bluuebunny/crossref_metadata_2025_split huggingface dataset:
A “Hired Girl” Testifies Against the “Son of a Prominent Family”: Bastardy and Rape on the Nineteenth-Century Nebraska Plains
Authors: Devlin Donna Rae 
Published: December 2021

Abstract
In Red Cloud, Nebraska, in 1887, Anna “Annie” Sadilek (later Pavelka) pressed bastardy charges against the “son of a prominent family,” even though she could have, according to her pre-trial testimony, pressed charges for rape. To the literary world, Sadilek is better known as Ántonia Shimerda, the powerful protagonist in Willa Cather’s 1918 novel, My Ántonia. However, it is Sadilek’s real-life experience that allows us to better understand life on the Nebraska Plains, specifically through an examination of the state’s rape laws and the ways these laws were subsequently interpreted by the courts. The Nebraska Supreme Court, between 1877 and 1886, established the need for the state to prove force as a primary component of the definition for rape, drew boundaries around acceptable reporting times, and solidified their stance on the requirement of corroborating testimony. These factors led Sadilek to charge Charley Kaley not with rape but with bastardy, a civil suit, which almost guaranteed a successful outcome for Sadilek and her child because it would not burden the county or state with their financial welfare. In analyzing Sadilek’s choices before the law, this article demonstrates the complexities of the gendered legal systems facing women like Sadilek who sought justice for crimes of a sexual nature. Additionally significant, this article draws attention to a space and place that lacks significant study in regard to the sexual power dynamics of the nineteenth-century Great Plains West, a multicultural contact zone highly susceptible to the influences of hypermasculine control.
A Methodology for Calculation of Internal Dose Following Exposure to Radioactive Fallout from the Detonation of a Nuclear Fission Device
Authors: Anspaugh Lynn R. , Bouville André , Thiessen Kathleen M. , Hoffman F. Owen , Beck Harold L. , Gordeev Konstantin I. , Simon Steven L. 
Published: December 2021

Abstract
The purpose of this paper is to provide a methodology for the calculation of internal doses of radiation following exposure to radioactive fallout from the detonation of a nuclear fission device. Reliance is on methodology previously published in the open literature or in reports not readily available, though some new analysis is also included. Herein, we present two methodologic variations: one simpler to implement, the other more difficult but more flexible. The intention is to provide in one place a comprehensive methodology. Pathways considered are (1) the ingestion of vegetables and fruits contaminated by fallout directly, (2) the ingestion of vegetables and fruits contaminated by continuing deposition by rain- or irrigation-splash and resuspension, (3) the ingestion of vegetables and fruits contaminated by absorption of radionuclides by roots after tillage of soil, (4) the non-equilibrium transfer of short-lived radionuclides through the cow-milk and goat-milk food chains, (5) the equilibrium transfer of long lived radionuclides through milk and meat food chains, and (6) inhalation of descending fallout. Uncertainty in calculated results is considered. This is one of six companion papers that describe a comprehensive methodology for assessing both external and internal dose following exposures to fallout from a nuclear detonation. Input required to implement the dose-estimation model for any particular location consists of an estimate of the post-detonation external gamma-exposure rate and an estimate of the time of arrival of the fallout cloud. The additional data required to make such calculations are included in the six companion papers.
Poly(ADP-Ribose) Polymerase Inhibition in Small Cell Lung Cancer
Authors: Guo Matthew Z. , Marrone Kristen A. , Spira Alexander , Scott Susan C. 
Published: December 2021

Abstract
Small cell lung cancer (SCLC) is a highly aggressive neuroendocrine malignancy with high and rapid relapse rates and poor outcomes. Treatment for SCLC has historically been limited by the lack of targetable driver genomic lesions, however recent developments in the underpinnings of genomic instability in SCLC and understanding of its transcriptional subtypes have led to increased interest in the use of poly(ADP-ribose) polymerase (PARP) inhibitors as a rationale therapy. Poly(ADP-ribose) polymerase inhibitors, historically designed to target BRCA1/2-mutated malignancies, capitalize on synthetic lethality in homologous recombination–deficient tumors. In this review, we outline the mechanistic rationale for the use of PARP inhibitors in treating SCLC and detail key clinical trials investigating their use in combination with chemotherapy and immunotherapy. We describe developments in the understanding of biomarkers for sensitivity to therapy and highlight further investigational directions for the use of PARP inhibitors in treating SCLC.
New Roles of Poly(ADP-Ribose) Polymerase Inhibitors in the Treatment of Breast Cancer
Authors: Harvey-Jones Elizabeth , Vinas Villaro Gemma , Tutt Andrew 
Published: December 2021

