Miracle-dz/UniFAR-FTUs huggingface dataset:
A vertebrate adaptive radiation is assembled from an ancient and disjunct spatiotemporal landscape

Significance Most biodiversity evolved in rapid bursts of new species, adaptations, and ecological niches. However, this process of adaptive radiation is poorly understood. We used large-scale genomic sequencing across the entire Caribbean range of pupfishes to understand why radiation in this group is restricted to a single Bahamian island. We found that twofold higher gene flow to this island brought in new combinations of ancient adaptive mutations needed for colonizing novel ecological niches of scale-eating and snail-eating. Adaptation occurred in stages: first selection on feeding behavior, then selection for trophic morphology, and finally refinement through gene coding change. We demonstrate that young, localized radiations can emerge from a vast pool of adaptive genetic variation spread across time and space. To investigate the origins and stages of vertebrate adaptive radiation, we reconstructed the spatial and temporal histories of adaptive alleles underlying major phenotypic axes of diversification from the genomes of 202 Caribbean pupfishes. On a single Bahamian island, ancient standing variation from disjunct geographic sources was reassembled into new combinations under strong directional selection for adaptation to the novel trophic niches of scale-eating and molluscivory. We found evidence for two longstanding hypotheses of adaptive radiation: hybrid swarm origins and temporal stages of adaptation. Using a combination of population genomics, transcriptomics, and genome-wide association mapping, we demonstrate that this microendemic adaptive radiation of novel trophic specialists on San Salvador Island, Bahamas experienced twice as much adaptive introgression as generalist populations on neighboring islands and that adaptive divergence occurred in stages. First, standing regulatory variation in genes associated with feeding behavior (prlh, cfap20, and rmi1) were swept to fixation by selection, then standing regulatory variation in genes associated with craniofacial and muscular development (itga5, ext1, cyp26b1, and galr2) and finally the only de novo nonsynonymous substitution in an osteogenic transcription factor and oncogene (twist1) swept to fixation most recently. Our results demonstrate how ancient alleles maintained in distinct environmental refugia can be assembled into new adaptive combinations and provide a framework for reconstructing the spatiotemporal landscape of adaptation and speciation.
Preferentially Expressed Antigen in Melanoma Immunostaining in a Series of Melanocytic Neoplasms

Abstract: In their 2018 article, Lezcano et al [AJSP 2018(11):1456] show that diffuse tumor cell nuclear reactivity for Preferentially expressed Antigen in Melanoma (PRAME) is a feature of melanoma and that benign and atypical melanocytic tumors are PRAME negative or show only focal positivity for PRAME. We report our observations of PRAME staining in 253 melanocytic tumors. Tumors were classified by hematoxylin and eosin sections. The nuclear PRAME staining of neoplastic melanocytes in each case was categorized as absent, focally present, or diffusely present. The results were compared with those of Lezcano et al 105 of 134 (78%) melanocytic nevi were completely PRAME negative. Of the 29 PRAME-positive benign lesions, 28 exhibited focal but not diffuse positivity, including atypical (n = 11) and dysplastic nevi (n = 11). One of 11 Spitz nevi showed diffuse positivity (9%). Thirty-nine of 51 (76%) invasive melanomas, 41 of 50 (82%) melanoma in situ, and 15 of 18 (83%) metastatic melanomas were diffusely PRAME positive. Excluding desmoplastic melanomas, 39 of 49 (80%) primary melanomas were diffusely PRAME positive. Our findings of PRAME staining in melanocytic neoplasia are in general agreement with those of Lezcano et al. Diffuse PRAME reactivity in neoplastic melanocytes is a feature of malignancy and was only otherwise seen in 1 Spitz nevus. Caution is advised in interpretation of PRAME reactivity in melanocytic tumors of uncertain classification because melanoma arising in association with nevus and some atypical melanocytic tumors may show focal or incomplete PRAME staining. Routine histopathological findings, clinical information, PRAME staining, and judicious application of molecular studies are steps leading to accurate classification of melanocytic neoplasia.
Coastal resilience surges as living shorelines reduce lateral erosion of salt marshes

