bluuebunny/crossref_metadata_2025_split huggingface dataset:
HuConTest: Testing Human Contamination in Great Ape Samples
Authors: Kuhlwilm Martin , Fontsere Claudia , Han Sojung , Alvarez-Estape Marina , Marques-Bonet Tomas 
Published: May 2021

Abstract
Modern human contamination is a common problem in ancient DNA studies. We provide evidence that this issue is also present in studies in great apes, which are our closest living relatives, for example in noninvasive samples. Here, we present a simple method to detect human contamination in short-read sequencing data from different species: HuConTest. We demonstrate its feasibility using blood and tissue samples from these species. This test is particularly useful for more complex samples (such as museum and noninvasive samples) which have smaller amounts of endogenous DNA, as we show here.
Variants in USP48 encoding ubiquitin hydrolase are associated with autosomal dominant non-syndromic hereditary hearing loss
Authors: Bassani Sissy , van Beelen Edward , Rossel Mireille , Voisin Norine , Morgan Anna , Arribat Yoan , Chatron Nicolas , Chrast Jacqueline , Cocca Massimiliano , Delprat Benjamin , Faletra Flavio , Giannuzzi Giuliana , Guex Nicolas , Machavoine Roxane , Pradervand Sylvain , Smits Jeroen J , van de Kamp Jiddeke M , Ziegler Alban , Amati Francesca , Marlin Sandrine , Kremer Hannie , Locher Heiko , Maurice Tangui , Gasparini Paolo , Girotto Giorgia , Reymond Alexandre 
Published: May 2021

Abstract
Non-Syndromic Hereditary Hearing Loss (NSHHL) is a genetically heterogeneous sensory disorder with about 120 genes already associated. Through exome sequencing (ES) and data aggregation, we identified a family with six affected individuals and one unrelated NSHHL patient with predicted-to-be deleterious missense variants in USP48. We also uncovered an eighth patient presenting unilateral cochlear nerve aplasia and a de novo splice variant in the same gene. USP48 encodes a ubiquitin carboxyl-terminal hydrolase under evolutionary constraint. Pathogenicity of the variants is supported by in vitro assays that showed that the mutated proteins are unable to hydrolyze tetra-ubiquitin. Correspondingly, three-dimensional representation of the protein containing the familial missense variant is situated in a loop that might influence the binding to ubiquitin. Consistent with a contribution of USP48 to auditory function, immunohistology showed that the encoded protein is expressed in the developing human inner ear, specifically in the spiral ganglion neurons, outer sulcus, interdental cells of the spiral limbus, stria vascularis, Reissner’s membrane and in the transient Kolliker’s organ that is essential for auditory development. Engineered zebrafish knocked-down for usp48, the USP48 ortholog, presented with a delayed development of primary motor neurons, less developed statoacoustic neurons innervating the ears, decreased swimming velocity and circling swimming behavior indicative of vestibular dysfunction and hearing impairment. Corroboratingly, acoustic startle response assays revealed a significant decrease of auditory response of zebrafish lacking usp48 at 600 and 800 Hz wavelengths. In conclusion, we describe a novel autosomal dominant NSHHL gene through a multipronged approach combining ES, animal modeling, immunohistology and molecular assays.
Driving Performance Under Treatment of Most Frequently Prescribed Drugs for Mental Disorders: A Systematic Review of Patient Studies
Authors: Brunnauer Alexander , Herpich Florian , Zwanzger Peter , Laux Gerd 
Published: May 2021

