bluuebunny/crossref_metadata_2025_split huggingface dataset:
De Novo Genome Assemblies From Two Indigenous Americans from Arizona Identify New Polymorphisms in Non-Reference Sequences
Authors: Köroğlu Çiğdem , Chen Peng , Traurig Michael , Altok Serdar , Bogardus Clifton , Baier Leslie J 
Published: August 2024

Abstract
There is a collective push to diversify human genetic studies by including underrepresented populations. However, analyzing DNA sequence reads involves the initial step of aligning the reads to the GRCh38/hg38 reference genome which is inadequate for non-European ancestries. In this study, using long-read sequencing technology, we constructed de novo genome assemblies from two indigenous Americans from Arizona (IAZ). Each assembly included ∼17 Mb of DNA sequence not present [nonreference sequence (NRS)] in hg38, which consists mostly of repeat elements. Forty NRSs totaling 240 kb were uniquely anchored to the hg38 primary assembly generating a modified hg38-NRS reference genome. DNA sequence alignment and variant calling were then conducted with whole-genome sequencing (WGS) sequencing data from 387 IAZ using both the hg38 and modified hg38-NRS reference maps. Variant calling with the hg38-NRS map identified ∼50,000 single-nucleotide variants present in at least 5% of the WGS samples which were not detected with the hg38 reference map. We also directly assessed the NRSs positioned within genes. Seventeen NRSs anchored to regions including an identical 187 bp NRS found in both de novo assemblies. The NRS is located in HCN2 79 bp downstream of Exon 3 and contains several putative transcriptional regulatory elements. Genotyping of the HCN2-NRS revealed that the insertion is enriched in IAZ (minor allele frequency = 0.45) compared to other reference populations tested. This study shows that inclusion of population-specific NRSs can dramatically change the variant profile in an underrepresented ethnic groups and thereby lead to the discovery of previously missed common variations.
Microplastic Leachate Negatively Affects Fertilization in the Coral Montipora capitata
Authors: Wilkins Keiko W , Yew Joanne Y , Seeley Meredith , Richmond Robert H 
Published: August 2024

Synopsis
Microplastic pollution is an emerging stressor of concern to coral reef ecosystems, which are already threatened by additional global and local level anthropogenic stressors. The effects of ingesting microplastics alone on corals have been well studied, but the effects of the chemical composition of these particles have been understudied. Many microplastic-associated chemicals are endocrine disrupters potentially posing a threat to organismal reproduction. Therefore, the goal of this study was to determine if differences exist between the effects of microplastics themselves and microplastic leachate on Montipora capitata fertilization due to changes in fatty acid quantity and composition. Assays were conducted two years in a row which exposed M. capitata gamete bundles to either one of four types of recently manufactured, virgin microspheres (nylon, polypropylene, high-density polyethylene, or low-density polyethylene) at three concentrations (50, 100, or 200 particles/L) or microplastic leachates, presumably including plastic additives from these microspheres. Gamete fertilization was not impacted by microplastic particles themselves, but some of the microplastic leachate treatments with the same polymer type significantly reduced fertilization rates for M. capitata. Additionally, a total of 17 fatty acids were seen in both years, but neither fatty acid quantity nor composition correlated with observed declines in fertilization. Instead, fertilization and fatty acid data independently varied by concentration and polymer type, likely due to the presence of different chemicals. This study is the first to directly test the toxicity of microplastic leachate to coral reproduction. These findings show that microplastic-associated chemicals are an important stressor affecting successful coral fertilization and fatty acid quantity and composition and provide evidence for the negative effects of microplastic leachate to coral reproduction. Thus, plastic additives could pose an additional threat to coral replenishment and persistence in coral reef ecosystems.
New findings on the genetic basis of feathered legs in chickens: association of CUBN gene mutations with feathered-leg phenotype
Authors: Huang Lan , Guo Qixin , Sun Jialuo , Wang Zhixiu , Jiang Yong , Chang Guobin , Bai Hao 
Published: August 2024

