bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive genomic profiling of Brazilian non‐small cell lung cancer patients (GBOT 0118/LACOG0418)
Authors: Mascarenhas Eldsamira , Gelatti Ana Caroline , Araújo Luiz Henrique , Baldotto Clarissa , Mathias Clarissa , Zukin Mauro , Werutsky Gustavo , Pacheco Patricia , Gomes Rafaela , de Castro Gilberto , Cordeiro de Lima Vladmir Cláudio 
Published: December 2020

AbstractBackgroundThe aim of this study was to carry out a descriptive analysis of the somatic genetic profile and co‐occurring mutations of non‐small cell lung cancer (NSCLC) samples from patients tested with comprehensive genomic profiling (CGP).MethodsThis was a retrospective cross‐sectional study of patients diagnosed with NSCLC from 2013 to 2018 in Brazil and whose samples were submitted to CGP (FoundationOne or FoundationACT) using either tumor or circulating tumor DNA (ctDNA) from plasma.ResultsWe recovered 513 CGP results from patients, 457 (89.1%) of which were from tumors and 56 (10.9%) from plasma. The median age of patients was 64 years old, of which 51.6% were males. TP53 mutations were identified in 53.6% of tumor samples, KRAS mutations in 24.2%, EGFR activating mutations were detected in 22.5%, STK11 mutations in 11.6%, PIK3CA mutations in 8.8%, ALK rearrangements in 5.4%, BRAF mutations in 5.2%, and ERBB2 alterations in 4.9%. The most commonly comutated gene was TP53. TP53 p.R337H was observed in 4.3% of samples and was associated with somatic mutations in EGFR and ERBB2 (P < 0.00001). Tumor mutational burden (TMB) analysis was available for 80.5% of samples tested, and 5.5% of samples had high TMB (≥ 20 mutations/Mb).In conclusion, this retrospective analysis of genomic data from NSCLC patients obtained by CGP showed that common abnormalities such as EGFR mutations and ALK rearrangements had similar frequency to those previously described by other groups using others strategies. Additionally, our data confirm an association between TP53 p.R337H, supposedly germline in nature, and somatic mutations in genes of the HER family.Key pointsSignificant findings of the study
This is the first report of the prevalence of driver mutations in Brazilian NSCLC patients using comprehensive genomic profiling (CGP).
The frequency of the most common driver mutations in this population was similar to that previously described in Brazil.
What this study adds
TP53 was the most commonly comutated gene across samples. TP53 p.R337H was associated with somatic mutations in EGFR and ERBB2.
Most samples had low TMB; only 5.5% of samples had high TMB.
Inferring extinction date of a species using non‐homogeneous Poisson processes with a change‐point
Authors: Kodikara Saritha , Demirhan Haydar , Wang Yan , Stone Lewi 
Published: December 2020

Abstract

Bayesian methods have been developed for inferring the true year of extinction of a species from sighting records that have both certain and uncertain sightings. These methods typically make the restrictive assumption that all sighting types (i.e. certain, valid uncertain, invalid uncertain) derive from constant rate Poisson processes.

In this study, the constant rate assumption in the homogeneous Poisson process is relaxed by allowing certain and uncertain sightings to follow independent non‐homogeneous Poisson processes. The model can thus identify whether any of the sighting rates were increasing, decreasing or constant. In addition, a change‐point is introduced to model the uncertain sightings, where the sighting rates before and after the change‐point vary.

We have used Markov Chain Monte Carlo (MCMC) sampling to generate the posterior distributions for model parameters including species extinction time. The proposed method was applied to the sighting records of the black‐footed ferret Mustela nigripes and the ivory‐billed woodpecker Campephilus principalis (IBW) species.