A growing suite of research has demonstrated that nature‐based shoreline stabilization methods can increase resilience of coastal ecosystems by improving their capacity to return to predisturbance states. Previous work suggests that during hurricanes, living shorelines promote vertical accretion and experience less damage than traditional shoreline stabilization alternatives. Nevertheless, there is limited research looking at the impacts of major storm events on living shorelines and most studies have investigated a small number of sites. This study used in situ real‐time kinematic (RTK)‐GPS surveys to quantify the resilience (via the lateral change in shore position) of 17 living shoreline sites before and after a Category 1 hurricane event (Hurricane Florence, 2018). By doing so, this study seeks to understand the capacity of living shorelines (marsh with seaward breakwater or sill) to provide storm protection as compared to unaltered natural fringing salt marshes. After Hurricane Florence, living shorelines on average experienced significantly less lateral erosion compared to unprotected control segments (shoreline change rates of 0.015 and −0.31 m year−1, respectively). This study also explores how environmental siting variables (i.e., scarp presence, fetch, and bottom sediment) and sill design variables (i.e., sill material, width, and height) influence short‐ and long‐term erosion. living shorelines were found to reduce erosion of fringing marsh edge among projects with a range of installation ages, structural materials, sill widths, and sill heights, and they were able to provide protection from erosion across a range of fetch, scarp, and bottom sediment conditions. Living shoreline siting and sill design may be suitable for broader environmental conditions than previously known. This study shows that living shorelines can increase resilience by reducing erosion of fringing salt marshes, promoting lateral building up of shoreline zones during short‐term disturbance events, and from their long‐term presence. Integr Environ Assess Manag 2022;18:82–98. © 2021 SETAC
Can breast cancer be stopped? Modifiable risk factors of breast cancer among women with a prior benign or premalignant lesion

Physical inactivity, high postmenopausal body mass index, alcohol consumption and use of menopausal hormone therapy are established risk factors for breast cancer. Less is known about whether these factors influence the risk of progression of benign and premalignant breast lesions to invasive breast cancer. This registry‐based cohort study was based on women with a precancerous lesion who were followed for breast cancer. The cohort consisted of 11 270 women with a benign lesion, 972 women with hyperplasia with atypia and 2379 women with carcinoma in situ diagnosed and treated after participation in BreastScreen Norway, 2006‐2016. Information on breast cancer risk factors was collected by a questionnaire administered with the invitation letter. Cox regression analysis was used to estimate the association between breast cancer and physical activity, body mass index, alcohol consumption, tobacco smoking and menopausal hormone therapy, adjusted for age. During follow‐up, 274 women with a benign lesion, 34 women with hyperplasia with atypia and 118 women with carcinoma in situ were diagnosed with invasive breast cancer. We observed an increased risk of breast cancer associated with use of menopausal hormone therapy for women with a benign or premalignant lesion. Alcohol consumption and tobacco smoking showed suggestive increased risk of breast cancer among women with a benign lesion. We were only to a limited degree able to identify associations between modifiable risk factors of breast cancer and the disease among women with a precancerous lesion, and a larger study is needed to confirm or refute associations.
Tetracyclines and photosensitive skin reactions: a narrative review.

Tetracyclines are a group of broad-spectrum antibiotics largely employed in infectious, dermatological and surgical fields. Some adverse events may occur during treatment, including photosensitivity reactions, which are divided in phototoxic or photoallergic. We performed a systematic search on Pubmed, Cochrane and Embase from database inception to 9 Aug 2020 aim to summarize all available papers on photosensitive reactions related to Tetracyclines in all clinical settings where they are used on human being. On the basis of our inclusion criteria, we selected only randomized controlled trials, open comparative trials and prospective cohort studies performed on both volunteers and patients, moreover we included a pharmacovigilance register. Thirty-eight articles met inclusion criteria, describing photo-sensitive effects due to Doxycycline, Minocycline, Tetracycline, Lymecycline, Sarecycline, Demethylchlortetracycline, Chlortetracycline and Metacycline, across 6 diagnoses (acne, Lyme disease, Gulf Veteran Illness, adbominal aortic aneurysms, traveler's diarrhea and pterygium) and several volunteers who were deliberately exposed to natural or artificial light sources. Not all drugs belonging to Tetracyclines class are available to date, moreover the studies included lacked a homogeneous design and most of them involved a scarce number of patients, including reactions induced in volunteers during photo-testing. Available data on incidence, severity and clinical relevance of Tetracyclines-related photo-sensitive reactions are scarce, heterogeneous and weak. What we can extrapolate is that some Tetracyclines are more often related to phototoxic skin reactions than others and some of those seem to have a very low risk of phototoxicity. This article is protected by copyright. All rights reserved.
Recovery of turpentine from the production of medium-density fibreboard