AbstractBackgroundMobility is important for daily life functioning, with particular challenges regarding road safety under pharmacological treatment in patients with a psychiatric disease.MethodsAccording to PRISMA guidelines, a systematic literature search on PubMed database (January 1970 to December 2020) was performed. Primary endpoints were driving performance in on-road tests, driving simulator performance, or psychomotor and visual perception functions assessed to estimate fitness to drive according to legal regulations in patient studies.ResultsForty studies were identified (1533 patients, 38% female, median age 45 years), of which more than 60% were cross-sectional and open-label trials. Under steady-state medication, 31% (range 27%–42.5%) of schizophrenic or schizoaffective patients under antipsychotics and 18% (range 16%–20%) of unipolar and bipolar patients under antidepressants showed severe impairment in skills relevant for driving. Data point to an advantage of second-generation antipsychotics compared with first-generation antipsychotics as well as modern antidepressants over tricyclic antidepressants with respect to driving. Most patients significantly improved or stabilized in driving skills within 2–4 weeks of treatment with non-sedative or sedative antidepressants. Diazepam significantly worsened driving the first 3 weeks after treatment initiation, whereas medazepam (low dose), temazepam, and zolpidem did not impair driving. In long-term users of sedating antidepressants or benzodiazepines, impairments in on-road tests were not evident.ConclusionThe available evidence suggests that psychopharmacologic medicines improve or at least stabilize driving performance of patients under long-term treatment when given on clinical considerations. To enhance treatment compliance, existing classification systems of medicinal drugs concerning impact on driving performance should also incorporate information about effects of long-term-treatment.
The Tangle-Free Hypothesis on Random Hyperbolic Surfaces
Authors: Monk Laura , Thomas Joe 
Published: May 2021

Abstract
This article introduces the notion of $L$-tangle-free compact hyperbolic surfaces, inspired by the identically named property for regular graphs. Random surfaces of genus $g$, picked with the Weil–Petersson probability measure, are $(a \log g)$-tangle-free for any $a&lt;1$. This is almost optimal, for any surface is $(4 \log g + O (1))$-tangled. We establish various geometric consequences of the tangle-free hypothesis at a scale $L$, among which the fact that closed geodesics of length $&lt; \frac L 4$ are simple, disjoint, and embedded in disjoint hyperbolic cylinders of width $\geq \frac{L}{4}$.
Face Processing and Social Functioning in Pediatric Brain Tumor Survivors
Authors: Hocking Matthew C , Albee May , Brodsky Cole , Shabason Emily , Wang Leah , Schultz Robert T , Herrington John 
Published: May 2021

Abstract

Objective
Pediatric brain tumor survivors (PBTS) experience deficits in social functioning. Facial expression and identity recognition are key components of social information processing and are widely studied as an index of social difficulties in youth with autism spectrum disorder (ASD) and other neurodevelopmental conditions. This study evaluated facial expression and identity recognition among PBTS, youth with ASD, and typically developing (TD) youth, and the associations between these face processing skills and social impairments.

Methods
PBTS (N = 54; ages 7–16) who completed treatment at least 2 years prior were matched with TD (N = 43) youth and youth with ASD (N = 55) based on sex and IQ. Parents completed a measure of social impairments and youth completed a measure of facial expression and identity recognition.

Results
Groups significantly differed on social impairments (p &lt; .001), with youth with ASD scoring highest followed by PBTS and lastly TD youth. Youth with ASD performed significantly worse on the two measures of facial processing, while TD youth and PBTS were not statistically different. The association of facial expression recognition and social impairments was moderated by group, such that PBTS with higher levels of social impairment performed worse on the expression task compared to TD and ASD groups (p &lt; .01, η2 = 0.07).

Conclusions
Variability in face processing may be uniquely important to the social challenges of PBTS compared to other neurodevelopmental populations. Future directions include prospectively examining associations between facial expression recognition and social difficulties in PBTS and face processing training as an intervention for PBTS.
muscle-ups: improved approximations of the matter field with the extended Press–Schechter formalism and Lagrangian perturbation theory
Authors: Tosone Federico , Neyrinck Mark C , Granett Benjamin R , Guzzo Luigi , Vittorio Nicola 
Published: May 2021