Based on a hypothesis test, the results of the model indicate that the species both went extinct in the years 1988 and 1956 respectively. Moreover, a decline in the certain sighting rate was also inferred for both these species, possibly indicating the decrease in the species abundance as it converges to extinction. Thus, earlier models that assume a constant sighting rate may well be biased. Uncertain sighting rates for the IBW were found to increase before extinction (indicating possibly some additional ecological attention received near extinction) and remained constant after extinction.
Agricultural modification to vegetation drives presence and abundance of a threatened fossorial legless lizard
Authors: Wong David T. Y. , Gruber Bernd , Sarre Stephen D. , Osborne William S. 
Published: December 2020

AbstractAgricultural modification is one of the main drivers of global biodiversity decline. Vegetation clearance, tillage, grazing, and the application of fertilisers and pesticides have significantly affected native plants and animals. Reptiles can be vulnerable to agricultural practices, and localised declines in reptile biodiversity have been detected. However, the causes of these declines are likely to be many and will vary among reptiles with different life histories. Fossorial reptiles (those that mainly live below ground) are likely to be particularly vulnerable to soil and ground cover disturbance and yet are little studied in the context of agricultural practices. Here, we test the proposition that habitat disturbance caused by agricultural modification is a good predictor of decline or absence of a fossorial lizard. Specifically, we used boosted regression trees to model the relationship between five habitat factors and site abundance of the threatened Pink‐tailed Worm‐lizard (Aprasia parapulchella; Pygopodidae). We found that vegetation characteristics were the best predictors of A. parapulchella abundance. In particular, the relative contributions to our model of percentage cover of native large tussock‐forming grasses and site floristic score were 46% and 33%, respectively. Other variables that contributed to the explanation of abundance were percentage cover of rocks (10%), number of turnable rocks (5%) and relative density of rocks occupied by ants of the size class known to occur with A. parapulchella (5%). Our findings suggest that agricultural management or restoration strategies that promote ground‐layer vegetation characteristic of low levels of modification are likely to be most beneficial for the conservation of this species. Our findings and methods may be applicable to understand and study the presence and abundance of other fossorial or semi‐fossorial reptiles with specialised habitat preferences. Further research is required to establish the generality of our findings with respect to other such species around the world.
Histology of corpuscles of Stannius in Lake Van fish (Alburnus tarichi Güldenstädt, 1814) (Cyprinidae)
Authors: Kaptaner Burak , Ünal Güler , Doğan Emine , Aykut Handan 
Published: December 2020

AbstractIn the present study, the location, histology and number of corpuscles of Stannius (Sc), which are endocrine glands associated with the kidneys of teleost fish, were investigated for the first time in Lake Van fish (Alburnus tarichi), an anadromous and endemic inhabiting Turkey's Lake Van Basin. The Sc, which were ovoid or spheroid and white or cream in colour, were found to vary in number between three and five among the examined fish. The glands were located in the caudal part of the kidney, and either partially or completely embedded, and found to be present on both the ventral and dorsal surface of either side of the caudal part of the kidney. The Sc were surrounded by a connective tissue capsule that penetrated and divided the gland into incomplete lobules. Two types of cells were determined in the parenchyma of the gland. Type‐I cells were predominant throughout the parenchyma and larger than the second (type‐II). In the type‐I cells, the cytoplasm was observed as weakly or moderately eosinophilic with haematoxylin and eosin staining and weakly or moderately acidophilic with Mallory's triple staining. In the type‐I cells, the cytoplasm exhibited weak to moderate periodic acid‐Schiff staining and slight or uniform staining with aldehyde fuchsin. The type‐II cells were round, had a darkly stained spherical nucleus and were dispersed among the type‐I cells. They displayed no cytoplasmic staining with the abovementioned stains.
Role of microRNAs in inflammatory upper airway diseases
Authors: Tubita Valeria , Callejas‐Díaz Borja , Roca‐Ferrer Jordi , Marin Concepció , Liu Zheng , Wang De Yun , Mullol Joaquim 
Published: December 2020

AbstractMicroRNAs (miRNAs) are a conserved family of small endogenous noncoding RNA molecules that modulate post‐transcriptional gene expression in physiological and pathological processes. miRNAs can silence target mRNAs through degradation or inhibition of translation, showing their pivotal role in the pathogenesis of many human diseases. miRNAs play a role in regulating immune functions and inflammation and are implicated in controlling the development and activation of T and B cells. Inflammatory chronic upper airway diseases, such as rhinitis and rhinosinusitis, are spread all over the world and characterized by an exaggerated inflammation involving a complex interaction between immune and resident cells. Until now and despite allergy, little is known about their etiology and the processes implicated in the immune response and tuning inflammation of these diseases. This review highlights the knowledge of the current literature about miRNAs in inflammatory chronic upper airways diseases and how this may be exploited in the development of new clinical and therapeutic strategies.
Swedish survey of infant sleep practices showed increased bed‐sharing and positive associations with breastfeeding
Authors: Wennergren Göran , Strömberg Celind Frida , Goksör Emma , Alm Bernt 
Published: December 2020

