bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic comparison of malignant melanoma and atypical Spitz tumor in the pediatric population
Authors: Church Alanna J. , Moustafa Danna , Pinches Robert Seth , Hawryluk Elena B. , Schmidt Birgitta A. R. 
Published: February 2022

AbstractBackground/ObjectivesThe diagnostic distinction between atypical Spitz tumor (AST) and malignant melanoma (MM) in pediatric tumors is challenging. Molecular tests are increasingly used to characterize these neoplasms; however, limited studies are available in pediatric patients. This study aimed to provide a genomic comparison of pediatric MM and AST in the context of comprehensive clinical annotation.MethodsPediatric patients diagnosed with MM (n=11) and AST (n=12) were compared to a cohort of 693 adult melanoma patients. DNA next‐generation sequencing assessed kinase gene fusions, tumor mutational burden, sequence variants, copy number alterations, structural variants, microsatellite instability, and mutational signatures.ResultsSeven AST cases and eight MM cases were successfully sequenced. Kinase gene fusions were identified in both the MM and AST cohorts (NTRK1, ROS1, and MET). MM cases had TERT, BRAF, and CDKN2A alterations, which were not identified in the AST cohort. Tumor mutational burden (TMB) analysis showed pediatric ASTs had an average of 2.82 mutations/Mb, pediatric MM had an average of 5.7 mutations/Mb, and adult MM cases averaged 18.8 mut/Mb. One pediatric MM case had an elevated TMB of 15 mutations/Mb and a UV mutational signature.ConclusionsThese data expand our understanding of pediatric malignant melanoma. The differences between the molecular signatures for AST and MM are not statistically significant, and histopathology remains the gold standard for the diagnosis of pediatric AST and MM at this time. With more data, molecular studies may provide additional support for diagnosis and targeted therapeutics.
Does immigration enforcement affect whereless‐educatedUS natives and Hispanic immigrants live?
Authors: Orrenius Pia M. , Zavodny Madeline 
Published: February 2022

AbstractPrevious research shows that unauthorized Hispanic immigrants are less likely to live in areas that implement tough immigration enforcement policies. Less is known about whether such policies affect where US citizens live. We examine whether implementation of employment‐ and police‐based enforcement measures affected less‐educated US citizens' and unauthorized Hispanic immigrants' interstate mobility during 2006–2018. The results indicate that Hispanic US citizens are repelled from states with police‐based enforcement, with the impact on inflows versus outflows depending on whether they are married to an unauthorized immigrant. White and Black US natives' mobility tends to respond less to enforcement measures. The data that support the findings of this study are openly available in OpenICPSR athttps://doi.org/10.3886/E158681V1. These data were derived from the following resources available in the public domain: IPUMS USA athttps://doi.org/10.18128/D010.V11.0.
Post-Strata Based on Sample Quantiles
Authors: Fuller Wayne A. 
Published: February 2022

AbstractThe standard method of creating post-strata is to define the boundaries of the strata on the basis of population characteristics of auxiliary variables. Estimation treats the post-strata as strata for standard stratified-sample estimation. Samples often contain empty post-strata requiring adjustment to the estimation procedure. To avoid empty post-strata, we propose using the sample distribution function of an auxiliary variable to define the post-strata. We show that the large-sample efficiency of the sample-based post-stratification procedure is the same as that of the equivalently defined population-based procedure. In the simulation, the sample-based procedure was slightly more efficient than the classical procedure. The Monte Carlo coverage of a nominal 95% interval was approximately 95% for the sample-based procedure and approximately 94% for the classical procedure.
Acute physiological and psychophysical responses to different modes of heat stress
Authors: Campbell Holly A. , Akerman Ashley P. , Kissling Lorenz S. , Prout Jamie R. , Gibbons Travis D. , Thomas Kate N. , Cotter James D. 
Published: February 2022

New Findings

What is the central question of this study?
What are the profiles of acute physiological and psychophysical strain during and in recovery from different modes of heating, and to what extent do these diminish after repeated exposure?

What is the main finding and its importance?
Mode of heating affects the strain profiles during heat stress and recovery. Exercise in the heat incurred the greatest cardiovascular strain during heating and recovery. Humid heat was poorly tolerated despite heat strain being no greater than in other heating modes, and tolerance did not improve with multiple exposures.

