bluuebunny/crossref_metadata_2025_split huggingface dataset:
Black holes and WIMPs: all or nothing or something else
Authors: Carr Bernard , Kühnel Florian , Visinelli Luca 
Published: July 2021

ABSTRACT
We consider constraints on primordial black holes (PBHs) in the mass range $(10^{-18}\!-\!10^{15})\, \mathrm{M}_{\odot }$ if the dark matter (DM) comprises weakly interacting massive particles (WIMPs) that form haloes around them and generate γ-rays by annihilations. We first study the formation of the haloes and find that their density profile prior to WIMP annihilations evolves to a characteristic power-law form. Because of the wide range of PBH masses considered, our analysis forges an interesting link between previous approaches to this problem. We then consider the effect of the WIMP annihilations on the halo profile and the associated generation of γ-rays. The observed extragalactic γ-ray background implies that the PBH DM fraction is $f^{}_{\rm PBH} \lesssim 2 \times 10^{-9}\, (m_{\chi } / {\rm TeV})^{1.1}$ in the mass range $2 \times 10^{-12}\, \mathrm{M}_{\odot }\, (m_{\chi } / {\rm TeV})^{-3.2} \lesssim M \lesssim 5 \times 10^{12}\, \mathrm{M}_{\odot }\, (m_{\chi } / {\rm TeV})^{1.1}$, where mχ and M are the WIMP and PBH masses, respectively. This limit is independent of M and therefore applies for any PBH mass function. For $M \lesssim 2\times 10^{-12}\, \mathrm{M}_{\odot }\, (m_{\chi }/ {\rm TeV})^{-3.2}$, the constraint on $f^{}_{\rm PBH}$ is a decreasing function of M and PBHs could still make a significant DM contribution at very low masses. We also consider constraints on WIMPs if the DM is mostly PBHs. If the merging black holes recently discovered by LIGO/Virgo are of primordial origin, this would rule out the standard WIMP DM scenario. More generally, the WIMP DM fraction cannot exceed 10−4 for $M \gt 10^{-9}\, \mathrm{M}_{\odot }$ and $m_{\chi } \gt 10\,$ GeV. There is a region of parameter space, with $M \lesssim 10^{-11}\, \mathrm{M}_{\odot }$ and $m_{\chi } \lesssim 100\,$ GeV, in which WIMPs and PBHs can both provide some but not all of the DM, so that one requires a third DM candidate.
Aberration-corrected ultrafine analysis of miRNA reads at single-base resolution: a k-mer lattice approach
Authors: Zhang Xuan , Ping Pengyao , Hutvagner Gyorgy , Blumenstein Michael , Li Jinyan 
Published: July 2021

Abstract
Raw sequencing reads of miRNAs contain machine-made substitution errors, or even insertions and deletions (indels). Although the error rate can be low at 0.1%, precise rectification of these errors is critically important because isoform variation analysis at single-base resolution such as novel isomiR discovery, editing events understanding, differential expression analysis, or tissue-specific isoform identification is very sensitive to base positions and copy counts of the reads. Existing error correction methods do not work for miRNA sequencing data attributed to miRNAs’ length and per-read-coverage properties distinct from DNA or mRNA sequencing reads. We present a novel lattice structure combining kmers, (k – 1)mers and (k + 1)mers to address this problem. The method is particularly effective for the correction of indel errors. Extensive tests on datasets having known ground truth of errors demonstrate that the method is able to remove almost all of the errors, without introducing any new error, to improve the data quality from every-50-reads containing one error to every-1300-reads containing one error. Studies on experimental miRNA sequencing datasets show that the errors are often rectified at the 5′ ends and the seed regions of the reads, and that there are remarkable changes after the correction in miRNA isoform abundance, volume of singleton reads, overall entropy, isomiR families, tissue-specific miRNAs, and rare-miRNA quantities.
Stabilization and structural changes of 2D DNA origami by enzymatic ligation
Authors: Rajendran Arivazhagan , Krishnamurthy Kirankumar , Giridasappa Amulya , Nakata Eiji , Morii Takashi 
Published: July 2021