The rate of production of oil and turpentine in the effluent from the plug screw feeder at the exit from the presteamer of a fibreboard pilot plant was determined after a steady state of operation had been reached. From these data, the recovery of turpentine from the plug screw feeder effluent, as a proportion of that available in the wood chips, was shown to be 27%. Turpentine levels in wood of Pinus radiata D. Don were determined and compared with previous data, along with causes of variations in these data. The presteamer plug screw feeder effluent from a medium-density fibreboard production line appears to be a useful source of turpentine.
Accidental Deaths Involving Trees

Abstract We examined all deaths in Connecticut involving tree mishaps (struck by a tree/tree limb, injuries associated with tree removal operations). Records of the Connecticut Office of the Chief Medical Examiner including autopsy, toxicology, and investigators' reports of deaths from 2004 to 2019 were reviewed. All underwent autopsy examination. There were 64 fatalities, with ages ranging from 4 to 90 years (mean, 50 years). The causes of death involved the following: 56 blunt injury (primary site: 25 head, 13 multiple locations, 11 torso, and 7 neck), 5 traumatic asphyxia, 2 electrocution, and 1 chainsaw injury. Deaths were classified into 3 groups: 21 nonprofessional woodcutters, 19 professional woodcutters, and 24 tree failures. Among all woodcutters (100% men), impact by a falling tree/limb (78%) was the most common fatal event, and the most common lethal injury site was the head (45%). For tree failures, 58% involved storm/high-wind events, whereas 42% were spontaneous. Of the tree failure events, 58% involved motor vehicles, with most (86%) occurring while driving. Ethanol was detected in 6 decedents with blood concentrations ranging from 0.02 to 0.19 gm%, of which 4 were nonprofessional and 2 were professional woodcutters. There were some seasonal differences among the 3 groups. Overall, fatalities of nonprofessional woodcutters, compared with professionals, were more likely to involve an older man (58 vs 40 years), working alone (67% vs 11%), and under the influence of ethanol (19% vs 11%) in late summer-autumn who dies of blunt head trauma from a falling tree or tree limb. Aggressive tree control management along highways has been used to attempt to decrease storm-related fatalities.
Association of GSTM1 and GSTT1 gene polymorphisms with COVID‐19 susceptibility and its outcome

Coronavirus disease 2019 (COVID‐19) caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection has become a global health issue and develops into a broad range of illnesses from asymptomatic to fatal respiratory diseases. SARS‐CoV‐2 infection is associated with oxidative stress that triggers cytokine production, inflammation, and other pathophysiological processes. Glutathione‐S‐transferase (GST) is an important enzyme that catalyzes the conjugation of glutathione (GSH) with electrophiles to protect the cell from oxidative damage and participates in the antioxidant defense mechanism in the lungs. Thus, in this study, we investigated the role of GSTM1 and GSTT1 gene polymorphism with COVID‐19 susceptibility, as well as its outcome. The study included 269 RT‐PCR confirmed COVID‐19 patients with mild (n = 149) and severe (n = 120) conditions. All subjects were genotyped for GSTM1 and GSTT1 by multiplex polymerase chain reaction (mPCR) followed by statistical analysis. The frequency of GSTM1−/−, GSTT1−/− and GSTM1−/−/GSTT1−/− was higher in severe COVID‐19 patients as compared to mild patients but we did not observe a significant association. In the Cox hazard model, death was significantly 2.28‐fold higher in patients with the GSTT1−/− genotype (p = 0.047). In combination, patients having GSTM1+/+ and GSTT1−/− genotypes showed a poor survival rate (p = 0.02). Our results suggested that COVID‐19 patients with the GSTT1−/− genotype showed higher mortality.
Access to sexual and reproductive health care among young adult sex workers in Toronto, Ontario: a mixed-methods study

