bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Rare Case of NUT Carcinoma and Review of the Literature
Authors: Zelman Brandon , Chen Hannah , Pambuccian Stefan , Massarani-Wafai Razan , Mehrotra Swati , Ananthanarayanan Vijayalakshmi 
Published: September 2021

Abstract
Nuclear protein in testis (NUT) carcinoma is a rare, aggressive, poorly differentiated malignant neoplasm. NUT carcinoma (NC) is hallmarked by its chromosomal translocation involving the NUT/NUTM1 gene, which leads to a fusion oncoprotein that blocks epithelial differentiation and maintains proliferation in tumor cells. The translocation occurs with members of the BET (bromodomain and extraterminal domain) protein family, with 70% of the cases forming the NUTM1-BRD4 fusion. It most frequently involves the thoracic cavity followed by the head and neck, with a preference for midline areas of the body, especially the sinonasal tract and mediastinum. This led to NC formerly being known as NUT midline carcinoma. However, studies have shown that NC can occur widely throughout the body, thus leading to the updated name. NUT carcinoma is histologically defined as a tumor of primitive appearing round monomorphic cells with possible foci of abrupt keratinization. Given its rarity and its morphologic and immunohistochemical overlap with other tumors, NC has been largely underdiagnosed and misdiagnosed in the past few decades. However, with the improvement of genetic testing and the availability of an anti-NUT monoclonal antibody for diagnostic immunohistochemistry, the number of cases classified as NCs has vastly increased in the recent past.
An Observational Study of the Association Between Exposure to Vacant Building Demolitions and Elevated Blood Lead Levels in Children Under Six in St Louis City
Authors: Branz Mikayla , Harris Jenine K. , Haslam Matt 
Published: September 2021

Context:
St Louis City has been demolishing vacant buildings at an increasing rate. Demolition can cause lead dust spread, and childhood lead exposure can have negative effects on cognition, growth, and development. Previous studies show an association between exposure to multiple demolitions and elevated blood lead levels (EBLLs) in children, but St Louis City does not monitor the effects of demolitions on children's blood lead levels.

Objectives:
The purpose of this study was to measure the association between exposure to demolitions and EBLLs in children younger than 6 years in St Louis City from 2017 to 2020.

Design/Setting/Participants:
We analyzed blood lead testing data for children 0 to 72 months of age (n = 22 192) and proximity to demolitions. Exposure was the presence of demolitions within 400 ft of a child's address in the 33 days before their first lead test.

Main Outcome Measure:
We used logistic regression to test the association between proximity to demolition and EBLLs (≥5 µg/dL).

Results:
The percentage of children living in proximity to 1 or more demolitions was slightly higher among those with EBLLs (n = 21; 1.3%) than among those without EBLLs (n = 250; 1.2%). However, after adjusting for age, sex, year home was built, season, neighborhood socioeconomic percentile, and neighborhood racial composition, the odds of EBLLs were not significantly different for children exposed to 1 or more demolitions (OR = 0.82; 95% CI, 0.5-1.25) compared with exposed to zero demolitions.

Conclusions:
Although this study found no association between exposure to demolitions and EBLLs, results should be interpreted with caution, given numerous limitations. Given the consequences of childhood lead exposure, it is recommended that St Louis City conduct a similar analysis on demolitions conducted after 2020 using systematically collected demolition dates. Targeted testing or soil and air monitoring could also be informative.
Dance of Dollars: State Funding Effects on Local Health Department Expenditures
Authors: Viall Abigail H. , Bekemeier Betty , Yeager Valerie , Carton Thomas 
Published: September 2021

Objective:
We examined changes in total local health department (LHD) expenditures in the state of Washington following introduction of a new state funding program to support core public health services and infrastructure.

Methods:
We used a pre/posttest design regression model to evaluate changes in LHD expenditures 1, 2, and 6 years into the new state program. To address potential endogeneity in the model, we repeated all 3 analyses using 2-stage least squares regression.

Results:
In the base case, overall spending among LHDs significantly increased with receipt of the new state funds in the first years of the program (2008 and 2009). However, those increases were not sustained over the longer term (2013). In subpopulation analyses, total LHD spending increased more among larger LHDs.