AbstractAimMany countries lack monitoring of infant sleep practices, despite associations with sudden infant death. We studied sleep positions, bed‐sharing and breastfeeding in a new birth cohort.MethodsData were obtained from a prospective, population‐based cohort study of children born in western Sweden in 2018. The parents of 9,465 six‐month‐old infants, via postal questionnaires, were asked about their infants’ sleeping positions at three and six months, including where they slept and any bed‐sharing arrangements. The data were compared with our earlier 2003–2004 birth cohort.ResultsQuestionnaires were completed by the parents of 3,590 (38%) infants. At three months, 54% of the infants slept in a separate cot in their parents’ room. A further 43% slept in their parents’ bed: 42% in baby nests and 42% in close contact with their parents. At six months, 33% bed‐shared, compared with 20% in 2003–2004 (p < 0.001). Bed‐sharing was positively associated with breastfeeding (odds ratio at three months: 1.5–2.8, 95% confidence interval: 1.1–4.5).ConclusionMost infants slept in separate cots during the first three months. However, bed‐sharing showed an increasing trend and baby nests were popular. Bed‐sharing was positively associated with breastfeeding, but the association may not be causal.
Millennial‐scale environmental changes in the northwestern Japan Sea during the last glacial cycle
Authors: Evstigneeva Tatiana A. , Cherepanova Marina V. , Gorbarenko Sergey A. , Shi Xuefa , Bosin Alexander A. , Utkin Igor V. 
Published: December 2020

High‐resolution analyses of pollen and diatoms in core LV 53‐29 from the northwestern Japan Sea trace climate, vegetation and oceanographic changes during the past 120 ka. The age model for the core was based on tephrochronology, colour lightness and magnetic susceptibility and was used to aid correlation with Dansgaard‐Oeschger cycles (warm Greenland interstadials (GIs) and cold Greenland stadials (GSs)). The palynological and diatom data from this core record the changing influences of the East Asian monsoon, eustatic fluctuations in sea level, and the impact of variations in the direction and intensity of marine currents. Increases in Quercus and Cryptomeria pollen reflect GIs. The highest values of Cryptomeria were recorded during Marine Isotope Stage (MIS) 5 and were associated with an increase in the intensity of the summer monsoon. The increase in Larix pollen is an indicator of GSs, and it occurs in all marine isotopic stages. Changes in diatom records indicate that oceanographic conditions in the northwestern Japan Sea differed from its southern and eastern regions. An increase in the cold‐water and polyhalobous Rhizosolenia hebetata indicates GIs, although the surface water temperatures were colder than today with normal salinity. Species of the genus Chaetoceros, which is characteristic of GSs, were abundant during MIS 2. The predominance of Chaetoceros taxa and the high total abundance of diatoms may reflect regional upwelling conditions. The absence of brackish‐water species at this time indicates a slight freshening of the surface water. The study of pollen, spores and diatoms in sediments from the northwestern Japan Sea illustrates the great potential of these proxies for identifying abrupt climate oscillations preserved in high‐temporal resolution marine records, particularly those related to interstadial and stadial conditions.
The impact of anatomic, patient and surgical factors on membrane perforation during lateral wall sinus floor elevation
Authors: Pizzini Andrea , Basma Hussein S. , Li Peng , Geurs Nicolaas C. , Abou‐Arraj Ramzi V. 
Published: December 2020

