bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic insights intoCronobacterspp. recovered from food and human clinical cases in Zhejiang province, China (2008–2021)
Authors: Li Yi , Lin Guankai , Zhang Leyi , Hu Yuqin , Hong Chengji , Xie Airong , Fang Lei 
Published: February 2023

AbstractAimsCronobacter spp. are emerging food-borne pathogens capable of causing life-threatening illness via several distinct routes. Although endeavors to reduce the incidence of Cronobacter infections are implemented, potential risk of these microorganisms on food safety remains poorly understood. Here, we evaluated the genomic features of clinical Cronobacter and the possible food reservoirs of these infections.Methods and resultsWhole-genome sequencing (WGS) data of all human clinical cases (n = 15) during 2008–2021 in Zhejiang were used and compared to sequenced Cronobacter genomes (n = 76) representing various food products. Cronobacter strains exhibited a high degree of genetic diversity by WGS-based subtyping. A variety of serotypes (n = 12) and sequence types (n = 36) were identified, including six novel STs (ST762-ST765, ST798, and ST803) first-time described in this study. Nine clinical clusters representing 12/15 (80%) patients match a potential food source. Genomic insights into virulence genes revealed species/hosts specificity signatures associated with autochthonous populations. Resistance to streptomycin, azithromycin, sulfanilamide isoxazole, cefoxitin, amoxicillin, ampicillin, and chloramphenicol, as well as multidrug resistance, was noted. WGS data can be used to predict resistance phenotypes in amoxicillin, ampicillin, and chloramphenicol, which were extensively used in clinical treatment.ConclusionsThe wide dissemination of pathogenic potential and antibiotic-resistant strains in multiple food sources emphasized the importance of rigorous food safety policies to reduce Cronobacter contamination in China.
Freshwater environment as a reservoir of extended-spectrum β-lactamase-producing Enterobacteriaceae
Authors: Cho Sohyun , Jackson Charlene R , Frye Jonathan G 
Published: February 2023

AbstractSurface water receives large quantities of wastes from human and animal sources, thus providing an ideal setting for the accumulation, development, and dissemination of antibiotic resistant bacteria, including extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae. The rapid spread of ESBL-producing Enterobacteriaceae, particularly Escherichia coli and Klebsiella pneumoniae, is a growing threat to public health, and there have been increasing reports on the prevalence and abundance of ESBL-producing Enterobacteriaceae in aquatic environments all over the globe. The objective of this review is to understand the extent of ESBL-producing Enterobacteriaceae contamination in aquatic environments and to enhance our knowledge on the role of the freshwater environment as a reservoir and transmission routes for these bacteria. In this review, we present the prevalence and distribution of ESBL-producing Enterobacteriaceae and their ESBL genes in the freshwater environment, potential sources of these bacteria in the aquatic environment, as well as their potential drivers in the environment, including anthropogenic and environmental factors.
Effects of feeding levels on ileal amino acid digestibility of extruded full fat soybeans in nongestating sows
Authors: Wang Ya , Ma Xiangyuan , Li Guowei , Sun Mengmeng , Xu Shengyu , Lin Yan , Hua Lun , Li Jian , Feng Bin , Fang Zhengfeng , Jiang Xuemei , Zhuo Yong , Che Lianqiang , Wu De 
Published: February 2023

Abstract
The objectives of this study were to investigate the effect of feeding levels on amino acid (AA) digestibility of extruded full fat soybeans (EFSB) fed to nongestating sows and to provide a reference for setting feed intake level when evaluating the quality of nutrients in the feed ingested by sows. Twelve nongestating sows (parity 3 to 5) were fitted with a T-cannula at the distal ileum. After recovery, sows were assigned to a replicated 6 × 3 incomplete Latin square design using two diets (nitrogen-free and EFSB) and three levels of feed intake (1.3, 2.0, and 3.4 times the maintenance requirement for metabolizable energy (ME)). The design included six dietary treatments and three periods, and each period contained two replicates for a total of six replicate sows per treatment. All diets contained 0.3% chromic oxide as an indigestible marker. In each period, ileal digesta samples were collected continuously for 12 h on days 6 and 7 after 5 d of acclimation to the experimental diet. Results of the experiment indicated that different feeding levels (1.3, 2.0, and 3.4 times the maintenance requirement for ME) had no effects on apparent ileal digestibility (AID) of AA and standardized ileal digestibility (SID) of AA, but feeding level did affect the endogenous AA loss estimated using the nitrogen-free diet method. Endogenous phenylalanine excretion was greater with 1.3 times than with 3.4 times the maintenance requirement for ME (P = 0.03), and endogenous tyrosine excretion was greater with 1.3 and 2.0 times than with 3.4 times the maintenance requirement for ME (P = 0.01). Increasing feed consumption resulted in greater loss of total endogenous AAs and crude protein (CP). In conclusion, feeding levels of 1.3 to 3.4 times the maintenance requirement for ME did not affect the AID and SID of AA of EFSB fed to nongestating sows.
Quantitative Analysis of Lysergic Acid Diethylamide and Metabolite in Urine by Automated Extraction and Liquid Chromatography–Tandem Mass Spectrometry
Authors: Patton Amy L , Brown Jordan , Heine Kimberley , Sartori David A , Karschner Erin L , Walterscheid Jeffrey P 
Published: February 2023

