bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulation CT-based radiomics for prediction of response after neoadjuvant chemo-radiotherapy in patients with locally advanced rectal cancer
Authors: Bonomo Pierluigi , Socarras Fernandez Jairo , Thorwarth Daniela , Casati Marta , Livi Lorenzo , Zips Daniel , Gani Cihan 
Published: April 2022

Abstract
Background
To report on the discriminative ability of a simulation Computed Tomography (CT)-based radiomics signature for predicting response to treatment in patients undergoing neoadjuvant chemo-radiation for locally advanced adenocarcinoma of the rectum.

Methods
Consecutive patients treated at the Universities of Tübingen (from 1/1/07 to 31/12/10, explorative cohort) and Florence (from 1/1/11 to 31/12/17, external validation cohort) were considered in our dual-institution, retrospective analysis. Long-course neoadjuvant chemo-radiation was performed according to local policy. On simulation CT, the rectal Gross Tumor Volume was manually segmented. A feature selection process was performed yielding mineable data through an in-house developed software (written in Python 3.6). Model selection and hyper-parametrization of the model was performed using a fivefold cross validation approach. The main outcome measure of the study was the rate of pathologic good response, defined as the sum of Tumor regression grade (TRG) 3 and 4 according to Dworak’s classification.

Results
Two-hundred and one patients were included in our analysis, of whom 126 (62.7%) and 75 (37.3%) cases represented the explorative and external validation cohorts, respectively. Patient characteristics were well balanced between the two groups. A similar rate of good response to neoadjuvant treatment was obtained in in both cohorts (46% and 54.7%, respectively; p = 0.247). A total of 1150 features were extracted from the planning scans. A 5-metafeature complex consisting of Principal component analysis (PCA)-clusters (whose main components are LHL Grey-Level-Size-Zone: Large Zone Emphasis, Elongation, HHH Intensity Histogram Mean, HLL Run-Length: Run Level Variance and HHH Co-occurence: Cluster Tendency) in combination with 5-nearest neighbour model was the most robust signature. When applied to the explorative cohort, the prediction of good response corresponded to an average Area under the curve (AUC) value of 0.65 ± 0.02. When the model was tested on the external validation cohort, it ensured a similar accuracy, with a slightly lower predictive ability (AUC of 0.63).

Conclusions
Radiomics-based, data-mining from simulation CT scans was shown to be feasible and reproducible in two independent cohorts, yielding fair accuracy in the prediction of response to neoadjuvant chemo-radiation.
SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing
Authors: Danis Daniel , Jacobsen Julius O. B. , Balachandran Parithi , Zhu Qihui , Yilmaz Feyza , Reese Justin , Haimel Matthias , Lyon Gholson J. , Helbig Ingo , Mungall Christopher J. , Beck Christine R. , Lee Charles , Smedley Damian , Robinson Peter N. 
Published: April 2022

AbstractStructural variants (SVs) are implicated in the etiology of Mendelian diseases but have been systematically underascertained owing to sequencing technology limitations. Long-read sequencing enables comprehensive detection of SVs, but approaches for prioritization of candidate SVs are needed. Structural variant Annotation and analysis (SvAnna) assesses all classes of SVs and their intersection with transcripts and regulatory sequences, relating predicted effects on gene function with clinical phenotype data. SvAnna places 87% of deleterious SVs in the top ten ranks. The interpretable prioritizations offered by SvAnna will facilitate the widespread adoption of long-read sequencing in diagnostic genomics. SvAnna is available athttps://github.com/TheJacksonLaboratory/SvAnna.
Phloem wedges in Malpighiaceae: origin, structure, diversification, and systematic relevance
Authors: Quintanar-Castillo Angélica , Pace Marcelo R. 
Published: April 2022