Abstract
The low thermal stability of DNA nanostructures is the major drawback in their practical applications. Most of the DNA nanotubes/tiles and the DNA origami structures melt below 60°C due to the presence of discontinuities in the phosphate backbone (i.e., nicks) of the staple strands. In molecular biology, enzymatic ligation is commonly used to seal the nicks in the duplex DNA. However, in DNA nanotechnology, the ligation procedures are neither optimized for the DNA origami nor routinely applied to link the nicks in it. Here, we report a detailed analysis and optimization of the conditions for the enzymatic ligation of the staple strands in four types of 2D square lattice DNA origami. Our results indicated that the ligation takes overnight, efficient at 37°C rather than the usual 16°C or room temperature, and typically requires much higher concentration of T4 DNA ligase. Under the optimized conditions, up to 10 staples ligation with a maximum ligation efficiency of 55% was achieved. Also, the ligation is found to increase the thermal stability of the origami as low as 5°C to as high as 20°C, depending on the structure. Further, our studies indicated that the ligation of the staple strands influences the globular structure/planarity of the DNA origami, and the origami is more compact when the staples are ligated. The globular structure of the native and ligated origami was also found to be altered dynamically and progressively upon ethidium bromide intercalation in a concentration-dependent manner.
An intradialytic non-immersive virtual reality exercise programme: a crossover randomized controlled trial
Authors: Martínez-Olmos Francisco J , Gómez-Conesa Antonia A , García-Testal Alicia , Ortega-Pérez-de-Villar Lucía , Valtueña-Gimeno Noemí , Gil-Gómez José A , Garcia-Maset Rafael , Segura-Ortí Eva 
Published: July 2021

Abstract

Background
Chronic kidney disease is closely related to a high risk of death and disability, poor physical performance and frailty. The main objective of this research was to analyse how intradialytic administration of a non-immersive virtual reality (VR) exercise programme would affect physical function and adherence to exercise in these patients.

Methods
A total of 56 individuals participated in two 12-week periods in a crossover randomized controlled trial. Each patient underwent a functional capacity evaluation before and after each study period. The functional tests administered included the 4-m gait speed test, Short Physical Performance Battery (SPPB), timed up-and-go (TUG) test, one-legged stance test (OLST) for balance, sit-to-stand 10 (STS-10) and sit-to-stand 60 (STS-60) tests and 6-min walking test (6MWT). Adherence to the exercise programme was also recorded. To assess the effect of VR exercise on the functional test outcomes over time, the patients were analysed using a two-way repeated-measures analysis of variance with time and treatment as the within-participant factors.

Results
By the end of the 12 weeks of exercise, compared with the control period, 33 participants showed significant change in physical function as measured through the 4-m gait speed test (0.14 m/s), SPPB (1.2 points), TUG (−1.7 s), OLST (7.1 s), STS-10 (−5.8 s), STS-60 (5 repetitions) and 6MWT (85.2 m), with adherence rates exceeding 70%. There were no changes in the biochemical data or in the medications in the period of the study.

Conclusion
An intradialytic non-immersive VR exercise programme improves patient physical function.
Prevalence of vitamin D deficiency and impact on clinical outcomes after kidney transplantation: a systematic review and meta-analysis
Authors: Yin Saifu , Wang Xianding , Li Linde , Huang Zhongli , Fan Yu , Song Turun , Lin Tao 
Published: July 2021

Abstract

Context
The prevalence of vitamin D deficiency (VDD) and its impact on clinical outcomes after kidney transplant (KT) remain poorly defined.

Objectives
We conducted a meta-analysis to evaluate the impact of early VDD on clinical outcomes after KT.

Data Sources
Electronic databases (PubMed, Embase, Web of Science, and The Cochrane Library) were systematically searched for eligible publications up to April 30, 2020.

Data Extraction
Relative risk was presented as hazard ratios (HRs) or odds ratios (ORs) and 95%CIs for dichotomous outcomes. Mean difference (MD) and 95%CIs were presented for continuous outcomes.

Results
A total of 28 studies (13 prospective and 15 retrospective) were included. VDD was common early after KT, with a prevalence of 52% (95%CI: 41%–64%) at transplant, 34% (95%CI: 17%–51%) at 3 months, and 23% (95%CI: 10%–35%) at 6 months. Early VDD was associated with higher mortality rate after KT (HR, 1.56; 95%CI: 1.32–1.84; P &lt; 0.001). In addition, early VDD led to higher risk of bacterial infection (OR, 1.82; 95%CI: 1.40–2.36; P &lt; 0.001), BK polyomavirus infection (OR, 2.11, 95%CI: 1.23–3.61; P = 0.006), and cytomegalovirus infection (OR, 1.69; 95%CI: 1.24–2.31; P = 0.001). Early VDD increased the risk of acute rejection as well (HR, 2.28; 95%CI: 1.57–3.30; P &lt; 0.001). Recipients with early VDD had lower estimated glomerular filtration rates (mean difference: −5.06; 95%CI: −7.28 to 2.83 mL/min; P &lt; 0.001). Sensitivity analyses showed good stability of the pooled results.

