thereby increasing the ability of these cells to adapt to the oxidative challenges of the metastatic cascade and efficiently metastasize. Mechanistically, we found that metastatic signals lead to a histone H3.3 variant-mediated epigenetic regulation of the NADK promoter, resulting in increased NADK levels in cells with metastatic ability. Together, our work presents a previously uncharacterized role for NADK as an important contributor to breast cancer progression and suggests that NADK constitutes an important and much needed therapeutic target for metastatic breast cancers.
Engagement of health workers and peer educators from the National Adolescent Health Programme-Rashtriya Kishor Swasthya Karyakram during the COVID-19 pandemic: findings from a situational analysis
Authors: Arora Monika , Dringus Stefanie , Bahl Deepika , Rizvi Zoya , Maity Heeya , Lama Smritima , Mason-Jones Amanda J. , Kumar Deepak , Koul Prairna , Bassi Shalini 
Published: April 2022

AbstractBackgroundTo understand the impact of COVID-19 on implementation of the peer education programme of the National Adolescent Health Programme-Rashtriya Kishor Swasthya Karyakram; repurposing of the RKSK health workers and Peer Educators (PE) in COVID-19 response activities and; adolescents′ health and development issues.MethodsVirtual in-depth interviews were conducted with stakeholders (n=31) (aged 15 to 54) engaged in the implementation of the peer education programme at state, district, block, and village levels in Madhya Pradesh and Maharashtra (India). These interviews were thematically coded and analysed to address the research objectives.ResultsDespite most peer education programme activities being stopped, delayed, or disrupted during the pandemic and subsequent lockdown, some communication networks previously established, helped facilitate public health communication regarding COVID-19 and RKSK, between health workers, peer educators, and adolescents. There was significant repurposing of RKSK health workers and Peer Educators’ role towards COVID-19 response-related activities. Peer educators, with support from health workers, were involved in disseminating COVID-19 information, maintaining migrant and quarantine records, conducting household surveys for finding COVID-19 active cases and providing essential items (grocery, sanitary napkins, etc.) to communities and adolescents.ConclusionPeer Educators with support from community health workers are able to play a crucial role in meeting the needs of the communities during a pandemic. There is a need to further engage, involve and build the skills of Peer Educators to support the health system. PEs can be encouraged by granting more visibility and incorporating their role more formally by paying them within the public health system in India.
In silicoanalysis ofBacopa monnieri(L.) Wettst. compounds for drug development against Neurodegenerative Disorders
Authors: Sangeet Satyam , Khan Arshad , Mahanta Saurov , Roy Nabamita , Das Sanjib Kumar , Mohanta Yugal Kishore , Saravanan Muthupandian , Tag Hui , Hui Pallabi Kalita 
Published: April 2022

ABSTRACTNeurotrophins play a crucial role in the development and regulation of neurons. Alterations in the functioning of these Neurotrophins leads to several Neurodegenerative Disorders. Albeit engineered medications which are accessible for the treatment of Neurodegenerative Disorders, due to their numerous side-effects, it becomes imperative to formulate and synthesize novel drug candidates. Plants could be utilized as an alternative for these manufactured medications because of their low incidental effects in contrast with the engineered drugs.Bacopa monnierihas been traditionally known to be utilized to treat Neurodegenerative Disorders. Therefore, in current study anin-silicobased study was carried out to evaluate the pharmacological effect ofBacopa monnieri. Molecular Docking was carried out to screen the active phytochemicals ofBacopa monnieriwhich can act as potential drug candidates against the causative proteins of Neurodegenerative Disorders. A total of 105 biologically active phytochemicals fromBacopa monnieriwere docked against the receptors of brain-derived neurotrophic factor, neurotrophin-3, neurotrophin-4, and nerve growth factor. Based on molecular docking study it was observed that the phytocompounds Vitamin E, Benzene propanoic acid, 3,5-bis(1,1dimethylethyl)4-hydroxy-, methyl ester (BPA), Stigmasterol, and Nonacosane ofBacopa monnierisignificantly fits to the active residues of the four selected drug targets. Further Molecular Dynamics simulation study was performed to examine the stability of the binding of these phytochemicals with the selected targets. Drug likeness properties as well as related physico-chemical properties were analyzed through ADMETox study. Our findings suggested that the phytocompounds Vitamin E, BPA, Stigmasterol and Nonacosane significantly bind against brain-derived neurotrophic factor, neurotrophin-3, neurotrophin4, and nerve growth factor, respectively which may be the potential drug candidates for the treatment of neurodegenerative disorders.Graphic Abstract
One-sided design of protein-protein interaction motifs using deep learning
Authors: Syrlybaeva Raulia , Strauch Eva-Maria 
Published: April 2022

AbstractProtein-protein interactions are part of most processes in life and thereby the ability to generate new ones to either control, detect or inhibit them has universal applications. However, to develop a new binding protein to bind to a specific site at atomic detail without any additional input is a challenging problem. After DeepMind entered the protein folding field, we have seen rapid advances in protein structure predictions thanks to the implementation of machine learning algorithms. Neural networks are part of machine learning and they can learn the regularities from their input data. Here, we took advantage of their capabilities by training multiple neural networks on co-crystal structures of natural protein complexes. Inspired by image caption algorithms, we developed an extensive set of NN-based models, referred to as iNNterfaceDesign. It predicts the positioning and the secondary structure for the new binding motifs and then designs the backbone atoms followed by amino acid sequence design. Our methods are capable of recapitulating native interactions, including antibody-antigen interactions, while they also capable to produce more diverse solutions to binding at the same sites. As it was trained on natural complexes, it learned their features and can therefore also highlight preferential binding sites, as found in natural protein-protein interactions. Our method is generally applicable, and we believe that this is the first deep learning model for one-sided design of protein-protein interactions.Abstract figure
Convergent genomic signatures of adaptation to an extreme environment in cyprinoid fishes
Authors: Tong Chao , Li Miao 
Published: April 2022

AbstractCyprinoids are a worldwide distributed and diverse group of freshwater fish with more than 3,000 species. Although primarily freshwater, some cyprinoid species had convergently evolved to thrive in extreme environments and underlying genetic mechanisms remain unclear. Here, we leveraged 32 cyprinoid fish genomes to identify common genomic changes associated with convergent adaptation to highly saline and alkaline water in two East Asian cyprinoid fish species, Gymnocypris przwalskii and Leuciscus waleckii, representing two independent extremophile fish lineages. We found that genome-wide rate of nonsynonymous substitution and signal of intensified selection is higher in extremophile relative to non-extremophile fish taxa. We further tested gene-wide molecular convergence and found hundreds of genes tended to experience convergent shifts in selections in extremophile fish taxa, including convergent acceleration and positive selection. These genes were associated with several key functions, such as nervous system development, reproduction, ion transport and immune response, and included genes that previously have been implicated for saline or alkaline tolerance in fish. Additionally, comparative transcriptomic analyses defined the convergent roles of differentially expressed genes under selection in extremophile fish taxa during convergent adaptation. Taken together, our work provides insights into the genomic basis of convergent adaptation to extreme environments in fish.