AbstractObjectivesThis retrospective study aimed to evaluate the influence of anatomical, patient and surgical factors on the occurrence of membrane perforation (MP) during lateral window sinus floor elevation (LWSFE).Material and methodsA review of LWSFE patient records between 2014 and 2019 accounted for MP occurrence, window surface area (WSA), intravenous sedation use, osteotomy instrument type and clinician experience. Preoperative cone beam computed tomography (CBCT) scans were analyzed for lateral wall thickness (LWT), LFM and LAM angles formed between lateral and medial walls at the floor and anterior wall, respectively, sinus width at 5‐, 10‐ and 15‐mm (LM‐5, LM‐10 and LM‐15) from the floor, residual bone height (RBH), sinus pathologies, septa and arterial anastomoses. The generalized estimating equation (GEE) approach with a sandwich variance–covariance estimator was used to evaluate the associations with MP.ResultsMP occurred in 25.74% of 202 LWSFE procedures (166 patients). Mean 1.6 mm‐LWT, 3.2 mm‐RBH, 95°‐LFM, 75.5°‐LAM, 12 mm‐LM‐5, 20.79% septa, 16.83% arterial anastomosis, 37.62% sinus pathology and 29.21% intravenous sedations, 85.24% WSA ≥ 40 mm2 and 57% >10 procedures/clinician were reported. Greater MP rates were encountered as follows: 38.3% (LWT ≥ 1.5 mm), 38% (LFM < 90°), 59.6% (LAM < 70°), 45.4% (LM‐5 < 10 mm) and 36.4% (WSA ranged > 80 mm2), with statistically significant associations with all these outcomes (p < .05). The presence of pathologies was also associated with MP (p = .013). Associations between MP and the presence of septa and arterial anastomoses, age/gender, right/left sinus, RBH, clinician's experience, instrument type and intravenous sedation use could not be demonstrated.ConclusionsMP is significantly associated with thicker lateral walls, narrower sinuses, larger windows and existing sinus pathology.
Using Concept Maps in Teaching Operations Management Courses
Authors: Essila Jean C. , Alhourani Farouq , Motwani Jaideep 
Published: December 2020

ABSTRACTTeaching quantitative subjects such as operations management (OM) can be quite challenging. In this article, we present a novel approach that uses simplified concept maps for teaching OM. This application of concept maps was investigated to determine if it helps students to answer questions and to solve OM problems more effectively. Our study used a controlled experimental design with students divided into two groups, one taught using concept maps and another group taught using traditional techniques. Student learning was measured with pre‐ and posttests consisting of both multiple‐choice and constructed‐response items. The performance of the two groups was compared using an independent samples t‐test and analysis of covariance to control for the covariate “pretest.” The results indicate that use of simplified concept mapping significantly improved student learning of OM course material. We therefore recommend its adoption as an active‐learning pedagogical technique that can lead to positive change in the OM classroom.
Undergraduate neurology teaching: Comparison of an inpatient versus outpatient clinical setting
Authors: Martins Isabel Pavão , Fonseca Ana Catarina , Pires Luísa , Ferro José M. 
Published: December 2020

AbstractBackgroundNeurology is often perceived as a difficult discipline by medical students, yet it is an essential part of medical training. While the most common disorders of the nervous system can be observed in the outpatient setting, positive neurological signs are more likely to be found in neurology wards. We aimed to compare the impact of a neurology outpatient versus inpatient rotation setting on the grades obtained by medical students as a proxy measure of the learning outcomes.MethodsWe compared the results obtained by fourth year medical students in practical (OSCE) and multiple choice question (MCQ) exams in neurology, between students whose main (total of 24 h contact) teaching allocation was either the outpatient or inpatient setting, controlling for students’ gender, teacher, academic year and student’ previous achievement (measured by their scores on practical evaluation).ResultsA total of 1127 students were included, of whom 644 (57.14%) were allocated mainly to the neurology ward and 483 (42.86%) to the outpatient clinic. Students assigned to the ward obtained significantly higher grades in the OSCE and MCQ exams than those placed in the outpatient clinic. Teaching setting was an independent predictor of both classifications after adjustment.ConclusionsThe teaching setting had a significant impact on the learning outcomes. This may be due to a higher likelihood of observing abnormal neurological signs or to more student‐centered teaching on the ward. These results highlight the importance of a balanced distribution of students by different clinical settings.
Spatiotemporal context and firm performance: The mediating effect of strategic interaction
Authors: Gu Jiafeng 
Published: December 2020