AbstractBackgroundPhloem wedges furrowing the wood are one of the most notorious, widespread types of cambial variants in Angiosperms. Many lianas in Malpighiaceae show these variations in the arrangement of the secondary tissues. Here we explore their ontogeny, structure, and evolution in Malpighiaceae, where phloem wedges appeared multiple times, showing how they have contributed to the anatomical diversification of the family. Using a broad sampling with 143 species from 50 genera, covering all major lineages in Malpighiaceae, we crossed data from ontogeny, stem anatomy, and phylogenetic comparative methods to determine ontogenetic trajectories, final anatomical architectures, and evolution within the most recent phylogeny for the family.ResultsPhloem wedges appeared exclusively in lianas and disappeared in shrub lineages nested within liana lineages. At the onset of development, the vascular cambium is regular, producing secondary tissues homogeneously across its girth, but soon, portions of the cambium in between the leaf insertions switch their activity producing less wood and more phloem, initially generating phloem arcs, which progress into phloem wedges. In the formation of these wedges, two ontogenetic trajectories were found, one that maintains the continuity of the cambium, and another where the cambium gets dissected. Phloem wedges frequently remain as the main cambial variant in several lineages, while in others there are additional steps toward more complex cambial variants, such as fissured stems, or included phloem wedges, the latter a novel type of interxylary phloem first described for the family.ConclusionsPhloem wedges evolved exclusively in lianas, with two different ontogenies explaining the 10 independent origins of phloem wedges in Malpighiaceae. The presence of phloem wedges has favored the evolution of even more complex cambial variants such as fissured stems and interxylary phloem.
Quantifying lung cancer heterogeneity using novel CT features: a cross-institute study
Authors: Wang Zixing , Yang Cuihong , Han Wei , Sui Xin , Zheng Fuling , Xue Fang , Xu Xiaoli , Wu Peng , Chen Yali , Gu Wentao , Song Wei , Jiang Jingmei 
Published: April 2022

Abstract
Background
Radiomics-based image metrics are not used in the clinic despite the rapidly growing literature. We selected eight promising radiomic features and validated their value in decoding lung cancer heterogeneity.

Methods
CT images of 236 lung cancer patients were obtained from three different institutes, whereupon radiomic features were extracted according to a standardized procedure. The predictive value for patient long-term prognosis and association with routinely used semantic, genetic (e.g., epidermal growth factor receptor (EGFR)), and histopathological cancer profiles were validated. Feature measurement reproducibility was assessed.

Results
All eight selected features were robust across repeat scans (intraclass coefficient range: 0.81–0.99), and were associated with at least one of the cancer profiles: prognostic, semantic, genetic, and histopathological. For instance, “kurtosis” had a high predictive value of early death (AUC at first year: 0.70–0.75 in two independent cohorts), negative association with histopathological grade (Spearman’s r: − 0.30), and altered expression levels regarding EGFR mutation and semantic characteristics (solid intensity, spiculated shape, juxtapleural location, and pleura tag; all p < 0.05). Combined as a radiomic score, the features had a higher area under curve for predicting 5-year survival (train: 0.855, test: 0.780, external validation: 0.760) than routine characteristics (0.733, 0.622, 0.613, respectively), and a better capability in patient death risk stratification (hazard ratio: 5.828, 95% confidence interval: 2.915–11.561) than histopathological staging and grading.

Conclusions
We highlighted the clinical value of radiomic features. Following confirmation, these features may change the way in which we approach CT imaging and improve the individualized care of lung cancer patients.
Prognostic stratification of patients with AJCC 2018 pN1 disease in stage III oral squamous cell carcinoma
Authors: Tsai Ming-Hsien , Chuang Hui-Ching , Lin Yu-Tsai , Huang Tai-Lin , Fang Fu-Min , Lu Hui , Chien Chih-Yen 
Published: April 2022

Background Oral cancer with pT1-3N1 without extracapsular extension of the lymph node is classified as stage III according to the eighth edition of the AJCC staging system. Outcomes of a subgroup of patients classified as having stage III oral cancer with single nodal metastasis are observed to be various clinically. Therefore, such clinical outcomes for subgroup analyses in this cohort are necessary. Methods Patients with pT1-3N1 (based on the eighth edition of the AJCC staging system) oral cancer who underwent surgery between 2007 and 2016 were enrolled retrospectively for survival analyses. Results A total of 105 patients—including 28 patients with pT1N1 disease and 77 patients with pT2-3N1 disease—participated in the study. Pathological T classification was the only statistically significant prognosticator according to univariate analysis. The patients with pT1N1 disease showed better 5-year overall survival (OS), disease specific survival (DSS), and disease free survival (DFS) than those with pT2-3N1 disease (pT1N1 vs pT2-3N1, OS: 96.4% vs 72.2%, p = 0.004; DSS: 96.4% vs 77.3%, p = 0.021; DFS: 84.6% vs 62.3%, p = 0.023). Besides, there was no potential clinicopathological confounder which is significant associated with different pathological T classifications in this unique cohort. Conclusions Patients in the pT1N1 subgroup have significantly favorable prognosis than those with pT2-3N1 disease. Down-staging and reclassifying pT1N1 subgroup patients with oral cancer may be considered in tumor staging. Graphical Abstract
TNF-α inhibitor induced pigmented purpuric dermatoses: a case report
Authors: Jhaveri Divita , Zhao Frances 
Published: April 2022

Abstract
Background
We present a rare case of TNF-α inhibitor induced pigmented purpuric dermatoses (PPD) and explore its mechanisms and management.