Abstract
Chickens are the most thoroughly domesticated vertebrate species, and after long-continued natural and artificial selection, they now show rich phenotypic diversity. In particular, feathered legs present in domestic chickens are a characteristic that is carefully selected by advanced breeders. Previous studies have identified the key mutations responsible for feathered legs on chromosomes 13 and 15; however, not all chickens can be easily distinguished based on these two markers. In this study, whole-genome resequencing of 29 Bamaxiaogu chickens (BXCs) yielded 12,201,978 valid single-nucleotide polymorphisms (SNPs) and 2,792,426 valid insertions and deletions (InDels). Population structure analysis based on SNPs revealed that the test samples came from the same natural population. Based on these findings, we used an SNP- and InDel-based genome-wide association study (GWAS) to investigate the genetic basis of feathered legs in chickens. GWAS results revealed that 2 SNPs located in the introns of cubilin (CUBN; SNP1, chr2:19885382T&gt;A) and recombinant Ras suppressor protein 1 (RSU1) genes (SNP2, chr2:20002551G&gt;A), as well as an InDel (InDel1, chr2:19884383TG&gt;T) on CUBN, were all significantly associated with the presence of feathered legs. Diagnostic testing demonstrated that SNP1 effectively differentiated between chickens with feathered legs and those with clean legs (leg without feathers) within the BXC population and may thus be considered an effective marker of feathered legs in BXC. In contrast, other loci did not show the same discriminatory power. This study not only presents a new variant of feathered legs but also provides valuable novel insights into the underlying mechanisms of variation in the feathered-legs trait among chickens.
Examining imidacloprid behaviorally resistant house flies (Musca domestica L.) (Diptera: Muscidae) for neonicotinoid cross-resistance
Authors: Torres Jaqueline N , Hubbard Caleb B , Murillo Amy C 
Published: August 2024

Abstract
The house fly (Musca domestica L.) is a ubiquitous fly species commonly associated with confined animal and urban waste storage facilities. It is known for its pestiferous nature and ability to mechanically vector numerous disease-causing pathogens. Effective control of adult house fly populations has traditionally relied upon insecticidal food baits; however, due to the overuse of insecticides, resistance has proven to yield many insecticidal baits and chemical classes less effective. Imidacloprid, the most widely used neonicotinoid, has been formulated and commonly used in house fly baits for over 2 decades. However, widespread evidence of physiological and behavioral resistance to imidacloprid has been documented. While previous studies have investigated the mechanisms of behavioral resistance to imidacloprid in the house fly, it remains unclear whether behavioral resistance is specific to imidacloprid or if behavioral cross-resistance exists to other compounds within the neonicotinoid class of insecticides. The current study used no-choice and choice-feeding bioassays to examine a lab-selected imidacloprid behaviorally resistant house fly colony for cross-resistance to other insecticides in the neonicotinoid chemical class. All flies exhibited high mortality (97–100%) in no-choice assays, even when exposed to imidacloprid, indicating physiological susceptibility to all tested neonicotinoids. House flies exhibited high mortality (98–100%) in choice assays when exposed to all neonicotinoid insecticides tested besides imidacloprid. These results confirm that imidacloprid behavioral resistance is specific to the compound imidacloprid and that alternative neonicotinoids remain viable options for control. Our study showed no evidence of behavioral cross-resistance to other compounds in the neonicotinoid class.
Where There’s Hope, There’s Life
: On the Importance of Hope in Health Care
Authors: Clarke Steve , Oakley Justin 
Published: August 2024

Abstract
It is widely supposed that it is important to ensure that patients undergoing medical procedures hope that their treatments will be successful. But why is hope so important, if indeed it is? After examining the answers currently on offer in the literature, we identify a hitherto unrecognized reason for supposing that it is important that patients possess hope for a successful treatment, which draws on prospect theory, Kahneman and Tversky’s hugely influential descriptive theory about decision-making in situations of risk and uncertainty. We also consider some concerns about patient consent and the potential manipulation of patients that are raised by our account.
A rare case of chicken wishbone in Meckel’s diverticulum causing partial perforation and diverticulitis
Authors: Mamukadze Irada , Park Sean , Flessland Olivia , Moberg Libby , Jentz Amy 
Published: August 2024