Abstract
Since the proof of concept of synthetic lethality between poly(ADP-ribose) polymerase inhibition and loss of BRCA1/2 homologous recombination (HR) function in preclinical models and early phase clinical trials, poly(ADP-ribose) polymerase inhibitors (PARPi) are increasing part of standard-of-care treatment for advanced breast cancers with BRCA gene mutations. The field has also recently seen benefits for PARPi in early breast cancer in those with germline BRCA1 and BRCA2 pathogenic mutations, and signals that synthetic lethal affects may occur in tumors with deficiencies in HR caused by germline, somatic, or epigenetic dysregulation of a number of HR genes. Despite the evidence of the synthetic lethal effects of PARPi, they are not always effective in HR defective cancers, and as they become part of standard of care in breast cancer, the study of prevalence of distinct mechanisms of resistance to PARPi and cross-resistance with other DNA-damaging agents such as platinum in breast cancer will be important and may inform therapy choices.
PARP Inhibition in Advanced Prostate Cancer
Authors: Fenton Sarah E. , Chalmers Zachary R. , Hussain Maha 
Published: December 2021

Abstract
In May 2020, the poly(ADP-ribose) polymerase (PARP) inhibitors rucaparib and olaparib were Food and Drug Administration approved for the management of metastatic castration-resistant prostate cancers. Rucaparib was approved for tumors that harbor alterations in BRCA1 and BRCA2 following progression on chemotherapy and androgen receptor–directed therapy, whereas olaparib was approved for tumors that harbor alterations in a broader range of DNA damage repair genes following progression on androgen receptor–directed therapy. Loss-of-function mutations in genes such as BRCA1 and BRCA2 increase reliance on PARP-mediated mechanisms of DNA repair, and inhibition of this pathway results in the accumulation of lethal levels of DNA damage. This dependence is advantageous in the management of prostate cancer, as mutations in DNA damage repair genes are frequent. This review summarizes the role of PARP in cell homeostasis, methods of targeting PARP in cancer cells, and current clinical trials in the management of advanced prostate cancer with PARP inhibitors.
The Clinical Challenges, Trials, and Errors of Combatting Poly(ADP-Ribose) Polymerase Inhibitors Resistance
Authors: Pham Melissa M. , Hinchcliff Emily , Avila Monica , Westin Shannon N. 
Published: December 2021

Abstract
The use of poly(ADP-ribose) polymerase inhibitor (PARPi) exploits synthetic lethality in solid tumors with homologous recombination repair (HRR) defects. Significant clinical benefit has been established in breast and ovarian cancers harboring BRCA1/2 mutations, as well as tumors harboring characteristics of “BRCAness.” However, the durability of treatment responses is limited, and emerging data have demonstrated the clinical challenge of PARPi resistance. With the expanding use of PARPi, the significance of PARP therapy in patients pretreated with PARPi remains in need of significant further investigation. Molecular mechanisms contributing to this phenomenon include restoration of HRR function, replication fork stabilization, BRCA1/2 reversion mutations, and epigenetic changes. Current studies are evaluating the utility of combination therapies of PARPi with cell cycle checkpoint inhibitors, antiangiogenic agents, phosphatidylinositol 3-kinase/AKT pathway inhibitors, MEK inhibitors, and epigenetic modifiers to overcome this resistance. In this review, we address the mechanisms of PARPi resistance supported by preclinical models, examine current clinical trials applying combination therapy to overcome PARPi resistance, and discuss future directions to enhance the clinical efficacy of PARPi.
Composite Tissue Columella Wedge Excision for Nasal Tip Overprojection
Authors: Röjdmark Jonas , Fischer Sebastian 
Published: December 2021

Background:
The overprojected nasal tip is a challenge in facial surgery. Although several techniques are available, none has been proven to be superior. The aim of this study was to introduce a novel approach to overcome nasal tip overprojection and to evaluate its safety and efficacy.

Methods:
All patients with protruding nasal tip who underwent correction by means of a novel columella wedge technique were included in this study. In addition to detailed description of the novel surgical approach, its efficacy was analyzed by comparison of preoperative and postoperative nose dimensions. In addition, patients were examined during follow-up, and complication and revision rates were determined.