Conclusions:
Between 2006 and 2013, new state investments in core public health functions increased Washington State LHD expenditures in the short term, but those increases did not persist over time. For public health financial modernization efforts to translate into public health infrastructure modernization successes, the way new investments are structured may be as important as the amount of funding added.
Addressing Health Disparities: The Health Department Nurse Lead Executive's Relationship to Improved Community Health
Authors: Kett Paula M. , Bekemeier Betty , Herting Jerald R. , Altman Molly R. 
Published: September 2021

Context:
The nurse-trained local health department (LHD) lead executive has been shown to be positively associated with LHD performance; however, no other research has explored whether this association translates to improved community health.

Objective:
To investigate the relationship between the type of LHD leadership—whether or not the lead executive is a nurse—and changes in health outcomes.

Design:
This study used a multivariate panel time series design. Each model was estimated as a pooled time series and using time and unit fixed effects, with a 1-year lag used for all covariates and the main predictor.

Setting:
A national, county-level data set was compiled containing variables pertaining to the LHD, community demographics, and health outcomes for the years 2010-2018.

Participants:
The unit of analysis was the LHD. The data set was restricted to those counties with measurable mortality rates during at least 8 of the 9 time periods of the study, resulting in a total of 626 LHDs.

Main Outcome Measures:
The outcomes of interest were changes in 15- to 44-year-old all-cause mortality, infant mortality, and entry into prenatal care.

Results:
In models with combined time and unit fixed effects, a significant relationship exists between a nurse-led LHD and reduced mortality in the 15- to 44-year-old Black population (−5.2%, P < .05) and a reduction in the Black-White mortality ratio (−6%, P < .05). In addition, there is a relationship between the nurse-led LHD and a reduction in the percentage of the population with late or no entry to prenatal care.

Conclusions:
The evidence presented here helps connect the known positive association between nurse lead executives and LHD performance to improvements in community health. It suggests that nurse leaders are associated with health improvements in line with addressing health inequities.
Diagnostic Accuracy of Longitudinal Evaluation of Central Nervous System Sonoelastography in Preterm and Term Neonates
Authors: Ozkan Mehmet Burak , Ozkan Elif Özyazici 
Published: September 2021

Objectives
The objective of this study was to evaluate the brain elasticity of the central nervous system in preterm and term neonates.

Methods
Seventy-seven healthy preterm and term neonates (mean gestational age [GA], 37.5 weeks; range, 32.6–40.5 weeks) were included in the study. Periventricular and subcortical white matter, cortical gray matter, and ventricle and subdural spaces were examined with strain elastography ratios. Each patient underwent sonography evaluation twice. The mean age at the time of sonographic evaluation was 9 days (range, 4–15 days) for the first evaluation and 37 days (range, 31–47 days) for the second evaluation. The ratios were correlated with GA, birth weight.

Results
The caudate nucleus and cortical gray matter strain ratios were significantly higher than the periventricular and subcortical white matter strain ratios (P < 0.001). There was a positive relationship between GA and periventricular white matter elastographic scores on the two measurements (P = 0.022 and 0.018, respectively). The term neonates have higher strain rations compared with the preterm neonates at the first assessment (P < 0.01). At the evaluation of the area under the curve for the sonographic examination for the receiver operating characteristic curve, the periventricular white matter was 0.742 (95% confidence interval, 0.689–0.790), and it was 0.773 (95% confidence interval, 0.722–0.818) for the subcortical white matter.

Conclusions
Neonatal brain development, maturation, and myelination can be assessed by strain elastography. These findings should be evaluated with further larger cohorts that could help to prevent neonatal brain damages.
Extended Lymphadenectomy Improves Survival After Induction Chemoradiation for Esophageal Cancer
Authors: Kamel Mohamed K. , Harrison Sebron , Lee Benjamin , Port Jeffrey L. , Stiles Brendon M. , Altorki Nasser K. 
Published: September 2021

Objectives:
The aim of this study was to explore the potential value of extended nodal-dissection following neoadjuvant chemoradiation (CRT), by analyzing data from the National Cancer Database (NCDB).

Background:
A CROSS-trial post-hoc analysis showed that the number of dissected lymph nodes was associated with improved survival in patients undergoing upfront surgery but not in those treated with neoadjuvant CRT.