Abstract
Recently, lysergic acid diethylamide (LSD) has become a resurgent drug of abuse. The detection of LSD is problematic because of the low dosage taken by users, light and heat sensitivity of the analyte and the lack of efficient analytical methods. Presented here is the validation of an automated sample preparation method for the analysis of LSD and its primary urinary metabolite, 2-oxo-3-hydroxy-LSD (OHLSD), in urine samples by liquid chromatography–tandem mass spectrometry. Analytes were extracted from urine using an automated Dispersive Pipette XTRaction method on Hamilton STAR and STARlet liquid handling systems. The limit of detection for both analytes was administratively defined at the lowest calibrator used in the experiments, and the limit of quantitation was 0.05 ng/mL for both analytes. All validation criteria were acceptable per Department of Defense Instruction 1010.16 requirements. This method offers an efficient, sensitive analytical solution to routinely evaluate large numbers of urine specimens for LSD in workplace drug deterrence programs.
Demographic and Socioeconomic Risk Factors for Granulomatous Mastitis in the United States: A Case-Control Study
Authors: Capiro Nina , Naik Priyanka , Lo Amanda , Sayre James , Shaheen Magda , Thomas Mariam , Roth Antoinette 
Published: February 2023

AbstractObjectiveGranulomatous mastitis (GM) is a benign breast disease that can have an extended clinical course impacting quality of life and causing breast disfigurement. Granulomatous mastitis has been studied throughout the world; however, less is known about GM patients in the United States. We aim to identify demographic and socioeconomic factors associated with GM in the United States.MethodsAn IRB-approved retrospective case-control study was performed of 92 patients with biopsy-proven GM at two institutions in Los Angeles, California: a safety-net hospital and an academic institution. Age-matched controls were selected from patients presenting for diagnostic breast imaging. Demographic and socioeconomic characteristics were collected. Data were analyzed using univariable test for odds ratios (ORs) with 95% confidence intervals (CIs) and multivariable conditional logistic regression.ResultsPatients with GM were more likely to prefer Spanish language (OR 6.20, 95% CI: 2.71%–14.18%), identify as Hispanic/Latina (OR 5.18, 95% CI: 2.38%–11.30%), and be born in Mexico (OR 3.85, 95% CI: 1.23%–12.02%). Cases were more likely to have no primary care provider (OR 3.76, 95% CI: 1.97%–7.14%) and use California Medicaid for undocumented adults (OR 3.65, 95% CI: 1.89%–7.08%). In the multivariable analysis, participants who preferred Spanish language had four times higher odds of GM versus those who preferred English language (OR 4.32, 95% CI: 1.38%–13.54%).ConclusionPatients with GM may have barriers to health care access, such as preferring Spanish language, being an undocumented immigrant, and not having a primary care provider. Given these health care disparities, further research is needed to identify risk factors, etiologies, and treatments for this subset of GM patients.
Estimating phylogenies from genomes: A beginners review of commonly used genomic data in vertebrate phylogenomics
Authors: Carter Javan K , Kimball Rebecca T , Funk Erik R , Kane Nolan C , Schield Drew R , Spellman Garth M , Safran Rebecca J 
Published: February 2023