AbstractHeat stress is common and arises endogenously and exogenously. It can be acutely hazardous while also increasingly advocated to drive health and performance‐related adaptations. Yet, the nature of strain (deviation in regulated variables) imposed by different heating modes is not well established, despite the potential for important differences. We, therefore, compared three modes of heat stress for thermal, cardiovascular and perceptual strain profiles during exposure and recovery when experienced as a novel stimulus and an accustomed stimulus. In a crossover design, 13 physically active participants (five females) underwent 5 days of 60‐min exposures to hot water immersion (40°C), sauna (55°C, 54% relative humidity) and exercise in the heat (40°C, 52% relative humidity), and a thermoneutral water immersion control (36.5°C), each separated by ≥4 weeks. Physiological (thermal, cardiovascular, haemodynamic) and psychophysical strain responses were assessed on days 1 and 5. Sauna evoked the warmest skin (40°C; P < 0.001) but exercise in the heat caused the largest increase in core temperature, sweat rate, heart rate (post hoc comparisons all P < 0.001) and systolic blood pressure (P ≤ 0.002), and possibly decrease in diastolic blood pressures (P ≤ 0.130), regardless of day. Thermal sensation and feeling state were more favourable on day 5 than on day 1 (P ≤ 0.021), with all modes of heat being equivalently uncomfortable (P ≥ 0.215). Plasma volume expanded the largest extent during immersions (P < 0.001). The current data highlight that exercising in the heat generates a more complex strain profile, while passive heat stress in humid heat has lower tolerance and more cardiovascular strain than hot water immersion.
Comparison of ALitretinoin with PUVA as the first-line treatment in patients with severe chronic HAnd eczema (ALPHA): study protocol for a randomised controlled trial
Authors: Smith Isabelle L , Gilberts Rachael , Brown Sarah , Fernandez Catherine , Nixon Jane , Reynolds Catherine , Smith Catherine , Lear John T , Sunderland Lesley , Green Cathy , Goodfield Mark , Cowdell Fiona , Hampton Philip , Barker Amy , Vargas-Palacios Armando , Tubeuf Sandy , Wittmann Miriam 
Published: February 2022

IntroductionHand eczema (HE) is one of the most common skin disorders and an important cause for morbidity and occupational disability. The 1-year prevalence of HE is estimated to be up to 10% and it is estimated that 5%–7% of those develop severe chronic HE. However, current clinical evidence is not compelling enough to guide clinical practice. In a survey among 194 UK dermatologists the most frequent first choice approaches were psoralen combined with ultraviolet A (UVA) treatment (PUVA), oral steroids and alitretinoin (AL). When asked which strategy was most efficient for long-term outcome 20% of clinicians indicated they did not know; 43% of clinicians reported AL and 30% reported PUVA.Methods and analysisALPHA is a multicentre, open, prospective, two-arm parallel group, randomised controlled trial comparing PUVA and AL with a planned sample size re-estimation. Between 500 and 780 participants will be randomised on a 1:1 basis. The physician’s global assessment (PGA) will direct treatment after randomisation, non-responders will be treated according to usual clinical practice; providing valuable pilot data on second line therapeutic approaches to inform future trials.Assessments will be conducted up to 52 weeks post randomisation. The primary outcome measure is the Hand Eczema Severity Index at 12 weeks. Secondary outcome measures include modified Total Lesion Symptom Score, PGA, time to relapse, patient reported outcome measures and DNA extraction and assessment of genetic variants. A substudy on molecular inflammatory mediators will provide information on subgroup specific treatment responses. Photographs will be taken and HE severity assessed by a central review panel.Ethics and disseminationEthics approval was obtained from Leeds West Research Ethics Committee (14/YH/1259).Trial results will be disseminated at relevant clinical conferences and societies, published in peer-reviewed journals and through relevant patient groups.Trial registration numberISRCTN80206075.
Inflamed and non-inflamed classes of HCC: a revised immunogenomic classification
Authors: Montironi Carla , Castet Florian , Haber Philipp K , Pinyol Roser , Torres-Martin Miguel , Torrens Laura , Mesropian Agavni , Wang Huan , Puigvehi Marc , Maeda Miho , Leow Wei Qiang , Harrod Elizabeth , Taik Patricia , Chinburen Jigjidsuren , Taivanbaatar Erdenebileg , Chinbold Enkhbold , Solé Arqués Manel , Donovan Michael , Thung Swan , Neely Jaclyn , Mazzaferro Vincenzo , Anderson Jeffrey , Roayaie Sasan , Schwartz Myron , Villanueva Augusto , Friedman Scott L , Uzilov Andrew , Sia Daniela , Llovet Josep M 
Published: February 2022