Case presentation
A 44-year-old woman presented with non-pruritic non-tender petechial rash on bilateral lower limbs after being started on Adalimumab, with the rash progressing to worsen on Golimumab, both used for managing her seronegative peripheral arthritis. Laboratory panel revealed a negative vasculitis screen and skin biopsy confirmed the condition. After ceasing the TNF-α inhibitors and changing to Secukinumab, an Interleukin-17 inhibitor, the lesions stopped erupting and slowly resolved.

Conclusion
PPD is a benign skin condition and has been associated with various medications and exposure to chemicals in the literature. Different mechanisms have been proposed in the literature however its exact aetiology is unknown. To date, there is no standardized treatment however patients should be reassured that PPD is benign and will often regress by itself once the causative agent has been removed.
Breast-feeding practices and maternal employment in health facilities of Lira District, Northern Uganda
Authors: Omute Tom , Kirungi Gloria 
Published: April 2022

Abstract
Background
In Uganda, many working mothers stop breast-feeding before the end of the mandatory maternity leave of 60 days. Inadequate breast-feeding is a risk factor for infant morbidity and mortality. Thus, understanding of the factors that influence breast-feeding is essential so as to advocate for the appropriate breast-feeding practices. This cross-sectional study assessed the pre-lacteal feeding (PLF), early initiation of breast-feeding (EIBF) and exclusive breast-feeding (EBF) and the associated factors for PLF, EIBF and EBF among working mothers in health facilities in Lira District, Northern Uganda.

Results
Among 376 mothers who participated, the prevalence of PLF, EIBF and EBF was 23.2%, 67.0% and 43.9%, respectively. Mode of delivery was significantly associated with PLF (AOR = 0.39, 95% CI 0.22–0.68, p < 0.01), while mode of delivery (AOR = 3.77, 95% CI 2.19–6.47, p < 0.01), length of daily working time (AOR = 0.49, 95% CI 0.29–0.82, p < 0.01) and paid maternity leave (AOR = 0.45, 95% CI 0.22–0.95, p < 0.05) were the statistically significant factors associated with EIBF. Age-group, income level, mode of delivery (AOR = 0.26, 95% CI 0.09–0.74, p < 0.05), distance to workplace (AOR = 0.45, 95% CI 0.26–0.78, p < 0.01), paid maternity leave (AOR = 0.45, 95% CI 0.22–0.95, p < 0.01), breast-feeding space (AOR = 0.30, 95% CI 0.16–0.59, p < 0.05) and breast-feeding break (AOR = 0.84, 95% CI 0.47–1.50, p < 0.01) were the significant factors associated with EBF.

Conclusions
Exclusive breast-feeding and pre-lacteal feeding among working mothers in health facilities in Lira District are lower than the national averages, but prevalence of early initiation of breast-feeding is higher than the national average.
Gut microbiota of ring-tailed lemurs (Lemur catta) vary across natural and captive populations and correlate with environmental microbiota
Authors: Bornbusch Sally L. , Greene Lydia K. , Rahobilalaina Sylvia , Calkins Samantha , Rothman Ryan S. , Clarke Tara A. , LaFleur Marni , Drea Christine M. 
Published: April 2022

Abstract
Background
Inter-population variation in host-associated microbiota reflects differences in the hosts’ environments, but this characterization is typically based on studies comparing few populations. The diversity of natural habitats and captivity conditions occupied by any given host species has not been captured in these comparisons. Moreover, intraspecific variation in gut microbiota, generally attributed to diet, may also stem from differential acquisition of environmental microbes—an understudied mechanism by which host microbiomes are directly shaped by environmental microbes. To more comprehensively characterize gut microbiota in an ecologically flexible host, the ring-tailed lemur (Lemur catta; n = 209), while also investigating the role of environmental acquisition, we used 16S rRNA sequencing of lemur gut and soil microbiota sampled from up to 13 settings, eight in the wilderness of Madagascar and five in captivity in Madagascar or the U.S. Based on matched fecal and soil samples, we used microbial source tracking to examine covariation between the two types of consortia.