ABSTRACT
Lagrangian algorithms to simulate the evolution of cold dark matter (CDM) are invaluable tools to generate large suites of mock halo catalogues. In this paper, we first show that the main limitation of current semi-analytical schemes to simulate the displacement of CDM is their inability to model the evolution of overdensities in the initial density field, a limit that can be circumvented by detecting halo particles in the initial conditions. We thus propose ‘MUltiscale Spherical Collapse Lagrangian Evolution Using Press–Schechter’ (muscle-ups), a new scheme that reproduces the results from Lagrangian perturbation theory on large scales, while improving the modelling of overdensities on small scales. In muscle-ups, we adapt the extended Press and Schechter formalism to Lagrangian algorithms of the displacement field. For regions exceeding a collapse threshold in the density smoothed at a radius R, we consider all particles within a radius R collapsed. Exploiting a multiscale smoothing of the initial density, we build a halo catalogue on the fly by optimizing the selection of halo candidates. This allows us to generate a density field with a halo mass function that matches one measured in N-body simulations. We further explicitly gather particles in each halo together in a profile, providing a numerical, Lagrangian-based implementation of the halo model. Compared to previous semi-analytical Lagrangian methods, we find that muscle-ups improves the recovery of the statistics of the density field at the level of the probability density function, the power spectrum, and the cross-correlation with the N-body result.
On the formation of terrestrial planets between two massive planets: the case of 55 Cancri
Authors: Zhou Lei , Dvorak Rudolf , Zhou Li-Yong 
Published: May 2021

ABSTRACT
Considering the huge computational resources required by smoothed particle hydrodynamics (SPH) simulations and the overestimation of post-collision materials from perfect merging, we develop a statistical method to deal with collisions during the formation of planetary systems by introducing random material loss. In this method, the mass and water content lost by the sole outcome from every merger vary randomly within a range dependent on the total mass and water content of colliding bodies. The application of the random loss method to the planet formation in the Solar system shows a good consistency with existing SPH results. We also apply this method to the extrasolar planetary system 55 Cancri that hosts (at least) five planets and study the formation of terrestrial planets between the outermost two planets. A disc with 500 Mars mass embryos in dynamically cold orbits before the late-stage accretion phase is assumed. Scenarios with different amounts of planetary embryos and different loss parameters are adopted in our simulations. The statistical result from hundreds of simulations shows that an Earth-like planet with water inventory of roughly 6 Earth ocean could form between 55 Cnc f and d. It may reside between 1.0 and 2.6 au but the most likely region extends from 1.5 to 2.1 au. Thus, the probability of this planet being in the potentially habitable zone (0.59–1.43 au) is relatively low, only around 10 per cent. Planets 55 Cnc f and d could also be shaped and gain some water from giant impacts and consequently the orbits of them may also change accordingly.
WISDOM Project – IX. Giant molecular clouds in the lenticular galaxy NGC 4429: effects of shear and tidal forces on clouds
Authors: Liu Lijie , Bureau Martin , Blitz Leo , Davis Timothy A , Onishi Kyoko , Smith Mark , North Eve , Iguchi Satoru 
Published: May 2021

ABSTRACT
We present high spatial resolution (≈12 pc) Atacama Large Millimeter/submillimeter Array 12CO(J = 3–2) observations of the nearby lenticular galaxy NGC 4429. We identify 217 giant molecular clouds within the 450 pc radius molecular gas disc. The clouds generally have smaller sizes and masses but higher surface densities and observed linewidths than those of Milky Way disc clouds. An unusually steep size–linewidth relation ($\sigma \propto R_{\rm c}^{0.8}$) and large cloud internal velocity gradients (0.05–0.91 km s−1 pc−1) and observed virial parameters (〈αobs,vir〉 ≈ 4.0) are found, which appear due to internal rotation driven by the background galactic gravitational potential. Removing this rotation, an internal virial equilibrium appears to be established between the self-gravitational (Usg) and turbulent kinetic (Eturb) energies of each cloud, i.e. $\langle \alpha _{\rm sg,vir}\equiv \frac{2E_{\rm turb}}{\vert U_{\rm sg}\vert }\rangle \approx 1.3$. However, to properly account for both self and external gravity (shear and tidal forces), we formulate a modified virial theorem and define an effective virial parameter $\alpha _{\rm eff,vir}\equiv \alpha _{\rm sg,vir}+\frac{E_{\rm ext}}{\vert U_{\rm sg}\vert }$ (and associated effective velocity dispersion). The NGC 4429 clouds then appear to be in a critical state in which the self-gravitational energy and the contribution of external gravity to the cloud’s energy budget (Eext) are approximately equal, i.e. $\frac{E_{\rm ext}}{\vert U_{\rm sg}\vert }\approx 1$. As such, 〈αeff,vir〉 ≈ 2.2 and most clouds are not virialized but remain marginally gravitationally bound. We show this is consistent with the clouds having sizes similar to their tidal radii and being generally radially elongated. External gravity is thus as important as self-gravity to regulate the clouds of NGC 4429.
IKT 16 aka PSR J0058–7218: discovery of a 22 ms energetic rotation-powered pulsar in the Small Magellanic Cloud
Authors: Maitra C , Esposito P , Tiengo A , Ballet J , Haberl F , Dai S , Filipović M D , Pilia M 
Published: May 2021