ObjectiveWe previously reported a characterisation of the hepatocellular carcinoma (HCC) immune contexture and described an immune-specific class. We now aim to further delineate the immunogenomic classification of HCC to incorporate features that explain responses/resistance to immunotherapy.DesignWe performed RNA and whole-exome sequencing, T-cell receptor (TCR)-sequencing, multiplex immunofluorescence and immunohistochemistry in a novel cohort of 240 HCC patients and validated our results in other cohorts comprising 660 patients.ResultsOur integrative analysis led to define: (1) the inflamed class of HCC (37%), which includes the previously reported immune subclass (22%) and a new immune-like subclass (15%) with high interferon signalling, cytolytic activity, expression of immune-effector cytokines and a more diverse T-cell repertoire. A 20-gene signature was able to capture ~90% of these tumours and is associated with response to immunotherapy. Proteins identified in liquid biopsies recapitulated the inflamed class with an area under the ROC curve (AUC) of 0.91; (2) The intermediate class, enriched inTP53mutations (49% vs 29%, p=0.035), and chromosomal losses involving immune-related genes and; (3) the excluded class, enriched inCTNNB1mutations (93% vs 27%, p<0.001) andPTK2overexpression due to gene amplification and promoter hypomethylation.CTNNB1mutations outside the excluded class led to weak activation of the Wnt-βcatenin pathway or occurred in HCCs dominated by high interferon signalling and type I antigen presenting genes.ConclusionWe have characterised the immunogenomic contexture of HCC and defined inflamed and non-inflamed tumours. Two distinctCTNNB1patterns associated with a differential role in immune evasion are described. These features may help predict immune response in HCC.
Resistance to bacterial spot (Xanthomonas gardneri) on foliage and fruit of commercial processing tomato cultivars
Authors: Simonton Tina E. , Robinson Darren , Gillard Chris , Jordan Katerina , Trueman Cheryl L. 
Published: February 2022

Bacterial spot of tomato (Xanthomonas gardneri Šutić) is an economically important disease of processing tomatoes in Ontario, Canada, resulting in premature defoliation and fruit damage. Breeding efforts for host resistance focus on assessments of foliar health as opposed to fruit health but anecdotal reports from industry suggest a poor relationship between fruit and foliar resistance. To investigate this, nine commercial cultivars were inoculated at the vegetative (foliar experiment) or reproductive (fruit experiment) stages in replicated field experiments from 2016 to 2018. In the foliar experiment, the standardized area under the disease progress curve (sAUDPC) for defoliation was 51% to 54% higher for ‘TSH18’ than ‘H9706’, ‘Hypeel 696’, and ‘H3406’, but equivalent to ‘CC337’. Fruit disease incidence was 49% and 47% lower for ‘CC337’ than ‘TSH18’ and ‘H9706’, but equivalent to ‘H3406’ and ‘Hypeel 696’. Fruit disease severity was 63% and 60% lower for ‘CC337’ than ‘H9706’and ‘H3406’, respectively, but equivalent to ‘TSH18’ and ‘Hypeel 696’. However, in the fruit experiment, fruit disease incidence was equivalent among cultivars, while the disease severity index for ‘H9706’ (3.4) was higher than ‘Hypeel 696’ (0.7). Furthermore, rank correlation analysis between sAUDPC and fruit disease variables failed to meet the criteria for a significant and strong relationship (r ≥ 0.8 or ≤ −0.8 and P ≤ 0.05). Additional research is needed to better understand the mechanisms of fruit infection by X. gardneri. In the meantime, scientists should consider the limitations of assessing only foliar damage as an evaluation method for bacterial spot management tools in tomato.
Analogue of the pole-skipping phenomenon in acoustic black holes
Authors: Yuan Haiming , Ge Xian-Hui 
Published: February 2022

