Temporal dynamics of woolly mammoth genome erosion prior to extinction.

A number of species have recently recovered from near-extinction. Although these species have avoided the immediate extinction threat, their long-term viability remains precarious due to the potential genetic consequences of population declines, which are poorly understood on a timescale beyond a few generations. Woolly mammoths (Mammuthus primigenius) became isolated on Wrangel Island around 10,000 years ago and persisted for over 200 generations before becoming extinct around 4,000 years ago. To study the evolutionary processes leading up to the mammoths' extinction, we analyzed 21 Siberian woolly mammoth genomes. Our results show that the population recovered quickly from a severe bottleneck and remained demographically stable during the ensuing six millennia. We find that mildly deleterious mutations gradually accumulated, whereas highly deleterious mutations were purged, suggesting ongoing inbreeding depression that lasted for hundreds of generations. The time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked populations.

Disentangling Signatures of Selection Before and After European Colonization in Latin Americans.

Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. Although classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations, we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ∼4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico, and Peru. Our approach replicates previous reports of selection in the human leukocyte antigen region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.

A genome-wide association study identifies novel gene associations with facial skin wrinkling and mole count in Latin Americans.

BACKGROUND: Genome-wide association studies (GWASs) have identified genes influencing skin ageing and mole count in Europeans, but little is known about the relevance of these (or other genes) in non-Europeans. OBJECTIVES: To conduct a GWAS for facial skin ageing and mole count in adults < 40 years old, of mixed European, Native American and African ancestry, recruited in Latin America. METHODS: Skin ageing and mole count scores were obtained from facial photographs of over 6000 individuals. After quality control checks, three wrinkling traits and mole count were retained for genetic analyses. DNA samples were genotyped with Illumina's HumanOmniExpress chip. Association testing was performed on around 8 703 729 single-nucleotide polymorphisms (SNPs) across the autosomal genome. RESULTS: Genome-wide significant association was observed at four genome regions: two were associated with wrinkling (in 1p13·3 and 21q21·2), one with mole count (in 1q32·3) and one with both wrinkling and mole count (in 5p13·2). Associated SNPs in 5p13·2 and in 1p13·3 are intronic within SLC45A2 and VAV3, respectively, while SNPs in 1q32·3 are near the SLC30A1 gene, and those in 21q21·2 occur in a gene desert. Analyses of SNPs in IRF4 and MC1R are consistent with a role of these genes in skin ageing. CONCLUSIONS: We replicate the association of wrinkling with variants in SLC45A2, IRF4 and MC1R reported in Europeans. We identify VAV3 and SLC30A1 as two novel candidate genes impacting on wrinkling and mole count, respectively. We provide the first evidence that SLC45A2 influences mole count, in addition to variants in this gene affecting melanoma risk in Europeans.

A laboratory study of the scouting ability of two reciprocating glide path instruments in mesial root canals of extracted mandibular molars.

AIM: To evaluate in a laboratory setting the performance of two reciprocating glide path systems, WaveOne Gold Glider (WO) and R-Pilot (RP), to create a glide path in mesial root canals of mandibular molars and to assess the torsional resistance of instruments after performing the glide path. METHODOLOGY: A total of 60 mesial root canals of extracted human mandibular molars were divided into two groups (n = 30) according to the glide path system to be used. The data from the volume of each canal, acquired by microcomputed tomography (micro-CT), were validated statistically for the anatomical pairing of the groups. Preparation time, frequency in gaining apical patency, plastic deformation rate of instruments, and canal transportation and centring ability were recorded and compared statistically. The torsional fatigue of the instruments after use was also evaluated. Data were analysed using Fisher's exact test and Mann-Whitney U-test with a 5% significance level. RESULTS: No significant differences were found between groups regarding the time required to perform the glide path, the frequency distributions of the canals classified as patent and the instruments with plastic deformation after use (P > 0.05). No significant differences were found between groups regarding the degree of canal transportation and centring ability at the cervical, middle and apical thirds (P > 0.05). The RP groups had significantly greater maximum torsional strength values compared with the WO groups (P < 0.05). The used WO group had greater angular deflection to fracture when compared to the new WO group (P < 0.05). A significant difference was also found in the percentage of loss of angular deflection in a comparison of the WO group with the RP group (P < 0.05). CONCLUSIONS: The WO and RP instruments performed the same in terms of preparation time, plastic deformation, gaining apical patency, degree of canal transportation and centring ability. The RP instruments had greater torsional strength, less angular deflection and lower percentage of loss in angular deflection than the WO. The used WO group had the greatest angular deflection values.