AbstractDespite the increasing feasibility of sequencing whole genomes from diverse taxa, a persistent problem in phylogenomics is the selection of appropriate genetic markers or loci for a given taxonomic group or research question. In this review, we aim to streamline the decision-making process when selecting specific markers to use in phylogenomic studies by introducing commonly used types of genomic markers, their evolutionary characteristics, and their associated uses in phylogenomics. Specifically, we review the utilities of ultraconserved elements (including flanking regions), anchored hybrid enrichment loci, conserved nonexonic elements, untranslated regions, introns, exons, mitochondrial DNA, single nucleotide polymorphisms, and anonymous regions (nonspecific regions that are evenly or randomly distributed across the genome). These various genomic elements and regions differ in their substitution rates, likelihood of neutrality or of being strongly linked to loci under selection, and mode of inheritance, each of which are important considerations in phylogenomic reconstruction. These features may give each type of marker important advantages and disadvantages depending on the biological question, number of taxa sampled, evolutionary timescale, cost effectiveness, and analytical methods used. We provide a concise outline as a resource to efficiently consider key aspects of each type of genetic marker. There are many factors to consider when designing phylogenomic studies, and this review may serve as a primer when weighing options between multiple potential phylogenomic markers.
Tea domain transcription factor TEAD4 mitigates TGF-β signaling and hepatocellular carcinoma progression independently of YAP
Authors: Luo Weicheng , Li Yi , Zeng Yi , Li Yining , Cheng Minzhang , Zhang Cheng , Li Fei , Wu Yiqing , Huang Chunhong , Yang Xiaolong , Kremerskothen Joachim , Zhang Jianmin , Zhang Chunbo , Tu Shuo , Li Zhihua , Luo Zhijun , Lin Zhenghong , Yan Xiaohua 
Published: February 2023

Abstract
Tea domain transcription factor 4 (TEAD4) plays a pivotal role in tissue development and homeostasis by interacting with Yes-associated protein (YAP) in response to Hippo signaling inactivation. TEAD4 and YAP can also cooperate with transforming growth factor-β (TGF-β)-activated Smad proteins to regulate gene transcription. Yet, it remains unclear whether TEAD4 plays a YAP-independent role in TGF-β signaling. Here, we unveil a novel tumor suppressive function of TEAD4 in liver cancer via mitigating TGF-β signaling. Ectopic TEAD4 inhibited TGF-β-induced signal transduction, Smad transcriptional activity, and target gene transcription, consequently suppressing hepatocellular carcinoma cell proliferation and migration in vitro and xenograft tumor growth in mice. Consistently, depletion of endogenous TEAD4 by siRNAs enhanced TGF-β signaling in cancer cells. Mechanistically, TEAD4 associates with receptor-regulated Smads (Smad2/3) and Smad4 in the nucleus, thereby impairing the binding of Smad2/3 to the histone acetyltransferase p300. Intriguingly, these negative effects of TEAD4 on TGF-β/Smad signaling are independent of YAP, as impairing the TEAD4–YAP interaction through point mutagenesis or depletion of YAP and/or its paralog TAZ has little effect. Together, these results unravel a novel function of TEAD4 in fine tuning TGF-β signaling and liver cancer progression in a YAP-independent manner.
Hysterectomy, bilateral oophorectomy, and breast cancer risk in a racially diverse prospective cohort study
Authors: Lovett Sharonda M , Sandler Dale P , O’Brien Katie M 
Published: February 2023

Abstract

Background
Gynecologic surgery is hypothesized to reduce risk of breast cancer; however, associations may be modified by subsequent hormone use. Our objective was to examine the association between gynecologic surgery and breast cancer incidence considering the use of hormone therapy.

Methods
The Sister Study is a prospective cohort of initially breast cancer–free women aged 35-74 years with a sister who had breast cancer. We used Cox proportional hazards models to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for the association between gynecologic surgery (no surgery, hysterectomy only, bilateral oophorectomy with or without hysterectomy) and incident breast cancer among 50 701 women.

Results
History of gynecologic surgery was common, with 13.8% reporting hysterectomy only and 18.1% reporting bilateral oophorectomy with or without hysterectomy. During follow-up (median = 11.4 years), 3948 cases were diagnosed. Compared with no surgery, bilateral oophorectomy was inversely associated with breast cancer (HR = 0.91, 95% CI = 0.83 to 1.00), and hysterectomy alone was positively associated (HR = 1.12, 95% CI = 1.02 to 1.23). Compared with no surgery and no hormone therapy, bilateral oophorectomy combined with estrogen only therapy (HR = 0.83, 95% CI = 0.74 to 0.94) was inversely associated with breast cancer, while hysterectomy combined with estrogen plus progestin therapy was positively associated with breast cancer (HR = 1.25, 95% CI = 1.01 to 1.55).