Abstract
Meckel’s diverticulum (MD), a rare congenital abnormality, can lead to issues like diverticulitis and bleeding. Foreign bodies in MD are even rarer, causing vague symptoms and perforation, requiring urgent surgery. This case report highlights a patient with a foreign body in MD, focusing on clinical presentation and management. A 55-year-old male presented with abdominal pain, nausea, and vomiting. Computed tomography scan revealed a foreign body perforating the small bowel. Exploratory laparotomy found a partially perforated MD with a foreign body. Diverticulectomy was performed, and the patient recovered, discharged the next day. Foreign bodies in MD are exceedingly rare and can cause inflammation, infection, and perforation, mimicking appendicitis. Diagnosis is challenging due to nonspecific symptoms, with imaging and clinical evaluation crucial. Surgical intervention, like diverticulectomy, is primary. Early diagnosis and prompt surgery are critical in managing MD complicated by foreign bodies, ensuring favorable outcomes. This report underscores symptom recognition and effective management strategies.
Challenges in diagnosis and management of invasive ductal carcinoma in axillary ectopic breast tissue: a case study
Authors: Suliman Alsadig , Osman MagdAlden , Ali Siddig , Hussein Sara , Osman Reem Mohamed , Tageldin Enas , Ali Lobna E 
Published: August 2024

Abstract
Ectopic breast tissue (EBT) is breast tissue located outside the normal anatomic boundaries of the breasts, developing due to incomplete embryological regression of the mammary ridges. EBT can develop anywhere along the milk line, with the axilla being the most common site. While generally benign, EBT can undergo malignant transformation. This case report discusses a 24-year-old female with locally advanced invasive ductal carcinoma in the axillary EBT, highlighting its clinical presentation, diagnostic process, and management in a resource-limited setting. The patient underwent wide local excision and axillary lymph node dissection followed by adjuvant chemotherapy and radiotherapy, achieving a favorable short-term outcome. This case underscores the importance of considering EBT in differential diagnosis of axillary masses and the need for tailored treatment strategies in such settings.
Spin evolution of neutron stars in transient low-mass X-ray binaries
Authors: Cui Zhe , Li Xiang-Dong 
Published: August 2024

ABSTRACT
Millisecond pulsar + helium white dwarf (MSP + He WD) binaries are thought to have descended from neutron star low-mass X-ray binaries (NS LMXBs). The NSs accreted from the progenitors of the WDs and their spin periods were accordingly accelerated to the equilibrium periods of order milliseconds. Thus, the initial spin periods of the ‘recycled’ NSs are critically determined by the average mass transfer rate in the LMXB phase. However, the standard picture neglects the possible spin-down of the NSs when the donor star decouples from its Roche lobe at the end of the mass transfer, as well as the transient behaviour of most LMXBs. Both imply more complicated spin evolution during the recycling process. In this work, we perform detailed calculations of the formation of MSP + He WD binaries. We take into account three magnetic braking (MB) prescriptions proposed in the literature, and examine the effects of both persistent and transient accretion. We find that the spin periods are not sensitively dependent on the efficiency of MB, but are considerably influenced by the accretion mode. In comparison with persistent accretion, transient accretion leads to shorter and longer spin periods of the NSs in narrow and wide systems, respectively. This may help account for the measured spin periods of MSPs in wide binaries, which seem to be longer than predicted by the persistent accretion model.
Comparing Gaia, NED, and SIMBAD source classifications in nearby galaxies
Authors: Hales J , Barmby P 
Published: August 2024