Effect of larger apical size on the quality of preparation in curved canals using reciprocating instruments with different heat thermal treatments.

AIM: To evaluate the influence of larger apical canal enlargement in curved canals using reciprocating systems subjected to various heat treatments. METHODOLOGY: Ninety mandibular premolars with root curvatures ranging from 20° to 30° were selected and scanned by microcomputed tomography (micro-CT) before and after root canal preparation with reciprocating systems (n = 30): Reciproc Blue (RB size 25, .08 taper and size 40, .06 taper; VDW, Munich, Germany), WaveOne Gold (WOG size 25, .07 taper and size 35, .06 taper; Dentsply Sirona, Ballaigues, Switzerland) and ProDesign R (PDR size 25, .06 taper and size 35, .05 taper; Easy Dental Equipment, Belo Horizonte, Brazil). Canal transportation, untouched areas, and apical and total root canal volumes were measured. Statistical analysis was performed with the nonparametric Kruskal-Wallis and Dunn's tests and a significance level set at 5%. RESULTS: The between-group comparison revealed no significant difference in untouched areas, canal transportation, and apical root canal volume among the groups (P > 0.05). However, WOG size 35, .06 taper was associated with a significant increase in the percentage of total canal volume in comparison to the PDR size 35, .05 taper (P < 0.05). The within-group comparison revealed a significant decrease in untouched areas, increase in apical and total root canal volume for all groups when using a larger instrument (P < 0.05). There was no significant difference in transportation among the groups and when a larger apical preparation was created (P > 0.05). CONCLUSIONS: Larger apical enlargement of curved canals was associated with a decrease in untouched areas, an increase in root canal volume and maintenance of canal trajectory. In addition, all systems were safe and provided similar root canal shapes.

The ability of three nickel-titanium mechanized systems to negotiate and shape MB2 canals in extracted maxillary first molars: a micro-computed tomographic study.

AIM: To evaluate the influence of three engine-driven NiTi file systems manufactured from different NiTi alloys for the preparation of second mesiobuccal (MB2) canals in extracted maxillary first molars using a micro-computed tomographic (micro-CT) scanner. METHODOLOGY: Thirty maxillary molars with two canals in the mesiobuccal root were selected and randomly divided into three groups (n = 10): Reciproc [REC; size 25, .08 taper; VDW, Munich, Germany], ProDesign R [PDR; size 25, .06 taper; Easy, Belo Horizonte, Brazil] and Mtwo [MO; size 25, .06 taper; VDW, Munich, Germany]. Before and after root canal preparation of the MB2 canal, the teeth were scanned using a micro-CT to evaluate canal transportation, centring ability, dentine thickness and volume change. The working time to achieve working length was also evaluated. All parameters were compared statistically using the Kruskal-Wallis and Dunn test for multiple comparisons, with a significance level of 5%. RESULTS: There was no significant difference amongst the groups regarding canal transportation and centring ability (P > 0.05). However, the PDR size 25, .06 taper group had significantly lower canal volume and volume of dentine removal compared with a MO size 25, .06 taper and REC size 25, .08 taper (P < 0.05). A root perforation was detected in MO size 25, .06 taper and REC size 25, .08 taper groups, respectively. Regarding the working time, the PDR size 25, .06 taper required a significantly longer time to achieve working length than MO size 25, .06 taper and REC size 25, .08 taper (P < 0.05). CONCLUSIONS: All NiTi systems had similar canal transportation, centring ability and increase in apical volume after preparation of MB2 canals. However, the PDR size 25, .06 taper had less volume of dentine removal, absence of root canal perforation and required a longer time to accomplish the root canal preparation.