ABSTRACT
We report here on the discovery with XMM–Newton of pulsations at 22 ms from the central compact source associated with IKT 16, a supernova remnant in the Small Magellanic Cloud (SMC). The measured spin period and spin period derivative correspond to 21.7661076(2) ms and 2.9(3) × 10−14 s s−1, respectively. Assuming standard spin-down by magnetic dipole radiation, the spin-down power corresponds to 1.1 × 1038 erg s−1 implying a Crab-like pulsar. This makes it the most energetic pulsar discovered in the SMC so far and a close analogue of PSR J0537–6910, a Crab-like pulsar in the Large Magellanic Cloud. The characteristic age of the pulsar is 12 kyr. Having for the first time a period measure for this source, we also searched for the signal in archival data collected in radio with the Parkes telescope and in γ-rays with the Fermi/LAT, but no evidence for pulsation was found in these energy bands.
Policing and Mental ill-health: Using Big Data to Assess the Scale and Severity of, and the Frontline Resources Committed to, mental ill-health-related calls-for-service
Authors: Langton Samuel , Bannister Jon , Ellison Mark , Haleem Muhammad Salman , Krzemieniewska-Nandwani Karolina 
Published: May 2021

AbstractAddressing public safety and welfare, inclusive of responding to incidents involving persons with mental ill-health (PMIH) has become an integral dimension of, and a significant challenge to, contemporary policing. Yet, little is known of the scale and severity of such PMIH-related policing demand, nor of the extent of frontline resource consumed in resolving such incidents. To address this shortfall, we deploy a bespoke text mining algorithm on police incident logs to estimate the proportion and severity of calls-for-service involving PMIH in a study of Greater Manchester, UK. Furthermore, and using Global Positioning System data, we then assess the amount of time spent by frontline officers responding to these calls. Findings suggest that existing police recording practices serve to significantly underestimate the scale and severity of PMIH-related demand. The amount of time spent dealing with PMIH-related incidents is both substantial and disproportionate relative to other forms of police demand.
Concurrent starch accumulation in stump and high fruit production in coffee (Coffea arabica)
Authors: Cambou Aurélie , Thaler Philippe , Clément-Vidal Anne , Barthès Bernard G , Charbonnier Fabien , Van den Meersche Karel , Aguilar Vega Maria E , Avelino Jacques , Davrieux Fabrice , Labouisse Jean-Pierre , de Melo Virginio Filho Elias , Deleporte Philippe , Brunet Didier , Lehner Peter , Roupsard Olivier 
Published: May 2021

Abstract
In coffee, fruit production on a given shoot drops after some years of high yield, triggering pruning to induce resprouting. The timing of pruning is a crucial farmer’s decision affecting yield and labour. One reason for fruit production drop could be the exhaustion of resources, particularly the non-structural carbohydrates (NSC).
To test this hypothesis in a Coffea L. arabica agroforestry system, we measured the concentrations of NSC, carbon (C) and nitrogen (N) in leaves, stems and stumps of the coffee plants, 2 and 5 years after pruning. We also compared shaded vs full sun plants. For that purpose, both analytical reference and visible and near infrared reflectance spectroscopy (VNIRS) methods were used.
As expected, concentrations of biochemical variables linked to photosynthesis activity (N, glucose, fructose, sucrose) decreased from leaves to stems, and then to stumps. In contrast, variables linked more closely to plant structure and reserves (total C, C:N ratio, starch concentration) were higher in long lifespan organs like stumps. Shading had little effect on most measured parameters, contrary to expectations. Concentrations of N, glucose and fructose were higher in 2-year-old organs. Conversely, starch concentration in perennial stumps was three times higher 5 years after pruning than 2 years after pruning, despite high fruit production. Therefore, the drop in fruit production occurring after 5–6 years was not due to a lack of NSC on plant scale. Starch accumulation in perennial organs concurrently to other sinks, such as fruit growth, could be considered as a ‘survival’ strategy, which may be a relic of the behaviour of wild coffee (a tropical shade-tolerant plant).
This study confirmed that VNIRS is a promisingly rapid and cost-effective option for starch monitoring (coefficient of determination for validation, R2val = 0.91), whereas predictions were less accurate for soluble sugars, probably due to their too similar spectral signature.
Multilevel, Percutaneous Posterior Cervical Interfacet Distraction and Fusion for Cervical Spondylotic Radiculopathy
Authors: Ramos Miguel Rafael David , Mendoza Christian Julius Patero , Yumol Jerik Villegas , Joson Rafael Sorreta , Ver Mikhail Lew Perez , Ver Mario Ratio 
Published: May 2021