Results:
Forty-two patients were included in this study. Columella wedge technique involved resection of a 2- to 5-mm section of the middle part of the columella. Postoperatively, nose projection and length decreased by 9 and 12 percent, respectively. The relation between projection and length of the nose changed from 0.68 preoperatively to 0.61 postoperatively. This difference was statistically significant (p = 0.002). After a mean follow-up of 28 months (range, 6 to 144 months), revision operations were necessary in seven patients (16.7 percent). No instabilities, impairment of breathing, or other complications occurred.

Conclusion:
The introduced columella wedge technique is efficient and safe for correction of the overprojected nasal tip.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
Present and future distribution of bat hosts of sarbecoviruses: implications for conservation and public health
Authors: Muylaert Renata L. , Kingston Tigga , Luo Jinhong , Vancine Maurício Humberto , Galli Nikolas , Carlson Colin J. , John Reju Sam , Rulli Maria Cristina , Hayman David T. S. 
Published: December 2021

AbstractGlobal changes in response to human encroachment into natural habitats and carbon emissions are driving the biodiversity extinction crisis and increasing disease emergence risk. Host distributions are one critical component to identify areas at risk of spillover, and bats act as reservoirs of diverse viruses. We developed a reproducible ecological niche modelling pipeline for bat hosts of SARS-like viruses (subgenus Sarbecovirus), given that since SARS-CoV-2 emergence several closely-related viruses have been discovered and sarbecovirus-host interactions have gained attention. We assess sampling biases and model bats’ current distributions based on climate and landscape relationships and project future scenarios. The most important predictors of species distribution were temperature seasonality and cave availability. We identified concentrated host hotspots in Myanmar and projected range contractions for most species by 2100. Our projections indicate hotspots will shift east in Southeast Asia in >2 °C hotter locations in a fossil-fueled development future. Hotspot shifts have implications for conservation and public health, as loss of population connectivity can lead to local extinctions, and remaining hotspots may concentrate near human populations.
TIMSCONVERT: A workflow to convert trapped ion mobility data to open data formats
Authors: Luu Gordon T. , Lizama-Chamu Itzel , McCaughey Catherine S. , Sanchez Laura M. , Wang Mingxun 
Published: December 2021

AbstractSummaryAdvances in mass spectrometry instrumentation have led to the development of mass spectrometers with ion mobility separation (IMS) capabilities and dual source instrumentation, but the current software ecosystem lacks interoperability with downstream data analysis using open-source software/pipelines. Here, we present TIMSCONVERT, a data conversion workflow from timsTOF fleX MS raw data files to size conscious mzML and imzML formats with minimal preprocessing to allow for compatibility with downstream data analysis tools, which we showcase with several examples using data acquired across different experiments and acquisition modalities on the timsTOF fleX.Availability and ImplementationTIMSCONVERT and its documentation can be found at https://github.com/gtluu/timsconvert and is available as a standalone command line interface, Nextflow workflow, and online in the Global Natural Products Social (GNPS) platform (https://proteomics2.ucsd.edu/ProteoSAFe/index.jsp?params={%22workflow%22%3A%20%22TIMSCONVERT%22}).ContactMingxun Wang, miw023@ucsd.eduSupplementary InformationSupplementary data are available at Bioinformatics online.
Outcomes Associated with Expanded Take-Home Eligibility for Outpatient Treatment with Medications for Opioid Use Disorder: A Mixed-Methods Analysis
Authors: Nguyen Oanh Kieu , Steiger Scott , Snyder Hannah , Perrotta Matthew , Suen Leslie W. , Joshi Neena , Castellanos Stacy , Shapiro Brad , Makam Anil N. , Knight Kelly R. 
Published: December 2021

