bluuebunny/crossref_metadata_2025_split huggingface dataset:
Haplotype-Resolved Genome of Sika Deer Reveals Allele-Specific Gene Expression and Chromosome Evolution
Authors: Han Ruobing , Han Lei , Zhao Xunwu , Wang Qianghui , Xia Yanling , Li Heping 
Published: November 2022

Abstract
Despite the scientific and medicinal importance of diploid sika deer (Cervus nippon), its genome resources are limited and haplotype-resolved chromosome-scale assembly is urgently needed. To explore mechanisms underlying the expression patterns of the allele-specific genes in antlers and the chromosome evolution in Cervidae, we report, for the first time, a high-quality haplotype-resolved chromosome-scale genome of sika deer by integrating multiple sequencing strategies, which was anchored to 32 homologous groups with a pair of sex chromosomes (XY). Several expanded genes (RET, PPP2R1A, PPP2R1B, YWHAB, YWHAZ, and RPS6) and positively selected genes (eIF4E, Wnt8A, Wnt9B, BMP4, and TP53) were identified, which could contribute to rapid antler growth without carcinogenesis. A comprehensive and systematic genome-wide analysis of allele expression patterns revealed that most alleles were functionally equivalent in regulating rapid antler growth and inhibiting oncogenesis. Comparative genomic analysis revealed that chromosome fission might occur during the divergence of sika deer and red deer (Cervus elaphus), and the olfactory sensation of sika deer might be more powerful than that of red deer. Obvious inversion regions containing olfactory receptor genes were also identified, which arose since the divergence. In conclusion, the high-quality allele-aware reference genome provides valuable resources for further illustration of the unique biological characteristics of antler, chromosome evolution, and multi-omics research of cervid animals.
A decomposition for Lévy processes inspected at Poisson moments
Authors: Boxma Onno , Mandjes Michel 
Published: November 2022

AbstractWe consider a Lévy process Y(t) that is not continuously observed, but rather inspected at Poisson(
$\omega$
) moments only, over an exponentially distributed time
$T_\beta$
with parameter
$\beta$
. The focus lies on the analysis of the distribution of the running maximum at such inspection moments up to
$T_\beta$
, denoted by
$Y_{\beta,\omega}$
. Our main result is a decomposition: we derive a remarkable distributional equality that contains
$Y_{\beta,\omega}$
as well as the running maximum process
$\bar Y(t)$
at the exponentially distributed times
$T_\beta$
and
$T_{\beta+\omega}$
. Concretely,
$\overline{Y}(T_\beta)$
can be written as the sum of two independent random variables that are distributed as
$Y_{\beta,\omega}$
and
$\overline{Y}(T_{\beta+\omega})$
. The distribution of
$Y_{\beta,\omega}$
can be identified more explicitly in the two special cases of a spectrally positive and a spectrally negative Lévy process. As an illustrative example of the potential of our results, we show how to determine the asymptotic behavior of the bankruptcy probability in the Cramér–Lundberg insurance risk model.
WALLABY Pilot Survey: Public release of HI kinematic models for more than 100 galaxies from phase 1 of ASKAP pilot observations
Authors: Deg N. , Spekkens K. , Westmeier T. , Reynolds T. N. , Venkataraman P. , Goliath S. , Shen A. X. , Halloran R. , Bosma A. , Catinella B , de Blok W. J. G. , Dénes H. , DiTeodoro E. M. , Elagali A. , For B.-Q. , Howlett C , Józsa G. I. G. , Kamphuis P. , Kleiner D. , Koribalski B , Lee-Waddell K. , Lelli F. , Lin X. , Murugeshan C. , Oh S. , Rhee J. , Scott T. C. , Staveley-Smith L. , van der Hulst J. M. , Verdes-Montenegro L. , Wang J. , Wong O. I. 
Published: November 2022