Mesotocin influences pinyon jay prosociality.

Many species exhibit prosocial behaviour, in which one individual's actions benefit another individual, often without an immediate benefit to itself. The neuropeptide oxytocin is an important hormonal mechanism influencing prosociality in mammals, but it is unclear whether the avian homologue mesotocin plays a similar functional role in birds. Here, we experimentally tested prosociality in pinyon jays (Gymnorhinus cyanocephalus), a highly social corvid species that spontaneously shares food with others. First, we measured prosocial preferences in a prosocial choice task with two different pay-off distributions: Prosocial trials delivered food to both the subject and either an empty cage or a partner bird, whereas Altruism trials delivered food only to an empty cage or a partner bird (none to subject). In a second experiment, we examined whether administering mesotocin influenced prosocial preferences. Compared to choices in a control condition, we show that subjects voluntarily delivered food rewards to partners, but only when also receiving food for themselves (Prosocial trials), and administration of high levels of mesotocin increased these behaviours. Thus, in birds, mesotocin seems to play a similar functional role in facilitating prosocial behaviours as oxytocin does in mammals, suggesting an evolutionarily conserved hormonal mechanism for prosociality.

The effect of mixing method on tricalcium silicate-based cement.

AIM: To evaluate the effect of three methods of mixing on the physical and chemical properties of tricalcium silicate-based cements. METHODOLOGY: The materials evaluated were MTA Angelus and Portland cement with 20% zirconium oxide (PC-20-Zr). The cements were mixed using a 3 : 1 powder-to-liquid ratio. The mixing methods were manual (m), trituration (tr) and ultrasonic (us) activation. The materials were characterized by means of scanning electron microscope (SEM) and energy dispersive X-ray spectroscopy. Flowability was analysed according to ANSI/ADA 57/2012. Initial and final setting times were assessed following ASTM C266/08. Volume change was evaluated using a micro-CT volumetric method. Solubility was analysed according to ADA 57/2012. pH and calcium ion release were measured after 3, 24, 72 and 168 h. Statistical analysis was performed using two-way analysis of variance. The level of significance was set at P = 0.05. RESULTS: The SEM analysis revealed that ultrasonic activation was associated with a homogeneous distribution of particles. Flowability, volume change and initial setting time were not influenced by the mixing method (P > 0.05). Solubility was influenced by the mixing method (P < 0.05). For pH, at 168 h, significant differences were found between MTA-m and PC-20-Zr-m (P < 0.05). For calcium ion release, PC-20-Zr-tr had higher values than MTA-m at 3 h, and MTA-tr had higher values than PC-20-Zr-m at 168 h (P < 0.05). CONCLUSIONS: The ultrasonic and trituration methods led to higher calcium ion release and pH compared with manual mixing for all cements, whilst the ultrasonic method produced smaller particles for the PC-20-Zr cement. Flow, setting times and volume change were not influenced by the mixing method used; however, it did have an impact on solubility.

Fusobacterium nucleatum prosthetic hip infection: Case report and review of the literature of unusual anaerobic prosthetic joint infection.

The anaerobic Gram-negative rod Fusobacterium nucleatum is an oral commensal and periodontal pathogen that has been associated with a wide variety of infections, yet it is extremely rare to be associated with prosthetic joint infection. After an exhaustive literature review, only two cases of prosthetic joint infection by F. nucleatum have been previously reported. To our knowledge, the case we report on here is the first combined with periprosthetic abscess and related with hemochromatosis. We therefore sought to provide a comprehensive literature review of case reports or series of less commonly encountered anaerobic microorganisms isolated from prosthetic joint infections.

Paediatric case series of drug reaction with eosinophilia and systemic symptoms (DRESS): 12-year experience at a single referral centre in Hong Kong and the first reported use of infliximab.