ABSTRACT
Gaia Data Release 3 (DR3) provides the first classifications for the sources in Gaia’s all-sky database. Most Gaia sources are stars in the Milky Way, but DR3 also contains many sources that belong to nearby galaxies, as well as background galaxies and quasars. In this work, we compare the Gaia classifications from the Discrete Source Classifier (CU8-DSC) module to the more detailed and heterogeneous classifications in NED (NASA Extragalactic Database) and/or SIMBAD (Set of Identifications, Measurements and Bibliography for Astronomical Data) for sources with sky positions within twice the Holmberg radius of nearby galaxies. Matching these catalogues gives approximately $3.2\times 10^5$ unique Gaia matches for $4\times 10^5$ sources over 1040 galaxies (excluding some large Local Group galaxies) in the Local Volume Galaxy catalogue. Matched sources contain a lower fraction of Gaia-classified stars and higher fractions of galaxies and quasars ($\sim 95$ per cent, 2 per cent, and 2 per cent, respectively) than DR3 overall. Considering NED (SIMBAD) classifications as truth values, the balanced accuracy of Gaia classification is 0.80 (0.83): the most common disagreements are literature-classified galaxies Gaia-classified as stars and literature-classified stars Gaia-classified as quasars. Purity (P) and completeness (C) metrics show that agreement between Gaia classification and NED/SIMBAD classification is best for stars ($P\, \mathrm{ and}\, C\sim 0.9$), and decreases for quasars ($P\lt 0.3$ and $0.7\lt C\lt 0.8$), galaxies ($0.7\lt P\lt 0.8$ and $0.3\lt C\lt 0.6$), white dwarfs ($0.04\lt P\lt 0.6$ and $C\sim 0.6$), and binary stars ($P\, \mathrm{ and}\, C\lt 0.1$). NED or SIMBAD sources classified only by detection wavelength are most often Gaia-classified as stars, while non-stellar components of galaxies appear in all Gaia classes.
Adult outcomes of childhood kidney replacement therapy in Europe from 2008 to 2019: an ERA Registry study
Authors: Montez de Sousa Iris R , Bonthuis Marjolein , Kramer Anneke , Ordoñez Flor Angel , de la Cerda Ojeda Francisco , Rydell Helena , Helve Jaakko , Groothoff Jaap W , Hommel Kristine , Buchwinkler Lukas , Segelmark Mårten , Arici Mustafa , Palsson Runolfur , Bell Samira , Trujillo-Alemán Sara , Bakkaloglu Sevcan A , Sørensen Søren S , Vila Anna , Ortiz Alberto , Stel Vianda S , Jager Kitty J 
Published: August 2024

ABSTRACT

Background
Young adults starting kidney replacement therapy (KRT) during childhood and reaching their 18th birthday (i.e. adult survivors of childhood KRT) form a challenging population of interest to nephrologists treating adults, as during this period there will be a transition to adult renal centres. Nonetheless, few studies have focused on the epidemiology of KRT in this group. We aimed to provide an update on these patients’ characteristics, treatment history, and graft and patient survival, to report their 5-year prognosis and expected remaining lifetime.

Methods
Data on KRT patients reaching their 18th birthday in 2008–19 were collected from 21 European countries/regions providing individual patient data to the European Renal Association (ERA) Registry. Patient characteristics and treatment trajectories were examined before and after turning 18 years old. Kaplan–Meier and Cox proportional hazards regression were used for patient and graft survival analyses.

Results
In total, 2944 patients were included. The proportion of adult survivors initiating KRT at a very young age (0–4 years) and undergoing pre-emptive kidney transplantation increased. Unadjusted 5-year patient survival was 96.9% [95% confidence interval (CI) 96.2–97.5]. Dialysis patients had a higher risk of death than kidney transplant recipients [adjusted hazard ratio 5.44 (95% CI 3.34–8.86)]. Between ages 18 and 23 years, about 21% of the adult survivors lost their kidney transplant and 34% of the dialysis patients continued this treatment. Compared with the general population, life expectancy for 18-year-old kidney transplant and dialysis patients was 17 and 40 years shorter, respectively.

Conclusion
Life expectancy of 18-year-old kidney transplant recipients was lower compared with the general population, yet having a functioning kidney graft at age 18 years resulted in better outcomes than being on dialysis. Nevertheless, between ages 18 and 23 years, about one-fifth of the kidney grafts failed and one-third of the patients remained on dialysis.
Effects of Vitamin D Supplementation and Baseline Vitamin D Status on Acute Respiratory Infections and Cathelicidin: A Randomized Controlled Trial
Authors: Laaksi Akseli , Kyröläinen Heikki , Pihlajamäki Harri , Vaara Jani P , Luukkaala Tiina , Laaksi Ilkka 
Published: August 2024

Abstract

Background
Vitamin D supplementation may lower the risk of acute respiratory infection (ARI), and the effects may be mediated through the induction of cathelicidin production.

Objective
To study the effect of vitamin D supplementation on ARI and cathelicidin concentration in a randomized controlled trial (RCT) and to study the associations between baseline serum 25 hydroxyvitamin D (25(OH)D) and ARIs and cathelicidin concentrations in a 14-week follow-up study.