Background: Young adult sex workers may benefit from sexual and reproductive health care services; however, little research has examined their access experiences. This study aimed to assess barriers to and facilitators of access to sexual and reproductive health care among young adult sex workers, and identify practices suggested by participants to improve services. Methods: This was a community-based mixed-methods study of adults aged 18–29 years who were currently or had previously been engaged in sex work, conducted in Toronto in 2017–2018. The study was guided by a Youth Advisory Committee of 4 youth with lived experience of sex work. Participants completed an online survey, or participated in a focus group or a one-on-one interview; all 3 modalities included parallel questions about barriers to and facilitators of access to sexual and reproductive health care. We summarized quantitative data using descriptive statistics and identified qualitative themes using thematic analysis, followed by triangulation of the 2 strands. Results: There were 54 survey respondents (response rate 48%) and 17 participants in the qualitative phase (14 in focus groups and 3 in interviews), for a total sample size of 71. Survey respondents reported suboptimal access to sexual and reproductive health care, with 8 (15%) reporting no regular source of care, and only 6 (11%) reporting that they disclose their sex work experience to providers. Actual or expected stigma regarding sex work on the part of providers was the dominant barrier to care, whereas nonjudgmental providers, particularly those who themselves have sex work experience, was a key facilitator. Participants suggested 7 practices to improve access to sexual and reproductive health care. Interpretation: Young adult sex workers face many barriers to accessing sexual and reproductive health care. Including people with sex work experience in the development of solutions will maximize the capacity to address the needs of this underserved population.
Swelling and elasticity of the cell walls of pulp fibres

Une augmentation du gonflement resulte de la pression osmotique generee dans la paroi de la cellule lorsque les contre-ions des groupes acides font l'objet d'echanges entre la forme hydrogene et la forme sodium. Ce phenomene de tension-extension a ete utilise pour obtenir un module d'elasticite de la paroi de la cellule gonflee d'eau. Il a ete trouve que le module des pâtes kraft jamais sechees diminuait de 10 a 2 MPa pendant que le rendement etait reduit de 100% a 65%, par la suite le module etait presque constant.
Cancer stem cell marker DCLK1 reprograms small extracellular vesicles toward migratory phenotype in gastric cancer cells

Doublecortin‐like kinase 1 (DCLK1) is a putative cancer stem cell marker, a promising diagnostic and prognostic maker for malignant tumors and a proposed driver gene for gastric cancer (GC). DCLK1 overexpression in a majority of solid cancers correlates with lymph node metastases, advanced disease and overall poor‐prognosis. In cancer cells, DCLK1 expression has been shown to promote epithelial‐to‐mesenchymal transition (EMT), driving disruption of cell‐cell adhesion, cell migration and invasion. Here, we report that DCLK1 influences small extracellular vesicle (sEV/exosome) biogenesis in a kinase‐dependent manner. sEVs isolated from DCLK1 overexpressing human GC cell line MKN1 (MKN1OE‐sEVs), promote the migration of parental (non‐transfected) MKN1 cells (MKN1PAR). Quantitative proteome analysis of MKN1OE‐sEVs revealed enrichment in migratory and adhesion regulators (STRAP, CORO1B, BCAM, COL3A, CCN1) in comparison to MKN1PAR‐sEVs. Moreover, using DCLK1‐IN‐1, a specific small molecule inhibitor of DCLK1, we reversed the increase in sEV size and concentration in contrast to other EV subtypes, as well as kinase‐dependent cargo selection of proteins involved in EV biogenesis (KTN1, CHMP1A, MYO1G) and migration and adhesion processes (STRAP, CCN1). Our findings highlight a specific role of DCLK1‐kinase dependent cargo selection for sEVs and shed new light on its role as a regulator of signaling in gastric tumorigenesis.
Transcranial magnetic stimulation alters multivoxel patterns in the absence of overall activity changes