ABSTRACTBackgroundAccess to medications for opioid use disorder (MOUD) in the U.S. is highly restricted. In March 2020, to reduce transmission of COVID-19, SAMHSA issued emergency regulations allowing up to two weeks of take-home doses for most patients.ObjectivesWe evaluated the benefits and unintended consequences of these new regulations expanding take-home eligibility to inform MOUD policy post-pandemicMethodsWe conducted a mixed-methods evaluation of an opioid treatment program in San Francisco caring for a diverse, low-income urban population. We assessed clinic-level intake, retention, and take-home prescribing; individual-level acute care utilization and mortality; and patient/provider perceptions of benefits, harms and challenges of the new regulations.ResultsClinic volume, intake and retention were largely unchanged after implementation of the new regulations, though the average monthly proportion of individuals receiving take-homes significantly increased from 31% to 47% (p<0.001). Among 506 established patients (≥90 days of care), the 10-month mortality was 2.7% among those who never received take-homes versus 3.2% among those newly started (p=0.79) and 0.8% among those with increases in take-homes (p=0.24). Individuals who never received take-homes had higher rates of emergency department visits (47.0%) and hospitalizations (19.7%) versus those with new starts (ED visits 29.2%, p<0.001; hospitalizations 14.3%, p=0.19) or increases in take-homes (ED visits 17.5%, p<0.001; hospitalizations 10.0%, p=0.02). Both patients and providers reported increased treatment flexibility, leading to increased engagement and stabilization.ConclusionsGiven the benefit and lack of appreciable harms, policymakers should consider extending expanded MOUD take-home eligibility after COVID-19, with careful monitoring for unintended outcomes.
High correlation between binding IgG (anti-RBD/S) and neutralizing antibodies against SARS-CoV-2 six months after vaccination
Authors: Guiomar Raquel , Santos Ana João , Melo Aryse Martins , Costa Inês , Matos Rita , Rodrigues Ana Paula , Kislaya Irina , Silva Anabela Santos , Roque Carla , Silva Carla , Aguiar Joaquim , Graça Fátima , Graça Antônio Silva , Machado Ausenda 
Published: December 2021

AbstractVaccination is considered the most important measure to control the COVID-19 pandemic. Extensive follow-up studies with distinct vaccines and populations are able to promote robust and reliable data to better understand the effectiveness of this pharmacologic strategy. In this sense, we present data regarding binding and neutralizing antibodies throughout time, from vaccinated and previously infected (PI) health care workers (HCW) in Portugal. We analyzed serum samples of 132 HCW, vaccinated and with previous SARS-CoV-2 infection. Samples were collected before vaccination (baseline, M1), at second dose vaccine uptake (M2), and 25-70 days (M3) and 150-210 days (M4) after the second dose for vaccinated individuals. The IgG (anti-RBD/S) antibody geometric mean titer found on vaccinated HCW at M2 (814.7 AU/ml; 95% CI 649.8-1021.5) were significantly higher than those found on PI HCW at recruitment (M1) (252.6 AU/ml; 95% CI 108.7 - 587.1), and the neutralizing antibodies (nAb) were similar between these groups, 93.2 UI/ml (95% CI 73.2-118.5) vs. 84.1 UI/ml (95% CI 40.4-155.9), respectively. We detected about 10-fold higher IgG (anti-RBD/S) antibodies titers in M3 when compared with M2, with a slightly but significant decrease in titers from 36 days after the second dose vaccine uptake. The increase of nAb titers were correlated with IgG (anti-RBD/S) antibodies titers, however, contrasting to IgG (anti-RBD/S) antibodies titers, we did not detect a decrease in nAb titer from 36 days after a second vaccine dose uptake. At M4, was observed a decrease of 8-fold in binding IgG (anti-RBD/S) and nAb. No significant differences in antibody titers were observed by sex, age or chronic diseases. Our results suggest that IgG (anti-RBD/S) antibodies titers and nAb titers could be correlated, but ongoing follow up of the cohort, is required to better understand this correlation, and the duration of the immune response.
Measuring the impact of COVID-19 vaccination and immunity waning: a modelling study for Portugal
Authors: Caetano Constantino , Morgado Maria Luísa , Patrício Paula , Leite Andreia , Machado Ausenda , Torres André , Pereira João Freitas , Namorado Sónia , Sottomayor Ana , Peralta André , Nunes Baltazar 
Published: December 2021