Conclusions
We observed an inverse association between bilateral oophorectomy and breast cancer risk. The positive association between hysterectomy and breast cancer may be due to concomitant estrogen plus progestin therapy.
Smoking as a prognostic factor for survival in patients with disseminated germ cell cancer
Authors: Bandak Mikkel , Nielsen Kristine Skovly , Kreiberg Michael , Wagner Thomas , Rosenvilde Josephine , Pisinger Charlotta , Johansen Christoffer , Daugaard Gedske , Lauritsen Jakob 
Published: February 2023

Abstract
We investigated the impact of smoking on overall survival (OS) in testicular germ cell cancer (TC) patients receiving first-line combination chemotherapy (bleomycin-etoposide-cisplatin [BEP]). Patients who received BEP for metastatic TC were identified in the Danish Testicular Cancer database. Information on smoking status at the time of diagnosis was obtained by medical record review. OS and cause of death were compared between current smokers and never-smokers. Of 1883 eligible patients, information on smoking status was available in 1156 patients, of whom 602 were current smokers. The 10-year OS was 92% in never-smokers compared with 83% in current smokers (P &lt; .001) (hazard ratio for death = 1.85, 95% confidence interval = 1.29 to 2.66, P = .001). A higher proportion of current smokers died of TC compared with nonsmokers (P &lt; .01). Smoking negatively affects survival after BEP in patients with disseminated TC. Vigorous smoking cessation programs are advocated in TC patients.
p27Kip1 V109G as a biomarker for CDK4/6 inhibitors indication in hormone receptor–positive breast cancer
Authors: Mouron Silvana , Bueno Maria J , Muñoz Manuel , Torres Raul , Rodríguez Sandra , Apala Juan V , Silva Jorge , Sánchez-Bayona Rodrigo , Manso Luis , Guerra Juan , Rodriguez-Lajusticia Laura , Malon Diego , Malumbres Marcos , Quintela-Fandino Miguel 
Published: February 2023

AbstractCDK4/6 inhibitors benefit a minority of patients who receive them in the breast cancer adjuvant setting. p27Kip1 is a protein that inhibits CDK/Cyclin complexes. We hypothesized that single-nucleotide polymorphisms that impaired p27Kip1 function could render patients refractory to endocrine therapy but responsive to CDK4/6 inhibitors, narrowing the patient subpopulation that requires CDK4/6 inhibitors. We found that the p27Kip1 V109G single-nucleotide polymorphism is homozygous in approximately 15% of hormone-positive breast cancer patients. Polymorphic patients experience rapid failure in response to endocrine monotherapy compared with wild-type or heterozygous patients in the first-line metastatic setting (progression-free survival: 92 vs 485 days, P &lt; .001); when CDK4/6 inhibitors are added, the differences disappear (progression-free survival: 658 vs 761 days, P = .92). As opposed to wild-type p27Kip1, p27Kip1 V109G is unable to suppress the kinase activity of CDK4 in the presence of endocrine inhibitors; however, palbociclib blocks CDK4 kinase activity regardless of the p27Kip1 status. p27Kip1 genotyping could constitute a tool for treatment selection.
Does Enforcement of the Cartel Prohibition in Healthcare Reflect Public and Political Attitudes Towards Competition? A Longitudinal Study From the Netherlands
Authors: van der Schors Wouter , Varkevisser Marco 
Published: February 2023

Abstract
In market-based healthcare systems, due to the high and increasing degree of integration between healthcare providers and purchasers, the enforcement of the cartel prohibition is both important and ever more complex. Competition authorities operate independently, but their approach to enforcement may be influenced by the public and political context. Within the setting of the Dutch healthcare system, we study how the cartel prohibition was enforced between 2004 and 2020 and focus on whether a relationship with public and political attitudes towards competition in healthcare can be observed. Using both qualitative and sentiment analyses, we assessed 38 formal and informal documents issued by the competition authority, 126 written parliamentary questions and almost 1,500 newspaper articles. Our findings reveal that during the first half of the study period (2004–2012), ex-post punitive formal enforcement of violations of the cartel prohibition, such as market-sharing and price-fixing agreements, predominated. During the second half of the study period (2012–2020); however, the competition authority’s focus seems to have shifted toward providing ex-ante informal guidance. We clearly observe negative public and political attitudes towards competition in healthcare as well as a distinct shift in enforcement of the cartel prohibition in Dutch health care. However, we are not able to test for a causal relationship between both observations.
Measuring top income shares in the UK
Authors: Advani Arun , Summers Andy , Tarrant Hannah 
Published: February 2023