Transcranial magnetic stimulation (TMS) has become one of the major tools for establishing the causal role of specific brain regions in perceptual, motor, and cognitive processes. Nevertheless, a persistent limitation of the technique is the lack of clarity regarding its precise effects on neural activity. Here, we examined the effects of TMS intensity and frequency on concurrently recorded blood‐oxygen‐level‐dependent (BOLD) signals at the site of stimulation. In two experiments, we delivered TMS to the dorsolateral prefrontal cortex in human subjects of both sexes. In Experiment 1, we delivered a series of pulses at high (100% of motor threshold) or low (50% of motor threshold) intensity, whereas, in Experiment 2, we always used high intensity but delivered stimulation at four different frequencies (5, 8.33, 12.5, and 25 Hz). We found that the TMS intensity and frequency could be reliably decoded using multivariate analysis techniques even though TMS had no effect on the overall BOLD activity at the site of stimulation in either experiment. These results provide important insight into the mechanisms through which TMS influences neural activity.
Elevated fibroblast growth factor‐inducible 14 expression transforms proneural‐like gliomas into more aggressive and lethal brain cancer

High‐grade gliomas (HGGs) are aggressive, treatment‐resistant, and often fatal human brain cancers. The TNF‐like weak inducer of apoptosis (TWEAK)/fibroblast growth factor‐inducible 14 (Fn14) signaling axis is involved in tissue repair after injury and constitutive signaling has been implicated in the pathogenesis of numerous solid cancers. The Fn14 gene is expressed at low levels in the normal, uninjured brain but is highly expressed in primary isocitrate dehydrogenase wild‐type and recurrent HGGs. Fn14 signaling is implicated in numerous aspects of glioma biology including brain invasion and chemotherapy resistance, but whether Fn14 overexpression can directly promote tumor malignancy has not been reported. Here, we used the replication‐competent avian sarcoma‐leukosis virus/tumor virus A system to examine the impact of Fn14 expression on glioma development and pathobiology. We found that the sole addition of Fn14 to an established oncogenic cocktail previously shown to generate proneural‐like gliomas led to the development of highly invasive and lethal brain cancer with striking biological features including extensive pseudopalisading necrosis, constitutive canonical and noncanonical NF‐κB pathway signaling, and high plasminogen activator inhibitor‐1 (PAI‐1) expression. Analyses of HGG patient datasets revealed that high human PAI‐1 gene (SERPINE1) expression correlates with shorter patient survival, and that the SERPINE1 and Fn14 (TNFRSF12A) genes are frequently co‐expressed in bulk tumor tissues, in tumor subregions, and in malignant cells residing in the tumor microenvironment. These findings provide new insights into the potential importance of Fn14 in human HGG pathobiology and designate both the NF‐κB signaling node and PAI‐1 as potential targets for therapeutic intervention.
Identifying Protein Subcellular Locations With Embeddings-Based node2loc

Identifying protein subcellular locations is an important topic in protein function prediction. Interacting proteins may share similar locations. Thus, it is imperative to infer protein subcellular locations by taking protein-protein interactions (PPIs)into account. In this study, we present a network embedding-based method, node2loc, to identify protein subcellular locations. node2loc first learns distributed embeddings of proteins in a protein-protein interaction (PPI)network using node2vec. Then the learned embeddings are further fed into a recurrent neural network (RNN). To resolve the severe class imbalance of different subcellular locations, Synthetic Minority Over-sampling Technique (SMOTE)is applied to artificially synthesize proteins for minority classes. node2loc is evaluated on our constructed human benchmark dataset with 16 subcellular locations and yields a Matthews correlation coefficient (MCC)value of 0.800, which is superior to baseline methods. In addition, node2loc yields a better performance on a Yeast benchmark dataset with 17 locations. The results demonstrate that the learned representations from a PPI network have certain discriminative ability for classifying protein subcellular locations. However, node2loc is a transductive method, it only works for proteins connected in a PPI network, and it needs to be retrained for new proteins. In addition, the PPI network needs be annotated to some extent with location information. node2loc is freely available at https://github.com/xypan1232/node2loc.