Methods:
The NCDB was queried (2004–2014) for patients who underwent esophagectomy following induction CRT. Predictors of overall survival (OS) were assessed. The optimal number of dissected LNs associated with highest survival benefit was determined by multiple regression analyses and receiveroperating characteristic curve analysis. The whole cohort was divided into 2 groups based on the predefined cutoff number. The two groups were propensity-matched (PMs).

Results:
Esophagectomy following induction-CRT was performed in 14,503 patients. The number of resected nodes was associated with improved OS in the multivariable analysis (hazard ratio for every 10 nodes: 0.95 (95% confidence interval: 0.93–0.98). The cutoff number of resected LNs that was associated with the highest survival benefit was 20 nodes. In the PM groups, patients in the “≥20 LNs” group had a 14% relative-increase in OS (P= 0.002), despite having more advanced pathological stages (stage II-IV: 76% vs 72%, P <0.001), and higher number of positive nodes (0–2 vs 0–1, P < 0.001).

Conclusions:
The total number of resected nodes is a significant determinant of improved survival following induction CRT in patients with either node negative or node positive disease. In the matched groups, patients with higher number of resected lymph nodes had higher OS rate, despite having more advanced pathological disease and higher number of resected positive lymph nodes.
Wastewater-Based Epidemiology and Whole-Genome Sequencing for Community-Level Surveillance of SARS-CoV-2 in Selected Urban Communities of Davao City, Philippines: A Pilot Study
Authors: Otero Maria Catherine B. , Murao Lyre Anni E. , Limen Mary Antoinette G. , Gaite Paul Lorenzo A. , Bacus Michael G. , Acaso Joan T. , Corazo Kahlil , Knot Ineke E. , Sajonia Homer , de los Reyes Francis L. , Jaraula Caroline Marie B. , Baja Emmanuel S. , Del Mundo Dann Marie N. 
Published: September 2021

ABSTRACT AND KEYWORDSBackgroundOver 50 countries have used Wastewater-Based Epidemiology (WBE) and Whole-Genome Sequencing (WGS) of SARS-CoV-2 for monitoring COVID-19 cases. COVID-19 surveillance in the Philippines relies on clinical monitoring and contact tracing, with both having limited use in early detection or prediction of community outbreaks. Thus, complementary public health surveillance methods that can provide community-level infection data faster and using lesser resources must be explored.ObjectivesThis study piloted and assessed WBE and WGS as approaches for COVID-19 surveillance in low-resource and low-sanitation communities in Davao City, Philippines.MethodsWeekly wastewater samples were collected from six barangay community sewer pipes or creeks from November to December 2020. Samples were concentrated using a PEG-NaCl precipitation method and analyzed by RT-PCR to detect the SARS-CoV-2 N, RdRP, and E genes. In addition, SARS-CoV-2 RNA-positive samples were subjected to WGS for genomic mutation surveillance. Public data from clinical surveillance were also reviewed to interpret WBE data.ResultsTwenty-two of the 24 samples (91.7%) obtained from the six barangays tested positive for SARS-CoV-2 RNA. The cycle threshold (Ct) values were correlated with RNA concentration and attack rate. Thirty-two SARS-CoV-2 mutations were detected in WGS, including novel non-synonymous mutations or indels in seven SARS-CoV-2 genes and ten mutations previously reported in the Philippines.DiscussionSARS-CoV-2 RNA was detected in community wastewater from the six barangays of Davao City, even when the barangays were classified as having a low risk of COVID-19 transmission and no new cases were reported. Despite the fragmented genome sequences analyzed, our genomic surveillance in wastewater confirmed the presence of previously reported mutations while identifying mutations not yet registered in clinical surveillance. The local context of a community must be considered when planning to adopt WBE and WGS as complementary COVID-19 surveillance methodologies, especially in low-sanitation and low-resource settings.
Ensemble forecast of COVID-19 in Karnataka for vulnerability assessment and policy interventions
Authors: Ganesan Sashikumaar , Subramani Deepak , Anandh Thivin , Ghose Divij , Babu Giridhara R 
Published: September 2021