Abstract
Information about the share of total income held by the richest 1%, or other top income groups, is increasingly used to discuss inequality levels and trends within and between nations. A top income share is the ratio of the total income held by the top income group divided by total personal income (the ‘income control total’). We compare two approaches to estimating income control totals: the ‘external’ approach used by the World Inequality Database, and an augmented ‘internal’ approach. We argue in favour of the latter, with reference to five desirable properties that a top share series would ideally possess. The choice matters: our augmented ‘internal’ approach yields estimates of the UK top 1% share that are around 2% points higher than the ‘external’ approach.
Missing data patterns in runners’ careers: do they matter?
Authors: Stival Mattia , Bernardi Mauro , Cattelan Manuela , Dellaportas Petros 
Published: February 2023

AbstractPredicting the future performance of young runners is an important research issue in experimental sports science and performance analysis. We analyse a dataset with annual seasonal best performances of male middle distance runners for a period of 14 years and provide a modelling framework that accounts for both the fact that each runner has typically run in 3 distance events (800, 1,500, and 5,000 m) and the presence of periods of no running activities. We propose a latent class matrix-variate state space model and we empirically demonstrate that accounting for missing data patterns in runners’ careers improves the out of sample prediction of their performances over time. In particular, we demonstrate that for this analysis, the missing data patterns provide valuable information for the prediction of runner’s performance.
Sexual function remains persistently low in women after treatment for colorectal cancer and anal squamous cell carcinoma
Authors: Savoie Marissa B , Paciorek Alan , Van Loon Katherine , Anwar Mekhail , Atreya Chloe E , Johnson P Connor , Kenfield Stacey A , Laffan Angela , Levin Anna O , Smith James F , Stanfield Dalila , Venook Alan , Zhang Li , Van Blarigan Erin L , Rowen Tami 
Published: February 2023

AbstractBackgroundWomen diagnosed with colorectal cancer (CRC) or anal squamous cell carcinoma (ASCC) are at high risk of sexual dysfunction after treatment, yet little is known about recovery and risk factors for chronic dysfunction.AimWe aimed to describe sexual function and sexual activity among women who underwent definitive treatment for CRC or ASCC, examine relationships between time since treatment completion and sexual function, and explore factors associated with desire and changes in sexual desire over time.MethodsAs part of a prospective cohort study of patients with gastrointestinal cancer at the University of California San Francisco, female-identifying participants who finished definitive treatment for CRC or ASCC completed the Female Sexual Function Index (FSFI) at 6- to 12-month intervals. We used multivariable linear mixed models to explore factors associated with the FSFI desire subscale.OutcomesOutcomes were rates of sexual activity, proportion at risk for sexual dysfunction (FSFI score &lt;26.55), total FSFI score, and FSFI desire subscale.ResultsAmong the 97 cancer survivors who completed at least 1 FSFI, the median age was 59 years, the median time since treatment end was 14 months, and 87% were menopausal. Fifty-five women (57%) had a history of colon cancer; 21 (22%), rectal cancer; and 21 (22%), ASCC. An additional 13 (13%) had a current ostomy. Approximately half the women were sexually active (n = 48, 49%). Among these 48 sexually active women, 34 (71%) had FSFI scores indicating risk for sexual dysfunction. Among the 10 sexually active women who completed a FSFI ≥2 years since end of treatment, the median total score was 22.6 (IQR, 15.6-27.3). None of the evaluated characteristics were associated with desire (age, tumor site, treatment, menopause status, or ostomy status).Clinical ImplicationsConsistent with prior studies, we found low desire scores after treatment for CRC or ASCC, with little recovery over time, suggesting that patients should not expect an eventual rebound of sexual function.Strengths and LimitationsStrengths of our study include longitudinal data and use of the validated FSFI. Women with ASCC composed 22% of our cohort, allowing for insight into this rare disease group. Limitations of this study include the small sample size, particularly for longitudinal analyses, and the enrollment of patients at variable times since treatment end.ConclusionWe observed a high prevalence of sexual health concerns, including low desire, after the treatment of CRC and ASCC that persisted for years after treatment was completed.