AbstractWe present the Widefield ASKAP L-band Legacy All-sky Blind surveY (WALLABY) Pilot Phase I Hikinematic models. This first data release consists of Hiobservations of three fields in the direction of the Hydra and Norma clusters, and the NGC 4636 galaxy group. In this paper, we describe how we generate and publicly release flat-disk tilted-ring kinematic models for 109/592 unique Hidetections in these fields. The modelling method adopted here—which we call the WALLABY Kinematic Analysis Proto-Pipeline (WKAPP) and for which the corresponding scripts are also publicly available—consists of combining results from the homogeneous application of theFATand3DBaroloalgorithms to the subset of 209 detections with sufficient resolution and$S/N$in order to generate optimised model parameters and uncertainties. The 109 models presented here tend to be gas rich detections resolved by at least 3–4 synthesised beams across their major axes, but there is no obvious environmental bias in the modelling. The data release described here is the first step towards the derivation of similar products for thousands of spatially resolved WALLABY detections via a dedicated kinematic pipeline. Such a large publicly available and homogeneously analysed dataset will be a powerful legacy product that that will enable a wide range of scientific studies.
Precision mitochondrial medicine
Authors: Chinnery Patrick F. 
Published: November 2022

Abstract
Mitochondria play a key role in cell homeostasis as a major source of intracellular energy (adenosine triphosphate), and as metabolic hubs regulating many canonical cell processes. Mitochondrial dysfunction has been widely documented in many common diseases, and genetic studies point towards a causal role in the pathogenesis of specific late-onset disorder. Together this makes targeting mitochondrial genes an attractive strategy for precision medicine. However, the genetics of mitochondrial biogenesis is complex, with over 1,100 candidate genes found in two different genomes: the nuclear DNA and mitochondrial DNA (mtDNA). Here, we review the current evidence associating mitochondrial genetic variants with distinct clinical phenotypes, with some having clear therapeutic implications. The strongest evidence has emerged through the investigation of rare inherited mitochondrial disorders, but genome-wide association studies also implicate mtDNA variants in the risk of developing common diseases, opening to door for the incorporation of mitochondrial genetic variant analysis in population disease risk stratification.
NOTES ON ATKIN–LEHNER THEORY FOR DRINFELD MODULAR FORMS
Authors: DALAL TARUN , KUMAR NARASIMHA 
Published: November 2022

AbstractWe settle a part of the conjecture by Bandini and Valentino [‘On the structure and slopes of Drinfeld cusp forms’, Exp. Math.31(2) (2022), 637–651] for
$S_{k,l}(\Gamma _0(T))$
when
$\mathrm {dim}\ S_{k,l}(\mathrm {GL}_2(A))\leq 2$
. We frame and check the conjecture for primes
$\mathfrak {p}$
and higher levels
$\mathfrak {p}\mathfrak {m}$
, and show that a part of the conjecture for level
$\mathfrak {p} \mathfrak {m}$
does not hold if
$\mathfrak {m}\ne A$
and
$(k,l)=(2,1)$
.
Extra virgin olive oil improves HDL lipid fraction but not HDL-mediated cholesterol efflux capacity: a double-blind, randomised, controlled, cross-over study (OLIVAUS)
Authors: Sarapis Katerina , George Elena S. , Marx Wolfgang , Mayr Hannah L. , Willcox Jane , Powell Katie L. , Folasire Oladayo S. , Lohning Anna E. , Prendergast Luke A. , Itsiopoulos Catherine , Thomas Colleen J. , Moschonis George 
Published: November 2022

AbstractOlive oil (OO) polyphenols have been shown to improve HDL anti-atherogenic function, thus demonstrating beneficial effects against cardiovascular risk factors. The aim of the present study was to investigate the effect of extra virgin high polyphenol olive oil (HPOO) v. low polyphenol olive oil (LPOO) on the capacity of HDL to promote cholesterol efflux in healthy adults. In a double-blind, randomised cross-over trial, fifty participants (aged 38·5 (sd 13·9) years, 66 % females) were supplemented with a daily dose (60 ml) of HPOO (320 mg/kg polyphenols) or LPOO (86 mg/kg polyphenols) for 3 weeks. Following a 2-week washout period, participants crossed over to the alternate treatment. Serum HDL-cholesterol efflux capacity, circulating lipids (i.e. total cholesterol, TAG, HDL, LDL) and anthropometrics were measured at baseline and follow-up. No significant between-group differences were observed. Furthermore, no significant changes in HDL-cholesterol efflux were found within either the LPOO and HPOO treatment arms; mean changes were 0·54 % (95 % CI (0·29, 1·37)) and 0·10 % (95 % CI (0·74, 0·94)), respectively. Serum HDL increased significantly after LPOO and HPOO intake by 0·13 mmol/l (95 % CI (0·04, 0·22)) and 0·10 mmol/l (95 % CI (0·02, 0·19)), respectively. A small but significant increase in LDL of 0·14 mmol/l (95 % CI (0·001, 0·28)) was observed following the HPOO intervention. Our results suggest that additional research is warranted to further understand the effect of OO with different phenolic content on mechanisms of cholesterol efflux via different pathways in multi-ethnic populations with diverse diets.
Substance use and psychotic-like experiences in young people: a systematic review and meta-analysis
Authors: Matheson Sandra L. , Laurie Mallory , Laurens Kristin R. 
Published: November 2022