AbstractWe present an ensemble forecast for Wave-3 of COVID-19 in the state of Karnataka, India, using the IISc Population Balance Model for infectious disease spread. The reported data of confirmed, recovered, and deceased cases in Karnataka from 1 July 2020 to 4 July 2021 is utilized to tune the model’s parameters, and an ensemble forecast is done from 5 July 2021 to 30 June 2022. The ensemble is built with 972 members by varying seven critical parameters that quantify the uncertainty in the spread dynamics (antibody waning, viral mutation) and interventions (pharmaceutical, non-pharmaceutical). The probability of Wave-3, the peak date distribution, and the peak caseload distribution are estimated from the ensemble forecast. Our analysis shows that the most significant causal factors are compliance to Covid-appropriate behavior, daily vaccination rate, and the immune escape new variant emergence-time. These causal factors determine when and how severe the Wave-3 of COVID-19 would be in Karnataka. We observe that when compliance to Covid-Appropriate Behavior is good (i.e., lockdown-like compliance), the emergence of new immune-escape variants beyond Sep ‘21 is unlikely to induce a new wave. A new wave is inevitable when compliance to Covid-Appropriate Behavior is only partial. Increasing the daily vaccination rates reduces the peak active caseload at Wave-3. Consequently, the hospitalization, ICU, and Oxygen requirements also decrease. Compared to Wave-2, the ensemble forecast indicates that the number of daily confirmed cases of children (0-17 years) at Wave-3’s peak could be seven times more on average. Our results provide insights to plan science-informed policy interventions and public health response.
Single-cell transcriptomics elucidates in vitro reprogramming of human intestinal epithelium cultured in a physiodynamic gut-on-a-chip
Authors: Shin Woojung , Su Zhe , Yi S. Stephen , Kim Hyun Jung 
Published: September 2021

AbstractThe microphysiological human gut-on-a-chip has demonstrated in vivo-relevant cellular fidelity of intestinal epithelium compared to its cultures in a static condition1, 2. Microfluidic control of morphogen gradients and mechanical cues robustly induced morphological histogenesis with villi-like three-dimensional (3D) microarchitecture, lineage-associated cytodifferentiation, and physiological functions of a human intestinal Caco-2 epithelium3, 4. However, transcriptomic dynamics that orchestrates morphological and functional reprogramming of the epithelium in a microphysiological culture remains elusive. Single-cell transcriptomic analysis revealed that a gut-on-a-chip culture that offers physiological motions and flow drives three distinctive subclusters that offer distinct gene expression and unique spatial representation in 3D epithelial layers. The pseudotemporal trajectory of individual cells visualized the evolutionary transition from ancestral genotypes in static cultures into more heterogeneous phenotypes in physiodynamic cultures on cell cycles, differentiation, and intestinal functions including digestion, absorption, drug transport, and metabolism of xenobiotics. Furthermore, the inversed transcriptomic signature of oncogenes and tumor-suppressor genes of Caco-2 cells verified that a gut-on-a-chip culture drives a postmitotic reprogramming of cancer-associated phenotypes. Thus, we discovered that a physiodynamic on-chip culture is necessary and sufficient for a cancer cell line to be reprogrammed to elicit in vivo-relevant heterogeneous cell populations with restored normal physiological signatures.
Dominating Lengthscales of Zebrafish Collective Behaviour
Authors: Yang Yushi , Turci Francesco , Kague Erika , Hammond Chrissy L. , Russo John , Royall C. Patrick 
Published: September 2021

AbstractCollective behaviour in living systems is observed across many scales, from bacteria to insects, to fish shoals. Zebrafish have emerged as a model system amenable to laboratory study. Here we report a three-dimensional study of the collective dynamics of fifty Zebrafish. We observed the emergence of collective behaviour changing between polarised to randomised, upon adaption to new environmental conditions. We quantify the spatial and temporal correlation functions of the fish and identify two length scales, the persistence length and the nearest neighbour distance, that capture the essence of the behavioural changes. The ratio of the two length scales correlates robustly with the polarisation of collective motion that we explain with a reductionist model of self–propelled particles with alignment interactions.
Atypical chemokine receptor 3 (ACKR3) induces the perturbation of rRNA biogenesis: a novel mechanism of colorectal tumorigenesis
Authors: Yang Juan , Li Ya-Nan , Pan Ting , Miao Rong-Rong , Zhang Yue-Ying , Wu Shu-Hua , Qu Xian-Jun , Cui Shu-Xiang 
Published: September 2021