Results
The diversity of lemur gut microbes varied markedly within and between settings. Microbial diversity was not consistently greater in wild than in captive lemurs, indicating that this metric is not necessarily an indicator of host habitat or environmental condition. Variation in microbial composition was inconsistent both with a single, representative gut community for wild conspecifics and with a universal ‘signal of captivity’ that homogenizes the gut consortia of captive animals. Despite the similar, commercial diets of captive lemurs on both continents, lemur gut microbiomes within Madagascar were compositionally most similar, suggesting that non-dietary factors govern some of the variability. In particular, soil microbial communities varied across geographic locations, with the few samples from different continents being the most distinct, and there was significant and context-specific covariation between gut and soil microbiota.

Conclusions
As one of the broadest, single-species investigations of primate microbiota, our study highlights that gut consortia are sensitive to multiple scales of environmental differences. This finding begs a reevaluation of the simple ‘captive vs. wild’ dichotomy. Beyond the important implications for animal care, health, and conservation, our finding that environmental acquisition may mediate aspects of host-associated consortia further expands the framework for how host-associated and environmental microbes interact across different microbial landscapes.
A pragmatic implementation research study for In Our DNA SC: a protocol to identify multi-level factors that support the implementation of a population-wide genomic screening initiative in diverse populations
Authors: Allen Caitlin G. , Judge Daniel P. , Levin Elissa , Sterba Katherine , Hunt Kelly , Ramos Paula S. , Melvin Cathy , Wager Karen , Catchpole Kenneth , Clinton Catherine , Ford Marvella , McMahon Lori L. , Lenert Leslie 
Published: April 2022

Abstract
Background
In 2021, the Medical University of South Carolina (MUSC) partnered with Helix, a population genetic testing company, to offer population-wide genomic screening for Centers for Disease Control and Preventions’ Tier 1 conditions of hereditary breast and ovarian cancer, Lynch syndrome, and familial hypercholesterolemia to 100,000 individuals in South Carolina. We developed an implementation science protocol to study the multi-level factors that influence the successful implementation of the In Our DNA SC initiative.

Methods
We will use a convergent parallel mixed-methods study design to evaluate the implementation of planned strategies and associated outcomes for In Our DNA SC. Aims focus on monitoring participation to ensure engagement of diverse populations, assessing contextual factors that influence implementation in community and clinical settings, describing the implementation team’s facilitators and barriers, and tracking program adaptations. We report details about each data collection tool and analyses planned, including surveys, interview guides, and tracking logs to capture and code work group meetings, adaptations, and technical assistance needs.

Discussion
The goal of In Our DNA SC is to provide population-level screening for actionable genetic conditions and to foster ongoing translational research. The use of implementation science can help better understand how to support the success of In Our DNA SC, identify barriers and facilitators to program implementation, and can ensure the sustainability of population-level genetic testing. The model-based components of our implementation science protocol can support the identification of best practices to streamline the expansion of similar population genomics programs at other institutions
Cancer Registry Data Linkage of Electronic Health Record Data From ASCO's CancerLinQ: Evaluation of Advantages, Limitations, and Lessons Learned
Authors: Charlton Mary E. , Kahl Amanda R. , McDowell Bradley D. , Miller Robert S. , Komatsoulis George , Koskimaki Jacob E. , Rivera Donna R. , Cronin Kathleen A. 
Published: April 2022