Abstract
This study aimed to systematically review and synthesise the available evidence on the prevalence and associations between psychotic-like experiences (PLEs) and substance use in children and adolescents aged ⩽17 years, prior to the typical age of development of prodromal symptoms of psychosis. As substance use has been associated with earlier age of psychosis onset and more severe illness, identifying risk processes in the premorbid phase of the illness may offer opportunities to prevent the development of prodromal symptoms and psychotic illness. MEDLINE, PsycINFO, and CINAHL databases were searched for chart review, case-control, cohort, twin, and cross-sectional studies. Study reporting was assessed using the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) checklist, and pooled evidence was evaluated using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach. Searches identified 55 studies that met inclusion criteria. Around two-in-five substance users reported PLEs [rate = 0.41, 95% confidence interval (CI) 0.32–0.51; low quality evidence], and one-in-five with PLEs reported using substances (rate = 0.19, 95% CI 0.12–0.28; moderate-to-high quality evidence). Substance users were nearly twice as likely to report PLEs than non-users [odds ratio (OR) 1.77, 95% CI 1.55–2.02; moderate quality evidence], and those with PLEs were twice as likely to use substances than those not reporting PLEs (OR 1.93, 95% CI 1.55–2.41; very low quality evidence). Younger age was associated with greater odds of PLEs in substance users compared to non-users. Young substance users may represent a subclinical at-risk group for psychosis. Developing early detection and intervention for both substance use and PLEs may reduce long-term adverse outcomes.
Focus interpretation in L1 and L2: The role of prosodic prominence and clefting
Authors: Yan Mengzhu , Warren Paul , Calhoun Sasha 
Published: November 2022

AbstractAlthough the importance of prosody in processing information structure (IS) has been shown in many languages including English and Mandarin, the interacting effects of prosody with other linguistic systems, such as syntax, are relatively under-studied, especially in L2. This paper reports two question-answer appropriateness rating experiments, investigating intermediate-to-high proficiency Mandarin listeners’ integration of prosodic prominence and clefting cues in the interpretation of focus in their L1 and L2 (English). It was found that prosodic prominence was more effective than clefting as a cue to focus in L1 Mandarin. However, clefting was as effective as prominence in L2, showing L1–L2 differences in integrating multiple cues. The findings are discussed in terms of Mennen’s L2 intonation learning theory (2015) and Bates and MacWhinney’s Competition Model (1989), which provide a framework for understanding difficulties in acquiring the use of particular cues in L2. The current study contributes to our limited knowledge of a crucial part of L2 learning: how L2 learners process IS.
Autonomous robot navigation based on a hierarchical cognitive model
Authors: Cai Jianxian , Yan Fenfen , Shi Yan , Zhang Mengying , Guo Lili 
Published: November 2022

AbstractWe propose a hierarchical cognitive navigation model (HCNM) to improve the self-learning and self-adaptive ability of mobile robots in unknown and complex environments. The HCNM model adopts the divide and conquers approach by dividing the path planning task into different levels of sub-tasks in complex environments and solves each sub-task in a smaller state subspace to decrease the state space dimensions. The HCNM model imitates animal asymptotic properties through the study of thermodynamic processes and designs a cognitive learning algorithm to achieve online optimum search strategies. We prove that the learning algorithm designed ensures that the cognitive model can converge to the optimal behavior path with probability one. Robot navigation is studied on the basis of the cognitive process. The experimental results show that the HCNM model has strong adaptability in unknown and environment, and the navigation path is clearer and the convergence time is better. Among them, the convergence time of HCNM model is 25 s, which is 86.5% lower than that of HRLM model. The HCNM model studied in this paper adopts a hierarchical structure, which reduces the learning difficulty and accelerates the learning speed in the unknown environment.
A heuristic gait template planning and dynamic motion control for biped robots
Authors: Han Lianqiang , Chen Xuechao , Yu Zhangguo , Gao Zhifa , Huang Gao , Zhang Jintao , Hashimoto Kenji , Huang Qiang 
Published: November 2022