AbstractAtypical chemokine receptor 3 (ACKR3), previously known as C-X-C chemokine receptor type 7 (CXCR7), has emerged as a key player in several biologic processes. Its atypical “intercepting receptor” signaling properties have established ACKR3 as the main regulator in pathophysiological processes in many diseases. However, much less is known the underlying mechanisms of ACKR3 in promoting tumorigenesis. We found, in both human and animal model, that activation of ACKR3 promotes colorectal tumorigenesis through the NOLC1-induced perturbations of rRNA biogenesis. As compared with adjacent non-neoplastic tissue, human colonic cancer tissues demonstrated higher expression of ACKR3, and high ACKR3 expression was associated with increased severity of colonic cancer. Villin-ACKR3 transgenic mice demonstrated the characteristics of ACKR3-induced colorectal cancer, showing the nuclear β-arrestin-1-activated perturbation of rRNA biogenesis. Activation of ACKR3 induced nuclear translocation of β-arrestin-1 (β-arr1), leading to the interaction of β-arr1 with nucleolar and coiled-body phosphoprotein 1 (NOLC1). As the highly phosphorylated protein in the nucleolus, NOLC1 further interacted with Fibrillarin, a highly conserved nucleolar methyltransferase responsible for ribosomal RNA methylation, leading to the increase of methylation in Histone H2A, resulting in the promotion of rRNA transcription of ribosome biogenesis. Conclusion: ACKR3 promotes colorectal tumorigenesis through the perturbation of rRNA biogenesis by nuclear β-arr1-induced interaction of NOLC1 with Fibrillarin.HIGH LIGHTSACKR3 is an atypical G protein-coupled receptor (GPCR)ACKR3 promotes colorectal tumorigenesisACKR3 induces nuclear translocation of β-arr1Nuclear β-arr1 interacts with NOLC1 to activate FibrillarinInteraction of NOLC1 to Fibrillarin leads to perturbation of rRNA biogenesis
Tradeoff breaking as model of evolutionary transitions in individuality and the limits of the fitness decoupling metaphor
Authors: Bourrat Pierrick , Doulcier Guilhem , Rose Caroline J. , Rainey Paul B. , Hammerschmidt Katrin 
Published: September 2021

AbstractEvolutionary transitions in individuality (ETIs) involve the formation of Darwinian collectives from Darwinian particles. The transition from cells to multicellular life is a prime example. During an ETI, collectives become units of selection in their own right. However, the underlying processes are poorly understood. One observation used to identify the completion of an ETI is an increase in collective-level performance accompanied by a decrease in particle-level performance, for example measured by growth rate. This seemingly counterintuitive dynamic has been referred to as “fitness decoupling” and has been used to interpret both models and experimental data. Using a mathematical approach, we show this concept to be problematic in that the fitness of particles and collectives can never decouple—calculations of particle and collective fitness performed over appropriate and equivalent time intervals are necessarily the same. By way of solution, we draw attention to the value of mechanistic approaches that emphasise traits, and tradeoffs among traits, as opposed to fitness. This trait-based approach is sufficient to capture dynamics that underpin evolutionary transitions. In addition, drawing upon both experimental and theoretical studies, we show that while early stages of transitions might often involve tradeoffs among particle traits, later—and critical—stages are likely to involve the rupture of such tradeoffs. Thus, tradeoff-breaking stands as a useful marker for ETIs.
Fluid-structure interaction simulation of tissue degradation and its effects on intra-aneurysm hemodynamics
Authors: Wang Haifeng , Uhlmann Klemens , Vedula Vijay , Balzani Daniel , Varnik Fathollah 
Published: September 2021

AbstractTissue degradation plays a crucial role in vascular diseases such as atherosclerosis and aneurysms. Computational modeling of vascular hemodynamics incorporating both arterial wall mechanics and tissue degradation has been a challenging task. In this study, we propose a novel finite element method-based approach to model the microscopic degradation of arterial walls and its interaction with blood flow. The model is applied to study the combined effects of pulsatile flow and tissue degradation on the deformation and intra-aneurysm hemodynamics. Our computational analysis reveals that tissue degradation leads to a weakening of the aneurysmal wall, which manifests itself in a larger deformation and a smaller von Mises stress. Moreover, simulation results for different heart rates, blood pressures and aneurysm geometries indicate consistently that, upon tissue degradation, wall shear stress increases near the flow-impingement region and decreases away from it. These findings are discussed in the context of recent reports regarding the role of both high and low wall shear stress for the progression and rupture of aneurysms.