Conclusion
VDD was common early after KT and associated with higher risk of death and adverse outcomes.
Experience From 211 Transcortical Selective Amygdalohippocampectomy Procedures: Relevant Surgical Anatomy and Review of the Literature
Authors: Ali Rushna , Englot Dario J , Yu Hong , Naftel Robert , Haas Kevin F , Konrad Peter E 
Published: July 2021

Abstract

BACKGROUND
Selective amygdalohippocampectomy (SelAH) is designed to treat medically refractory mesial temporal lobe epilepsy with reduced morbidity compared to standard anterior temporal lobectomy. At our institution, we perform SelAH via a transcortical approach via small corticectomy in the middle temporal gyrus.

OBJECTIVE
To discuss the surgical anatomy and nuances of SelAH, share our institutional experience, and perform a review of literature.

METHODS
Institutional experience was recorded by collecting demographic and outcome data from 1999 to 2017 under an Institutional Review Board protocol in a prospective manner using a REDCap database.

RESULTS
A total of 211 SelAH procedures were performed at our institution between 1999 and 2017. Of these patients, 54% (113/211) were females. The average age at surgery was 39.4 yr. Two-year Engel outcome data were available for 168 patients, of which 73% (123/168) had Engel I outcomes. Engel II outcomes were reported in 16.6% (28/168), III in 4.7% (8/168), and IV in 5.3% (9/168). Our review of literature showed that this is comparable to the seizure freedom rates reported by other groups. We then reviewed our surgical methodology based on operative reports and created illustrations of the surgical anatomy of temporal lobe approach. These illustrations were compared with postoperative magnetic resonance imaging to provide a better 3D understanding of the complex architecture of mesial temporal structures.

CONCLUSION
SelAH is a minimally invasive, safe, and effective approach for the treatment of medically refractory epilepsy with good surgical outcomes and low morbidity. We feel that mastering the complex anatomy of this approach helps achieve successful outcomes.
Golden Eagle dietary shifts following wildfire and shrub loss have negative consequences for nestling survivorship
Authors: Heath Julie A , Kochert Michael N , Steenhof Karen 
Published: July 2021

Abstract
Wildfires and invasive species have caused widespread changes in western North America’s shrub-steppe landscapes. The bottom–up consequences of degraded shrublands on predator ecology and demography remain poorly understood. We used a before–after paired design to study whether Golden Eagle (Aquila chrysaetos) diet and nestling survivorship changed following wildfires in southwestern Idaho, USA. We assessed burn extents from 1981 to 2013 and vegetation changes between 1979 (pre-burn) and 2014 (post-burn) within 3 km of Golden Eagle nesting centroids. We measured the frequency and biomass of individual prey, calculated diet diversity indexes, and monitored nestling survivorship at 15 territories in 1971–1981 and 2014–2015. On average, 0.70 of the area within 3 km of nesting centroids burned between 1981 and 2013, and the mean proportion of unburned shrubland decreased from 0.73 in 1979 to 0.22 in 2014. Diets in post-burn years were more diverse and had a lower proportion of some shrub-associated species, such as black-tailed jackrabbits (Lepus californicus) and mountain cottontails (Sylvilagus nuttallii), and a higher proportion of American Coots (Fulica americana), Mallards (Anas platyrhynchos), Piute ground squirrels (Urocitellus mollis), and Rock Pigeons (Columba livia) compared with pre-burn years. A high proportion of waterfowl represented a novel change in Golden Eagle diets, which are typically dominated by mammalian prey. Nestling survivorship was positively associated with the proportion of black-tailed jackrabbits and negatively associated with the proportion of Rock Pigeons in eagle diets. Rock Pigeons are a vector for Trichomonas gallinae, a disease-causing protozoan lethal to young eagles. Nesting attempts were more likely to fail (all young die) in the post-burn period compared with the pre-burn period. Dietary shifts are a common mechanism for predators to cope with landscape change, but shifts away from preferred prey to disease vectors affect nestling survivorship and could lead to population-level effects on productivity.
Enrichment Nature of Ultrapotassic Rocks in Southern Tibet Inherited from their Mantle Source
Authors: Li Weikai , Yang Zhiming , Chiaradia Massimo , Zhou Limin , Hou Zengqian 
Published: July 2021