AbstractBiped robots with dynamic motion control have shown strong robustness in complex environments. However, many motion planning methods rely on models, which have difficulty dynamically modifying the walking cycle, height, and other gait parameters to cope with environmental changes. In this study, a heuristic model-free gait template planning method with dynamic motion control is proposed. The gait trajectory can be generated by inputting the desired speed, walking cycle, and support height without a model. Then, the stable walking of the biped robot can be realized by foothold adjustment and whole-body dynamics model control. The gait template can be changed in real time to achieve gait flexibility of the biped robot. Finally, the effectiveness of the method is verified by simulations and experiments of the biped robot BHR-B2. The research presented here helps improve the gait transition ability of biped robots in dynamic locomotion.
Strategies to address non-communicable diseases in the Commonwealth of Independent States countries: a scoping review
Authors: Muratalieva Elvira , Nendaz Mathieu , Beran David 
Published: November 2022

Abstract

Aim:
The aim of this study is to review the literature in Commonwealth of Independent States (CIS) countries with regard to their response to non-communicable diseases (NCDs) and the implementation of the World Health Organization (WHO) Package of Essential Non-communicable (PEN) disease interventions for primary health care.

Background:
NCDs are estimated to account from 62% to 92% of total deaths in CIS countries. Current management of NCDs in CIS countries is focused on specialists and hospital care versus primary health care (PHC) as recommended by the WHO.

Methods:
This paper uses a scoping review of published and grey literature focusing on diabetes and hypertension in CIS countries. These two conditions are chosen as they represent a large burden in CIS countries and are included in the responses proposed by the WHO PEN.

Findings:
A total of 96 documents were identified and analysed with the results presented using the WHO Health System Building Blocks. Most of the publications identified focused on the service delivery (41) and human resources (20) components, while few addressed information and research (17), and only one publication was related to medical products. As for their disease of focus, most studies focused on hypertension (14) and much less on diabetes (3). The most studies came from Russia (18), followed by Ukraine (21) and then Kazakhstan (12). Only two countries Moldova and Kyrgyzstan have piloted the WHO PEN. Overall, the studies identified highlight the importance of the PHC system to better control and manage NCDs in CIS countries. However, these present only strategies versus concrete interventions. One of the main challenges is that NCD care at PHC in CIS countries continues to be predominantly provided by specialists in addition to focusing on treatment versus preventative services.
Broadband Dynamic Rupture Modeling With Fractal Fault Roughness, Frictional Heterogeneity, Viscoelasticity and Topography: The 2016 Mw 6.2 Amatrice, Italy Earthquake
Authors: Taufiqurrahman T. , Gabriel A.‐A. , Ulrich T. , Valentová L. , Gallovič F. 
Published: November 2022

AbstractAdvances in physics‐based earthquake simulations, utilizing high‐performance computing, have been exploited to better understand the generation and characteristics of the high‐frequency seismic wavefield. However, direct comparison to ground motion observations of a specific earthquake is challenging. We here propose a new approach to simulate data‐fused broadband ground motion synthetics using 3D dynamic rupture modeling of the 2016 Mw 6.2 Amatrice, Italy earthquake. We augment a smooth, best‐fitting model from Bayesian dynamic rupture source inversion of strong‐motion data (<1 Hz) with fractal fault roughness, frictional heterogeneities, viscoelastic attenuation, and topography. The required consistency to match long periods allows us to quantify the role of small‐scale dynamic source heterogeneities, such as the 3D roughness drag, from observational broadband seismic waveforms. We demonstrate that 3D data‐constrained fully dynamic rupture synthetics show good agreement with various observed ground‐motion metrics up to ∼5 Hz and are an important avenue toward non‐ergodic, physics‐based seismic hazard assessment.
Volume Estimation From Planform Characteristics of Washover Morphology
Authors: Lazarus Eli D. , Williams Hannah E. , Goldstein Evan B. 
Published: November 2022