Summary: DRESS (drug reaction with eosinophilia and systemic symptoms) is a rare but potentially life-threatening disorder characterized by fever, skin eruption, haematological abnormalities and multi-organ dysfunction after drug exposure. The pathophysiology is thought to be related to interactions between culprit drugs, viral reactivation and T-lymphocytes activation. We report 4 paediatric patients with DRESS who were treated at our centre over the past 12 years. Most cases improved after corticosteroids. Other immunosuppressive medications were attempted in refractory cases with varied outcomes. Patient 3 was the first reported case that involved the use of infliximab, a TNF-α inhibitor, for DRESS. Although clinical efficacy was not observed for this one patient, a previous study demonstrated that patients with DRESS, disease progression and HHV-6 reactivation had elevated pre-treatment TNF- α and IL-6 levels. Further research is needed to explore the role of these cytokines in DRESS.

The effects of global warming on allergic diseases.

Global warming is a public health emergency. Substantial scientific evidence indicates an unequivocal rising trend in global surface temperature that has caused higher atmospheric levels of moisture retention leading to more frequent extreme weather conditions, shrinking ice volume, and gradually rising sea levels. The concomitant rise in the prevalence of allergic diseases is closely related to these environmental changes because warm and moist environments favour the proliferation of common allergens such as pollens, dust mites, molds, and fungi. Global warming also stresses ecosystems, further accelerating critical biodiversity loss. Excessive carbon dioxide, together with the warming of seawater, promotes ocean acidification and oxygen depletion. This results in a progressive decline of phytoplankton and fish growth that in turn promotes the formation of larger oceanic dead zones, disrupting the food chain and biodiversity. Poor environmental biodiversity and a reduction in the microbiome spectrum are risk factors for allergic diseases in human populations. While climate change and the existence of an allergy epidemic are closely linked according to robust international research, efforts to mitigate these have encountered strong resistance because of vested economic and political concerns in different countries. International collaboration to establish legally binding regulations should be mandatory for forest protection and energy saving. Lifestyle and behavioural changes should also be advocated at the individual level by focusing on low carbon living; avoiding food wastage; and implementing the 4Rs: reduce, reuse, recycle, and replace principles. These lifestyle measures are entirely consistent with the current recommendations for allergy prevention. Efforts to mitigate climate change, preserve biodiversity, and prevent chronic diseases are interdependent disciplines.

Effectiveness of inactivated COVID-19 vaccine CoronaVac in children aged less than 3 years old during Omicron wave in Hong Kong.

The COVID-19 pandemic has affected people of all ages worldwide. However, there is still no information on the vaccine effectiveness (VE) of inactivated COVID-19 vaccines in children aged less than 3 years old. This study highlighted that 2 doses of CoronaVac were effective in preventing COVID-19, with a VE of 83.1 %.

[Sociodemographic, clinical and ultrasound characterization of thyroid nodule pathology and its association with malignancy in a Colombian high-complexity center]. / Caracterización sociodemográfica, clínica y ecográfica de la enfermedad de nódulos tiroideos y su relación con la malignidad en un centro de alta complejidad colombiano.

BACKGROUND AND OBJECTIVE: Thyroid nodules are among the most frequent conditions, with a 10% risk of malignancy. The objective is to describe the frequency of demographic, clinical, and ultrasonographic characteristics of thyroid nodule pathology in adults and to explore the relationship with tumor malignancy. METHODS: An analytical, retrospective cross-sectional study in adults with thyroid nodules and nodular fine-needle aspiration performed in adult patients from a Colombian reference center between 2009-2019. Data were obtained from the clinical history, descriptive measures of the patient's demographic, clinical, and ultrasound variables were estimated, and their relationship with the malignancy of the tumor was explored. RESULTS: A total of 445 patients and 515 nodules were included. The median age was 55 years (IQR 44-64), 86.8% of women, and 54.8% had a single lesion. Percentages of 80.2 and 19.8 were benign and malignant nodules, with a median of 15.7mm (IQR 11-25) and 12.7mm (IQR 8.5-18.3), respectively (p<0.001). Hypothyroidism and levothyroxine consumption were higher in those with malignant nodules (p<0.001). The echographic characteristics were statistically different between the nodules. In the malignant ones, there was a higher frequency of solid composition, hypoechogenicity, and irregular margins. In contrast, in the benign ones, the absence of echogenic focus stood out (p<0.001). CONCLUSION: The ultrasound characteristics are essential to define the risk of malignancy of a thyroid nodule. Therefore, considering the most frequent ones can help in the most appropriate approach to primary care.