AbstractPost-collisional ultrapotassic rocks (UPRs) in the Tibetan Plateau exhibit extreme enrichment in incompatible elements and radiogenic isotopes. Such enrichment is considered to be either inherited from a mantle source or developed during crustal evolution. In this study, to solve this debate we combined mineral textures and in situ geochemical composition of clinopyroxene phenocrysts in UPRs from southern Tibet to reveal their crustal evolution, enrichment cause and constrain metasomatism in their mantle source. Results show that the UPRs experienced an array of crustal processes, i.e., fractional crystallization, mixing, and assimilation. Fractional crystallization is indicated by decreases in Mg# and Ni and enrichment in incompatible elements (e.g. rare earth element (REE), Sr, Zr) toward the rims of normally zoned clinopyroxene phenocrysts (type-I). Magma mixing is evidenced by the presence of some clinopyroxene phenocrysts (type-II, -III) showing disequilibrium textures (e.g. reversed and overgrowth zoning), but in situ Sr isotope and trace element analysis of those disequilibrium zones indicate that late-stage recharged mafic magmas are depleted (87Sr/86Sr: 0.70659–0.71977) compared with the primitive ultrapotassic magmas (87Sr/86Sr: 0.70929–0.72553). Assimilation is revealed by the common presence of crustal xenoliths in southern Tibetan UPRs. Considering the much lower 87Sr/86Sr values (0.707759–0.709718) and incompatible element contents of these crustal xenoliths relative to their host UPRs, assimilation should have resulted in geochemical depletion of southern Tibetan UPRs rather than enrichment. The diluting impact of both assimilation and mixing is also supported by the modeling results based on the EC-E′RAχFC model combining the growth history of clinopyroxene. Trace elements ratios in clinopyroxenes also imply that the mantle source of southern Tibetan UPRs suffered an enriched and carbonatite-dominated metasomatism. Thus, we conclude that enrichment of southern Tibetan UPRs was inherited from the mantle source.
Gondomar and the Stage: Diego Sarmiento de Acuña and the Lost Theatrical Connection
Authors: Pérez Díez José A 
Published: July 2021

Abstract
Don Diego Sarmiento de Acuña, first Count of Gondomar (1567–1626), was twice appointed by the King of Spain to the delicate embassy in the court of James I in London, where he played a decisive role in Anglo-Spanish relations in the aftermath of the treaty of peace between the two monarchies signed in London in 1604. Beyond his uncontested political significance, Gondomar was also Spain’s premier bibliophile. His famous library comprised over 6000 volumes in nine languages, including a surprisingly large collection of plays. His interests in drama as an art form and in the theatre as a profession are well attested in his vast correspondence and the sizeable body of documents that have survived. While these interests have been noted, this is the first study that has attempted to analyse this body of evidence in a systematic way to suggest a closer connection to drama and the professional theatre of England and Spain. In particular, this study aims to shed some light on the untraced connections between Gondomar and the English playwrights and actors active in London during his time as ambassador. Gondomar’s library in London contained a number of recent and relatively rare works whose presence in the English metropolis at the right time might help to explain some cases of early adaptation of Spanish contemporary literature to the English drama of the period.
Risk of major adverse cardiovascular events in patients initiating biologics/apremilast for psoriatic arthritis: a nationwide cohort study
Authors: Pina Vegas Laura , Le Corvoisier Philippe , Penso Laetitia , Paul Muriel , Sbidian Emilie , Claudepierre Pascal 
Published: July 2021

Abstract

Objective
Several biological DMARDs (bDMARDs) have demonstrated anti-inflammatory effects in PsA. However, their comparative cardiovascular safety profiles remain unknown. We evaluated the risk of major adverse cardiovascular events (MACEs) in PsA patients on therapy with different classes of bDMARDs and apremilast.

Methods
This nationwide cohort study involved the administrative healthcare database of the French health insurance scheme linked to the hospital discharge database. All adults with PsA who were new users of bDMARDs/apremilast (neither in the year before the index date) during 2015–19 were included. Patients with previous cardiovascular diseases were excluded. End of follow-up was 31 December 2019. The primary endpoint was an occurrence of MACEs in a time-to-event analysis with propensity score-weighted Cox and Fine–Gray models.