AbstractOverwash is the cross‐shore transport of water and sediment from a waterbody over the crest of a sand or gravel barrier beach, and washover is the resulting sedimentary deposit. Washover volume, and alongshore patterns of washover distribution, are fundamental components of sediment budgets for low‐lying coastal barrier systems. Accurate sediment budgets are essential to forecasting barrier system sustainability under future climate‐driven forcing. However, comprehensive surveys of three‐dimensional washover morphology are challenging to deliver. Here, we use the results of a physical experiment, analysis of lidar data, and examples of washover characteristics reported in the literature to develop scaling relationships for washover morphometry that demonstrate volume can be reasonably inferred from planform measurements, for washover in natural (non‐built) and built barrier settings. Gaining three‐dimensional insight into washover deposits from two‐dimensional information unlocks the ability to analyze past aerial imagery and estimate contributions from washover flux to sediment budgets for past storms.
Increasing Drought Risks Over the Past Four Centuries Amidst Projected Flood Intensification in the Kabul River Basin (Afghanistan and Pakistan)—Evidence From Tree Rings
Authors: Khan Nasrullah , Nguyen Hung T. T. , Galelli Stefano , Cherubini Paolo 
Published: November 2022

AbstractIncreased flood risks have been projected, but with large uncertainties, in the Kabul River Basin (Afghanistan and Pakistan). To place future changes in a long‐term perspective, we produce a 382‐year precipitation reconstruction for the basin using seven tree‐ring chronologies of old‐growth conifers from the Hindu Kush Mountains, a monsoon‐shadow area. The reconstruction proves robust over rigorous cross‐validations (R2 = 0.60, RE = 0.60, CE = 0.53). The full reconstruction (1637–2018) reveals a steady decline in the low end of the precipitation distribution, implying increasing drought risks. We show that droughts are getting more severe, shorter, and more frequent, interspersed with more frequent pluvials in the past century. Drought risks, compounded with projected flood intensification, pose significant threats for this transboundary river. Therefore, future water management needs to account for both flood and drought risks and be informed by long‐term hydroclimatic variability.
Ecosystem Metabolism and Gradients of Temperature, Oxygen and Dissolved Inorganic Carbon in the Littoral Zone of a Macrophyte‐Dominated Lake
Authors: Martinsen Kenneth Thorø , Zak Nathalie Brandt , Baastrup‐Spohr Lars , Kragh Theis , Sand‐Jensen Kaj 
Published: November 2022

AbstractDense submerged macrophyte stands in lakes may promote alternating daytime stratification and nighttime convective mixing, driving extensive spatiotemporal variations in water temperature, oxygen, pH, and inorganic carbon (DIC). We set out to investigate environmental conditions and ecosystem metabolism in the macrophyte‐dominated littoral zone (0.6 m depth) of a shallow, mesotrophic lake and compared this with the pelagic zone (3.0 m deep). We found that, during summer, vertical water column gradients only occasionally occurred and were weak in the pelagic zone, while dense littoral macrophyte stands of charophytes exhibited strong diel changes and steep daytime temperature and oxygen depth gradients. Oxygen showed daytime surface supersaturation and bottom anoxia, alternating with nighttime mixing. In spring, before charophytes appeared, the vertical gradients were largely absent. Ecosystem metabolism was primarily positive in spring, but areal rates of daily gross primary production (GPP) and closely related respiration increased 6‐fold in summer. Ecosystem metabolism calculated based on oxygen or DIC was very similar, with a 1:1 M basis. Daytime DIC loss by CaCO3precipitation on charophyte surfaces averaged 6.3% of total DIC loss, and this loss was restored during nighttime. The contribution of shallow littoral macrophyte communities to whole‐lake summer GPP exceeded that estimated for phytoplankton. Environmental conditions in the macrophyte‐covered littoral zone differed markedly from pelagic waters with steep vertical gradients in temperature and chemistry during daytime including anoxic micro‐habitats in stark contrast to deep pelagic waters. The study highlights the significant influence of the littoral zone and macrophytes on whole‐lake ecosystem processes.