AbstractTraditional studies of firm performance typically focus on the effect of market structure and rarely consider the impact of the spatiotemporal context in industrial competition. Using a sample of 1,555 listed companies from 2015 to 2018 in China, this study shows that the profit center of gravity tends to move from southeast to northwest, and that there are negative effects on firm performance with distance from the profit center of gravity. Moreover, when controlling for organizational variables, strategic interaction at the local level significantly mediates the relationship between spatiotemporal context at the global level and firm performance at the microlevel. This investigation provides preliminary support for strategic interaction as a significant mediator between spatiotemporal context and firm performance, and further highlights the relevance of spatiotemporal context and strategic interaction in determining firm performance. The results of this study contribute to our understanding of the dynamic mechanism of spatiotemporal context affecting firm performance and the role of strategic interaction at the local level in this relationship, which can improve the existing insights into new economic geography.
Efficacy, tolerability, and safety of eptinezumab in patients with a dual diagnosis of chronic migraine and medication‐overuse headache: Subgroup analysis of PROMISE‐2
Authors: Diener Hans‐Christoph , Marmura Michael J. , Tepper Stewart J. , Cowan Robert , Starling Amaal J. , Diamond Merle L. , Hirman Joe , Mehta Lahar , Brevig Thomas , Sperling Bjørn , Cady Roger 
Published: December 2020

AbstractObjectiveTo evaluate the efficacy, tolerability, and safety of eptinezumab 100 and 300 mg compared with placebo in patients with the dual diagnosis of chronic migraine (CM) and medication‐overuse headache (MOH).BackgroundEptinezumab, a humanized monoclonal antibody targeting calcitonin gene‐related peptide, may be effective for treating patients with a dual diagnosis of CM and MOH.MethodsPROMISE‐2 (NCT02974153) was a double‐blind, randomized, placebo‐controlled, phase 3 study that comprised a screening visit, a 28‐day pretreatment period, and a 32‐week study duration. Patients in this exploratory analysis of a prespecified subgroup had confirmed diagnoses of both CM and MOH at screening. Patients were randomly assigned to receive intravenous eptinezumab 100, 300 mg, or placebo every 12 weeks. Efficacy outcomes included mean changes from baseline in monthly migraine days (MMDs) during weeks 1–12, migraine responder rates at week 12, and percentages of patients below International Classification of Headache Disorders thresholds for CM and MOH over weeks 1–24.ResultsThere were 431 patients who were diagnosed with CM and MOH as specified in the protocol and received eptinezumab 100 mg (n = 139), 300 mg (n = 147), or placebo (n = 145). During the baseline period, these patients experienced an average of 16.7 migraine days across treatment arms. Over weeks 1–12, eptinezumab‐treated patients experienced greater reductions from baseline in MMDs than placebo patients (100 mg, change from baseline = −8.4, difference from placebo [95% confidence interval (CI)] = −3.0 [−4.56, −1.52], p < 0.0001 vs. placebo; 300 mg, change from baseline = −8.6, difference from placebo [95% CI] = −3.2 [−4.66, −1.78], p < 0.0001 vs. placebo; placebo, −5.4). Compared with placebo, more eptinezumab‐treated patients were ≥50% migraine responders (100 mg, 84/139 [60.4%]; 300 mg, 91/147 [61.9%]; placebo, 50/145 [34.5%]) or ≥75% responders (100 mg, 38/139 [27.3%]; 300 mg, 44/147 [29.9%]; placebo, 21/145 [14.5%]) over weeks 1–12. Therapeutic benefits with eptinezumab were observed from day 1 after dosing, and improvements were sustained with an additional dose. For the full 24‐week treatment period, 71/139 (51.1%), 80/147 (54.4%), and 47/145 (32.4%) of 100, 300 mg, and placebo‐treated patients, respectively, were below CM thresholds, and of the patients who provided sufficient acute medication data, 47/93 (50.5%), 53/107 (49.5%), and 26/96 (27.1%), respectively, were below medication‐overuse thresholds.ConclusionsIn patients diagnosed with both CM and MOH, eptinezumab treatment resulted in greater reductions in MMDs, higher responder rates, and fewer patients meeting CM and MOH criteria, thus demonstrating the efficacy and clinical utility of eptinezumab in this patient population.