Results
Between 2015 and 2019, we included 9510 bDMARD new users [mean age 48.5 (s.d. 12.7) years; 42% men], including 7289 starting a TNF inhibitor, 1058 an IL-12/23 inhibitor and 1163 an IL-17 inhibitor, with 1885 apremilast new users [mean age 54.0 (s.d. 12.5) years; 44% men]. MACEs occurred in 51 (0.4%) patients. After propensity score weighting, the risk of MACEs was significantly greater with IL-12/23 (weighted hazard ratio 2.0, 95% CI 1.3, 3.0) and IL-17 (weighted hazard ratio 1.9, 95% CI 1.2, 3.0) inhibitors than TNF inhibitors, with no significant increased risk with apremilast (weighted hazard ratio 1.3, 95% CI 0.8, 2.2). Similar results were observed with the Fine–Gray competing risks survival model.

Conclusion
Analysis of a large database revealed a small overall number of MACEs, and the risk of MACEs was greater for PsA new users of IL-12/23 and IL-17 vs TNF inhibitors.
Clinical Spectrum of Neurological Manifestations in Pediatric COVID-19 Illness: A Case Series
Authors: Khan Afreen , Chakravarty Aparna , Jain Abhinav , Harish Rekha , Naqishbandi Rizwan , Ishani Twisha 
Published: July 2021

Abstract
We describe a cohort of three patients with variable neurological presentations by SARS-COV-2 infection. It includes one case each of acute cerebellitis, acute encephalomyelitis and arterial ischemic stroke. To the best of our knowledge, we report the first pediatric case of acute cerebellitis due to SARS-CoV-2 infection. All critically ill patients were treated with methylprednisolone pulse therapy and dexamethasone. Patient with acute cerebellitis in addition required intravenous immunoglobulin infusion. All the patients responded to the treatment with complete neurological recovery.
Neurological Manifestations of Pediatric Acute COVID Infections: A Single Center Experience
Authors: Dilber Beril , Aydın Zeynep Gökçe Gayretli , Yeşilbaş Osman , Sağ Elif , Aksoy Nurdan Kaykı , Gündoğmuş Fırat , Küçükalioğlu Burcu Parıltan , Yılmaz Semra Atasoy , Demirhan Yeşeren Nil , Çelik Nurşen , Karaca Abdullah , Ertem Neşe Yalçın , Özdemir Ramazan , Aksoy Halil İbrahim , Öztürk Emine Esra , Saygın Berna , Acar Filiz Aktürk 
Published: July 2021

Abstract

Background
Coronavirus disease 2019 (COVID-19) usually leads to a mild infectious disease course in children, while serious complications may occur in conjunction with both acute infection and neurological symptoms, which have been predominantly reported in adults. The neurological complications in these patients vary based on patient age and underlying comorbidities. Data on clinical features, particularly neurological features, and prognostic factors in children and adolescents are limited. This study provides a concise overview of neurological complications in pediatric COVID-19 cases.

Materials and methods
The retrospective study reviewed medical records of all patients who were admitted to our hospital and were diagnosed with COVID-19 by real-time reverse-transcription polymerase-chain-reaction (RT–PCR) assay between 11 March 2020 and 30 January 2021. Patients with a positive PCR result were categorized into two groups: outpatient departments patients and inpatient departments (IPD).

Results
Of the 2530 children who underwent RT–PCR during the study period, 382 (8.6%) were confirmed as COVID-19 positive, comprising 188 (49.2%) girls and 194 (50.8%) boys with a mean age of 7.14±5.84 (range, 0–17) years. Neurological complications that required hospitalization were present in 34 (8.9%) patients, including seizure (52.9%), headache (38.2%), dizziness (11.1%) and meningoencephalitis (5.8%).

Conclusion
The results indicated that neurological manifestations are not rare in children suffering from COVID-19. Seizures, headaches, dizziness, anosmia, ageusia and meningoencephalitis are major neurological manifestations during acute COVID-19 disease. Although seizures were the most common cause of hospitalization in IPD patients, the frequency of meningoencephalitis was quite high. Seizures were observed as febrile seizures for children under 6 years of age and afebrile seizures for those over 6 years of age. Febrile seizure accounted for half of all seizure children.