AbstractThe pole-skipping phenomenon is a special property of the retarded Green’s function of black hole perturbations. We turn to its analog in acoustic black holes, which may relate to experiments. The frequencies of these special points are located at negative integer (imaginary) Matsubara frequencies $$\omega =-i2\pi Tn$$

ω
=
-
i
2
π
T
n

, which are consistent with the imaginary frequencies of quasinormal modes (QNMs). This implies that the lower-half plane pole-skipping phenomena have the same physical meaning as the imaginary part of QNMs, which represents the dissipation of perturbation of acoustic black holes and is related to the instability time scale of perturbation.
Dynamical Taxonomy: Some Taxonomic Ranks to Systematically Classify Every Chaotic Attractor
Authors: Letellier Christophe , Stankevich Nataliya , Rössler Otto E. 
Published: February 2022

Characterizing accurately chaotic behaviors is not a trivial problem and must allow to determine the properties that two given chaotic invariant sets share or not. The underlying problem is the classification of chaotic regimes, and their labeling. Addressing these problems corresponds to the development of a dynamical taxonomy, exhibiting the key properties discriminating the variety of chaotic behaviors discussed in the abundant literature. Starting from the hierarchy of chaos initially proposed by one of us, we systematized the description of chaotic regimes observed in three- and four-dimensional spaces, which cover a large variety of known (and less known) examples of chaos. Starting with the spectrum of Lyapunov exponents as the first taxonomic ranks, we extended the description to higher ranks with some concepts inherited from topology (bounding torus, surface of section, first-return map, …).By treating extensively the Rössler and the Lorenz attractors, we extended the description of branched manifold — the highest known taxonomic rank for classifying chaotic attractor — by a linking matrix (or linker) to multicomponent attractors (bounded by a torus whose genus [Formula: see text]).
Paediatric Trigger-Locked Thumb
Authors: FERNANDES Carlton , DONG Katherine , RAYAN Ghazi 
Published: February 2022

Paediatric trigger-locked thumb (PT-LT) is a common paediatric thumb condition. It is an acquired flexion deformity of the interphalangeal joint because of a size mismatch between an enlarged flexor pollicis longus tendon and a stenotic oblique pulley. It may present clinically as paediatric locked thumb which is more common or infrequently as paediatric trigger thumb. Paediatric locked thumb is classified into two types based on the presence of metacarpophalangeal joint (MCPJ) hyperextension. Type I does not have MCPJ hyperextension, whereas type II is associated with MCPJ hyperextension. The treatment of PT-LT is determined by the patient’s age, time of onset, presentation, and type. Treatment modalities are observation, splinting, therapy, or surgery. Surgery involves dividing the A1 pulley and, most importantly, part of the oblique pulley. Level of Evidence: V (Therapeutic)
The influence of weathering on index properties and undrained shear strength for the Charmouth Mudstone Formation of the Lias Group at a site near Banbury, Oxfordshire, UK
Authors: Briggs Kevin M. , Blackmore Letisha , Svalova Aleksandra , Loveridge Fleur A. , Glendinning Stephanie , Powrie William , Butler Simon , Sartain Nick 
Published: February 2022

The Lias outcrop extends continuously from Dorset to Yorkshire in England, with outlying areas in Somerset and Wales. It underlies the transport routes between a number of major UK cities. Understanding the material properties of the Lias Group is therefore important for infrastructure construction and maintenance across England and Wales.
This study examines the influence of weathering on the engineering properties of the Charmouth Mudstone Formation (Lias Group) in light of recent developments in ground-investigation practice including: (i) the use of modern visual weathering classifications for soils and rocks; and (ii) the availability of large ground-investigation datasets from the construction of the High Speed Two (HS2) railway.
The variability in the undrained shear strength data was consistent with the moisture content, liquidity index and plasticity index of the samples, but they were poorer indicators than shown in previous studies. The visually-assessed weathering class and the depth below ground level were found to be more useful indicators of the undrained shear strength of the clay and mudstone samples of the Charmouth Mudstone Formation.