Methods
In the RCT study, the participants were randomized into 2 groups to receive either 20 µg of vitamin D3 or an identical placebo daily. Blood samples were obtained 3 times, at the beginning (study week 0), mid-term (study week 6), and at the end of the study period (study week 14). The follow-up study had 412 voluntary young men from 2 different locations and seasons (January and July). The primary outcomes were the number of ARIs diagnosed and the number of days off because of ARI.

Results
In the RCT, vitamin D supplementation had no effect on ARI or days off because of ARI. However, regardless of the group, vitamin D insufficiency (&lt;50 nmol/L) was associated with increased ARI. In the 14-week follow-up study, insufficient serum 25(OH)D at baseline was also associated with increased risk of ARI (odds ratio [OR], 2.1; 95% confidence interval [CI], 1.2–3.7) and also days-off duty (OR, 2.3; 95% CI, 1.3–4.0) and was inversely associated with cathelicidin concentration (OR, 0.49; 95% CI, .24–.99).

Conclusions
Sufficient serum 25(OH)D may be preventive against acute respiratory infection and the preventive effect could be mediated through the induction of cathelicidin production.
Clinical Trial Registry number: NCT05014048. https://clinicaltrials.gov/study/NCT05014048?term=NCT05014048&rank=1
“Let Us… Take Our Places in Public Affairs:” Black Women’s Political Activism in the Pacific Northwest, 1870–1920
Authors: Cobbins-Modica Quin’Nita 
Published: August 2024

Abstract
African American women in the Pacific Northwest played a significant role in local and national political campaigns before the ratification of the Nineteenth Amendment. Despite being a marginal population, they helped secure women’s voting rights and created a network of gendered partisan clubs and organizations throughout the region’s urban localities. Collectively, they sought to protect fundamental civil and human rights, expand women’s freedoms, and improve the lives of African Americans. By 1918, their organizing power and leadership within the Republican Party gave rise to the historic campaign of Alice S. Presto, the first documented Black woman to run for elective office in the United States. This article examines the early activism of western Black women and the ways they wielded their electoral and political influence to help shape the concepts of freedom and progressive politics in the American West.
Optimizing transcriptome-based synthetic lethality predictions to improve precision oncology in early-stage breast cancer: BC-SELECT
Authors: Kim Yewon , Nagy Matthew , Pollard Rebecca , Rajagopal Padma Sheila 
Published: August 2024

ABSTRACTPatients with early-stage triple-negative (TNBC) or HER2-positive (HER2+) breast cancer do not have tools to predict response before treatment. Pathologic complete response (pCR) is a proxy that still requires neoadjuvant treatment. BC-SELECT is a clinically focused computational tool that leverages genetic interactions, such as synthetic lethality (SL) or rescue (SR), to predict treatment response from gene expression data. BC-SELECT builds on existing related tools (SELECT, ENLIGHT) to navigate competing treatment options.BC-SELECT involves two main steps: (1) a “gene pair identification” step that identifies clinically relevant partner genes usingin vivoandin vitrodatasets for a drug target, and (2) “training/parameter tuning” using early-stage breast cancer clinical trials to develop predicted response scores to treatment. We evaluated BC-SELECT’s ability to predict responders to trastuzumab, poly (ADP-ribose) polymerase (PARP) inhibitors, and immunotherapy by training on three trials including 86 patients and validating on nine trials including 722 patients.BC-SELECT significantly predicted treatment response in 6/9 early-stage trials, including in all PARP inhibitors (ROC-AUCs 0.6-0.8; Odds Ratio (OR): 1.9-3.5) and immunotherapy (ROC-AUCs 0.7-0.8; OR: 3.2-7.1). BC-SELECT distinguished between responders and non-responders in 8/9 trials (FDR-corrected Wilcoxon rank-sum test p-value <0.1). BC-SELECT outperformed SELECT and ENLIGHT in predicting immunotherapy response. Specificity was comparable across subtypes, with HER2+ 0.64, TNBC 0.66, and hormone-receptor positive (HR+) 0.76.There are no standard-of-care pre-treatment predictors of response in TNBC and HER2+ breast cancer. Our findings position BC-SELECT as an eventual decision-support tool to prioritize treatments approved for patients with early-stage breast cancer.STATEMENT OF SIGNIFICANCEBC-SELECT is a clinically focused computational tool that leverages genetic interactions, such as synthetic lethality, to predict treatment response from gene expression data for PARP inhibitors and immunotherapy in early-stage breast cancer.