PURPOSE To evaluate the completeness of information for research and quality assessment through a linkage between cancer registry data and electronic health record (EHR) data refined by ASCO's health technology platform CancerLinQ. METHODS A probabilistic data linkage between Iowa Cancer Registry (ICR) and an Iowa oncology clinic through CancerLinQ data was conducted for cases diagnosed between 2009 and 2018. Demographic, cancer, and treatment variables were compared between data sources for the same patients, all of whom were diagnosed with one primary cancer. Treatment data and compliance with quality measures were compared among those with breast or prostate cancer; SEER-Medicare data served as a comparison. Variables captured only in CancerLinQ data (smoking, pain, and height/weight) were evaluated for completeness. RESULTS There were 6,175 patients whose data were linked between ICR and CancerLinQ data sets. Of those, 4,291 (70%) were diagnosed with one primary cancer and were included in analyses. Demographic variables were comparable between data sets. Proportions of people receiving hormone therapy (30% v 26%, P < .0001) or immunotherapy (22% v 12%, P < .0001) were significantly higher in CancerLinQ data compared with ICR data. ICR data contained more complete TNM stage, human epidermal growth factor receptor 2 testing, and Gleason score information. Compliance with quality measures was generally highest in SEER-Medicare data followed by the combined ICR-CancerLinQ data. CancerLinQ data contained smoking, pain, and height/weight information within one month of diagnosis for 88%, 52%, and 76% of patients, respectively. CONCLUSION Linking CancerLinQ EHR data with cancer registry data led to more complete data for each source respectively, as registry data provides definitive diagnosis and more complete stage information and laboratory results, whereas EHR data provide more detailed treatment data and additional variables not captured by registries.
Organ Preservation in Patients With Rectal Adenocarcinoma Treated With Total Neoadjuvant Therapy
Authors: Garcia-Aguilar Julio , Patil Sujata , Gollub Marc J. , Kim Jin K. , Yuval Jonathan B. , Thompson Hannah M. , Verheij Floris S. , Omer Dana M. , Lee Meghan , Dunne Richard F. , Marcet Jorge , Cataldo Peter , Polite Blase , Herzig Daniel O. , Liska David , Oommen Samuel , Friel Charles M. , Ternent Charles , Coveler Andrew L. , Hunt Steven , Gregory Anita , Varma Madhulika G. , Bello Brian L. , Carmichael Joseph C. , Krauss John , Gleisner Ana , Paty Philip B. , Weiser Martin R. , Nash Garrett M. , Pappou Emmanouil , Guillem José G. , Temple Larissa , Wei Iris H. , Widmar Maria , Lin Sabrina , Segal Neil H. , Cercek Andrea , Yaeger Rona , Smith J. Joshua , Goodman Karyn A. , Wu Abraham J. , Saltz Leonard B. 
Published: April 2022

PURPOSE Prospective data on the efficacy of a watch-and-wait strategy to achieve organ preservation in patients with locally advanced rectal cancer treated with total neoadjuvant therapy are limited. METHODS In this prospective, randomized phase II trial, we assessed the outcomes of 324 patients with stage II or III rectal adenocarcinoma treated with induction chemotherapy followed by chemoradiotherapy (INCT-CRT) or chemoradiotherapy followed by consolidation chemotherapy (CRT-CNCT) and either total mesorectal excision (TME) or watch-and-wait on the basis of tumor response. Patients in both groups received 4 months of infusional fluorouracil-leucovorin-oxaliplatin or capecitabine-oxaliplatin and 5,000 to 5,600 cGy of radiation combined with either continuous infusion fluorouracil or capecitabine during radiotherapy. The trial was designed as two stand-alone studies with disease-free survival (DFS) as the primary end point for both groups, with a comparison to a null hypothesis on the basis of historical data. The secondary end point was TME-free survival. RESULTS Median follow-up was 3 years. Three-year DFS was 76% (95% CI, 69 to 84) for the INCT-CRT group and 76% (95% CI, 69 to 83) for the CRT-CNCT group, in line with the 3-year DFS rate (75%) observed historically. Three-year TME-free survival was 41% (95% CI, 33 to 50) in the INCT-CRT group and 53% (95% CI, 45 to 62) in the CRT-CNCT group. No differences were found between groups in local recurrence-free survival, distant metastasis-free survival, or overall survival. Patients who underwent TME after restaging and patients who underwent TME after regrowth had similar DFS rates. CONCLUSION Organ preservation is achievable in half of the patients with rectal cancer treated with total neoadjuvant therapy, without an apparent detriment in survival, compared with historical controls treated with chemoradiotherapy, TME, and postoperative chemotherapy.
“I Can't Do Anything but Wait”: The Lived Experiences of Children of Transnational Migrants in Lombok, Indonesia
Authors: Beazley Harriot , Ball Jessica 
Published: April 2022

Abstract
This article contributes to debates about the temporal and affective implications of migration in Southeast Asia by presenting child-focused research concerned with children in rural Lombok, Indonesia, who have been “left behind” by their transnational migrating parents. The article explores the unpredictability of the temporality of migration and how parental absence can be indefinite or permanent, especially for parents who follow undocumented channels of migration. The article explores children’s lived experiences of waiting for their parents to return, often with no contact, and how multiple modes of waiting have become a distinctive part of children’s lives within transnational migrant communities.