Genomics of adaptive evolution in the woolly mammoth.

Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of traditional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.

Neanderthal introgression in SCN9A impacts mechanical pain sensitivity.

The Nav1.7 voltage-gated sodium channel plays a key role in nociception. Three functional variants in the SCN9A gene (encoding M932L, V991L, and D1908G in Nav1.7), have recently been identified as stemming from Neanderthal introgression and to associate with pain symptomatology in UK BioBank data. In 1000 genomes data, these variants are absent in Europeans but common in Latin Americans. Analysing high-density genotype data from 7594 Latin Americans, we characterized Neanderthal introgression in SCN9A. We find that tracts of introgression occur on a Native American genomic background, have an average length of ~123 kb and overlap the M932L, V991L, and D1908G coding positions. Furthermore, we measured experimentally six pain thresholds in 1623 healthy Colombians. We found that Neanderthal ancestry in SCN9A is significantly associated with a lower mechanical pain threshold after sensitization with mustard oil and evidence of additivity of effects across Nav1.7 variants. Our findings support the reported association of Neanderthal Nav1.7 variants with clinical pain, define a specific sensory modality affected by archaic introgression in SCN9A and are consistent with independent effects of the Neanderthal variants on Nav1.7 function.

Automatic landmarking identifies new loci associated with face morphology and implicates Neanderthal introgression in human nasal shape.

We report a genome-wide association study of facial features in >6000 Latin Americans based on automatic landmarking of 2D portraits and testing for association with inter-landmark distances. We detected significant associations (P-value <5 × 10-8) at 42 genome regions, nine of which have been previously reported. In follow-up analyses, 26 of the 33 novel regions replicate in East Asians, Europeans, or Africans, and one mouse homologous region influences craniofacial morphology in mice. The novel region in 1q32.3 shows introgression from Neanderthals and we find that the introgressed tract increases nasal height (consistent with the differentiation between Neanderthals and modern humans). Novel regions include candidate genes and genome regulatory elements previously implicated in craniofacial development, and show preferential transcription in cranial neural crest cells. The automated approach used here should simplify the collection of large study samples from across the world, facilitating a cosmopolitan characterization of the genetics of facial features.

Effective detection of abnormal gait patterns in Parkinson's disease patients using kinematics, nonlinear, and stability gait features.

BACKGROUND AND OBJECTIVES: Parkinson's disease (PD) is a neurodegenerative disease that produces movement disorders and it is the second most common neurodegenerative disease after Alzheimer's. Among other symptoms, PD affects gait patterns and produces bradykinesia, abnormal changes in posture, and shortened strides. In this study we present a comprehensive analysis of three different feature sets to model those abnormal gait patterns. The proposed approach is evaluated upon three groups of subjects: PD patients, young healthy controls (YHC), and elderly healthy controls (EHC). METHODS: Three feature sets are created: (1) kinematic measures including those that allow modeling time, distance and velocity of the strides, (2) nonlinear dynamics including different measures extracted from embedded attractors resulting from the time-series of the gait signals, and (3) different stability measures extracted in the time and frequency-domains. Support Vector Machine, Random Forest and XGBoost classifiers are trained to automatically discriminate between PD patients and healthy subjects. RESULTS: Among the considered feature sets, three individual measures emerge as the ones that yield accurate detection of PD and could potentially be used in clinical practice. Accuracies of up to 87.0% and 90.0% are found for the classification between PD vs. YHC and PD vs. EHC, respectively, considering individual measures. CONCLUSIONS: This study contributes to a better understanding of abnormal gait patterns observed in PD patients. Particularly the introduced approach shows good results that could be potentially used in clinical practice as a tool to support the diagnosis and follow-up of the patients.