Supplementary material:
Dataset for the Undrained Shear Strength and Index Properties of Charmouth Mudstone Formation Samples Excavated Near Banbury, Oxfordshire, UK, is available from the University of Bath Research Data Archive at
https://researchdata.bath.ac.uk/id/eprint/1012
Discovering the Roots: Uniform Closure Results for Algebraic Classes Under Factoring
Authors: Dutta Pranjal , Saxena Nitin , Sinhababu Amit 
Published: February 2022

Newton iteration is an almost 350-year-old recursive formula that approximates a simple root of a polynomial quite rapidly. We generalize it to a matrix recurrence (allRootsNI) that approximates all roots simultaneously. In this form, the process yields better circuit complexity in the case when the number of rootsris small but the multiplicities are exponentially large. Our method sets up a linear system inrunknowns and iteratively builds the roots as formal power series. For an algebraic circuit\( f(x_1,\ldots ,x_n) \)of sizes, we prove that each factor has size at most a polynomial insand the degree of the squarefree part off. Consequently, if\( f_1 \)is a\( 2^{\Omega (n)} \)-hard polynomial, then any nonzero multiple\( \prod _{i} f_i^{e_i} \)is equally hard for arbitrary positive\( e_i \)’s, assuming that\( \sum _i\deg (f_i) \)is at most\( 2^{O(n)} \).It is an old open question whether the class of poly(n) size formulas (respectively, algebraic branching programs) is closed under factoring. We show that given a polynomialfof degree\( n^{O(1)} \)and formula (respectively, algebraic branching program) size\( n^{O(\log n)} \), we can find a similar-size formula (respectively, algebraic branching program) factor in randomized poly(\( n^{\log n} \)) time. Consequently, if the determinant requires an\( n^{\Omega (\log n)} \)size formula, then the same can be said about any of its nonzero multiples.In all of our proofs, we exploit the following property of multivariate polynomial factorization. Under a random linear transformation\( \tau \), the polynomial\( f(\tau \overline{x}) \)completely factors via power series roots. Moreover, the factorization adapts well to circuit complexity analysis. Therefore, with the help of the strong mathematical characterizations and the ‘allRootsNI’ technique, we make significant progress towards the old open problems; supplementing the vast body of classical results and concepts in algebraic circuit factorization (e.g., [17,51,54,111]).
Challenges and Coping Strategies of Maritime Instructors and Students in An Online Distance Learning (ODL) Environment
Authors: Mundo David Gerald S. Del , Malangen Ardrian D. , Cruz Orlando Dela 
Published: February 2022

ABSTRACT

The COVID-19 pandemic has forced Higher Education Institutions (HEIs), Teachers and students to move into Online Distance Learning in the Philippines to continue providing quality education. The study centers on two factors the Challenges and Coping Strategies of Maritime Instructors and Students in an Online Distance Learning (ODL) Environment of Dr. Carlos S. Lanting College. A total of 157 respondents were involved in the study and distribution of questionnaires was done thru online. The descriptive and quantitative method of research is used in this study. As a result both the students and teachers used smartphones and laptop in Online Distance Learning but majority of the students have postpaid subscription service (42.38%) with an unstable and slow internet connectivity. Furthermore, the Challenges of Maritime Instructors and Students in an Online Distance Learning (ODL) Environment, the respondents generally answered “rarely” to the given statements as to academic requirements(M=2.08 and M=2.33), Learning Management System (M=1.96 and M=2.30), delivery of instructions (M=2.17 and 2.39) while data from learning environment (M=2.78 and M=2.73) is interpreted as "sometimes," inferring that the respondents perceived the learning environment as the biggest challenge out of the four. The coping strategies of Maritime Instructors and Students in ODL the students generally answered "sometimes" to the given scenarios while the instructors generally answered "often." Meanwhile, the results show that the instructors preferred utilizing the Internet to their advantage for researching lessons and similarly to the students, setting specific time to prepare for school work are the best coping strategies for them. There is no significant difference and relationship on the Challenges and Strategies of Maritime Instructors and Students in an Online Distance Learning (ODL) Environment. Thus, to address the challenge regarding the learning environment and the poor internet connection, the findings of the study recommend that students and instructors must set time to prepare for schoolwork, create notes to better understand/deliver a lesson, and find another place for better learning/teaching and lesser distractions.