AbstractVaccination strategies to control COVID-19 have been ongoing worldwide since the end of 2020. Understanding their possible effect is key to prevent future disease spread. Using a modelling approach, this study intends to measure the impact of the COVID-19 Portuguese vaccination strategy on the effective reproduction number and explore three scenarios for vaccine effectiveness waning. Namely, the no-immunity-loss, 1-year and 3-years of immunity duration scenarios. We adapted an age-structured SEIR deterministic model and used Portuguese hospitalisation data for the model calibration. Results show that, although the Portuguese vaccination plan had a substantial impact in reducing overall transmission, it might not be sufficient to control disease spread. A significant vaccination coverage of those above 5 years old, a vaccine effectiveness against disease of at least 80% and softer non-pharmaceutical interventions (NPIs), such as mask usage and social distancing, would be necessary to control disease spread in the worst scenario considered. The immunity duration scenario of 1-year displays a resurgence of COVID-19 hospitalisations by the end of 2021, the same is observed in 3-year scenario although with a lower magnitude. The no-immunity-loss scenario presents a low increase in hospitalisations. In both the 1-year and 3-year scenarios, a vaccination boost of those above 65 years old would result in a 53% and 38% peak reduction of non-ICU hospitalisations, respectively. These results suggest that NPIs should not be fully phased-out but instead be combined with a fast booster vaccination strategy to reduce healthcare burden.
The economic burden of protecting islands from invasive alien species
Authors: Bodey Thomas W , Angulo Elena , Bang Alok , Bellard Céline , Fantle-Lepczyk Jean , Lenzner Bernd , Turbelin Anna , Watari Yuya , Courchamp Franck 
Published: December 2021

AbstractBiological invasions represent a key threat to island ecosystems, with pronounced impacts across environments and economies. The ecological impacts have received substantial focus, but the economic costs have lacked synthesis at spatial and temporal scales. Here we utilise the InvaCost database, the most comprehensive global assessment of published economic costs of invasive species, to assess reported spend by cost types and socioeconomic sectors, and to examine temporal trends in spending, across islands that differ in their political geography - nation states, overseas territories or offshore islands of continental countries. We based this assessment on 1473 unique cost entries comprising 2914 annual costs totalling almost US$100 million in area-corrected costs between 1965-2020. We find that offshore islands of continental countries incur the greatest total and management costs. However, nation states incurred the greatest damage costs whilst substantially financing management actions, and spent an overall greater proportion of their GDP. In contrast, spending within overseas territories was significantly lower in all respects. The most impacted sector was authorities and stakeholders, demonstrating the key role of government in addressing island invasions. Temporal trends revealed continual increases in spending across all island types. This likely reflects ongoing introduction rates globally alongside an increased recognition of the importance of islands as biodiversity hotspots, and an appetite to tackle invasive species at larger and more socially complex scales. However, the high economic costs of invasions on islands substantiates the need to prevent them in order to avoid this dire threat to biodiversity and its burden on limited conservation resources.
Comparative analysis of gene prediction tools for viral genome annotation
Authors: González-Tortuero Enrique , Krishnamurthi Revathy , Allison Heather E. , Goodhead Ian B. , James Chloë E. 
Published: December 2021

AbstractThe number of newly available viral genomes and metagenomes has increased exponentially since the development of high throughput sequencing platforms and genome analysis tools. Bioinformatic annotation pipelines are largely based on open reading frame (ORF) calling software, which identifies genes independently of the sequence taxonomical background. Although ORF-calling programs provide a rapid genome annotation, they can misidentify ORFs and start codons; errors that might be perpetuated and propagated over time. This study evaluated the performance of multiple ORF-calling programs for viral genome annotation against the complete RefSeq viral database. Programs outputs varied when considering the viral nucleic acid type versus the viral host. According to the number of ORFs, Prodigal and Metaprodigal were the most accurate programs for DNA viruses, while FragGeneScan and Prodigal generated the most accurate outputs for RNA viruses. Similarly, Prodigal outperformed the benchmark for viruses infecting prokaryotes, and GLIMMER and GeneMarkS produced the most accurate annotations for viruses infecting eukaryotes. When the coordinates of the ORFs were considered, Prodigal scored high for all scenarios except for RNA viruses, where GeneMarkS generated the most reliable results. Overall, the quality of the coordinates predicted for RNA viruses was poorer than for DNA viruses, suggesting the need for improved ORF-calling programs to deal with RNA viruses. Moreover, none of the ORF-calling programs reached 90% accuracy for annotation of DNA viruses. Any automatic annotation can still be improved by manual curation, especially when the presence of ORFs is validated with wet-lab experiments. However, our evaluation of the current ORF-calling programs is expected to be useful for the improvement of viral genome annotation pipelines and highlights the need for more expression data to improve the rigor of reference genomes.