Study Design.
Retrospective review of patients who underwent multilevel posterior cervical interfacet distraction and fusion (PCIDF) using cages for cervical spondylotic radiculopathy (CSR).

Objective.
To determine clinical and radiographic outcomes following multilevel PCIDF.

Summary of Background Data.
Anterior cervical discectomy and fusion has long been the standard of treatment for CSR. Advancements in surgery have employed minimally invasive techniques such as endoscopic discectomy, foraminotomy, and PCIDF. Studies on single-level PCIDF have reported good clinical outcomes, short hospital stays, and rare complications, but its application in multilevel disease is still evolving.

Methods.
Patients with CSR and confirmed radiologic evidence of multilevel foraminal stenosis without central canal stenosis were reviewed. Two-year outcomes of multilevel PCIDF included Neck Disability Index, neck and arm Visual Analogue Scale (VAS), radiographic cervical alignment parameters, evidence of fusion, and incidence of adjacent segment degeneration were compared at different time points.

Results.
Thirty patients (mean age 54.6 ± 8.3) were included in the study with an average of 3.4 ± 0.8 levels treated. Mean surgical duration and intraoperative blood loss was 143.2 ± 69.7 minutes and 27.7 ± 28.7 mL, respectively, with an average length of stay at 1.8 ± 1.5 days. Neck Disability Index, VAS-neck, and VAS-arm all significantly improved at 2 weeks (P < 0.001) and was maintained until 2 years postoperatively. A significant decrease in segmental and C2-C7 lordosis, with a corresponding increase in sagittal vertical axis, was observed at 3 months postoperatively (P < 0.001) but did not deteriorate further on subsequent visits. Successful fusion was achieved in 90% of patients after 2 years. There was a 13.3% incidence of adjacent segment degeneration in the study cohort and one perioperative complication (3.3%).

Conclusion.
Our study suggests that multilevel PCIDF is safe and effective for CSR caused by foraminal stenosis. However, its potential to cause kyphosis and clinical impact on global sagittal alignment requires further scrutiny and long-term evaluation.

Level of Evidence: 4
Prenatal Phenotypical Discrepancy in Monozygotic Twins with Tuberous Sclerosis Complex
Authors: Xiong Shiyi , Wu Fengyu , Chen Guangquan , Wang Jian , Yang Yingjun , Xing Ya , Sun Luming 
Published: May 2021

Abstract
Tuberous sclerosis complex (TSC) is an autosomal-dominant genetic disorder characterized by the development of hamartomas in the brain, heart, skin, kidney, lung, retina, and so on. One fetus from family 1 had a cardiac rhabdomyoma from 21 weeks and 6 days of gestational age, and developed multiple rhabdomyomas and tubers in the brain at 23 weeks and 5 days. The counter monozygotic twin fetus remained negative throughout the pregnancy according to imaging examination. A nonsense mutation in TSC2 (c.4762C>T, p.Gln1588*) was identified in both twins, but not in the mother. Family 2 was one pair of twin fetuses caused by a microdeletion of exon 30 within TSC2 inherited from their apparently asymptomatic mother with mosaic status. The larger fetus was identified as having the first cardiac rhabdomyoma from 17 weeks and 4 days of gestational age. The smaller fetus developed multiple rhabdomyomas until 25 weeks and 6 days of gestational age. Both families terminated the pregnancy. Here, we provide intrauterine examples of clinical variability among monozygotic twins suffering from TSC.