Miracle-dz/UniFAR-FTUs huggingface dataset:
Mixed micropapillary patterns found in malignant pleural mesothelioma with possibly worsened prognostic implication

A 60-year-old male had dyspnea which was found to be due to right pleural effusion and pleural thickening. Surgical biopsy was performed, leading to a diagnosis of epithelioid mesothelioma. After three courses of chemotherapy, he underwent extrapleural pneumonectomy (Figure 1a). Pathological diagnosis was diffuse malignant epithelioid mesothelioma of the right pleura. Histologically, atypical epithelioid mesothelial cells were arranged in a tubulopapillary structure in most parts of the tumor according to the fifth World Health Organization classification (Figure 1b). Lymph node metastasis was observed in a subcarinal lesion (Figure 1c). A micropapillary pattern was also observed, characterized by the presence of a papillary structure with tufts lacking a central fibrovascular
Utilization of Palliative Care for Patients with COVID-19 and Acute Kidney Injury during a COVID-19 Surge

Visual Abstract Background and objectives AKI is a common complication of coronavirus disease 2019 (COVID-19) and is associated with high mortality. Palliative care, a specialty that supports patients with serious illness, is valuable for these patients but is historically underutilized in AKI. The objectives of this paper are to describe the use of palliative care in patients with AKI and COVID-19 and their subsequent health care utilization. Design, setting, participants, & measurements We conducted a retrospective analysis of New York University Langone Health electronic health data of COVID-19 hospitalizations between March 2, 2020 and August 25, 2020. Regression models were used to examine characteristics associated with receiving a palliative care consult. Results Among patients with COVID-19 (n=4276; 40%), those with AKI (n=1310; 31%) were more likely than those without AKI (n=2966; 69%) to receive palliative care (AKI without KRT: adjusted odds ratio, 1.81; 95% confidence interval, 1.40 to 2.33; P<0.001; AKI with KRT: adjusted odds ratio, 2.45; 95% confidence interval, 1.52 to 3.97; P<0.001), even after controlling for markers of critical illness (admission to intensive care units, mechanical ventilation, or modified sequential organ failure assessment score); however, consults came significantly later (10 days from admission versus 5 days; P<0.001). Similarly, 66% of patients initiated on KRT received palliative care versus 37% (P<0.001) of those with AKI not receiving KRT, and timing was also later (12 days from admission versus 9 days; P=0.002). Despite greater use of palliative care, patients with AKI had a significantly longer length of stay, more intensive care unit admissions, and more use of mechanical ventilation. Those with AKI did have a higher frequency of discharges to inpatient hospice (6% versus 3%) and change in code status (34% versus 7%) than those without AKI. Conclusions Palliative care was utilized more frequently for patients with AKI and COVID-19 than historically reported in AKI. Despite high mortality, consultation occurred late in the hospital course and was not associated with reduced initiation of life-sustaining interventions. Podcast This article contains a podcast at https://www.asn-online.org/media/podcast/CJASN/2022_02_24_CJN11030821. mp3
Characterizing mobile element insertions in 5675 genomes

Abstract Mobile element insertions (MEIs) are a major class of structural variants (SVs) and have been linked to many human genetic disorders, including hemophilia, neurofibromatosis, and various cancers. However, human MEI resources from large-scale genome sequencing are still lacking compared to those for SNPs and SVs. Here, we report a comprehensive map of 36 699 non-reference MEIs constructed from 5675 genomes, comprising 2998 Chinese samples (∼26.2×, NyuWa) and 2677 samples from the 1000 Genomes Project (∼7.4×, 1KGP). We discovered that LINE-1 insertions were highly enriched in centromere regions, implying the role of chromosome context in retroelement insertion. After functional annotation, we estimated that MEIs are responsible for about 9.3% of all protein-truncating events per genome. Finally, we built a companion database named HMEID for public use. This resource represents the latest and largest genomewide study on MEIs and will have broad utility for exploration of human MEI findings.
MulViMotion: Shape-Aware 3D Myocardial Motion Tracking From Multi-View Cardiac MRI

Recovering the 3D motion of the heart from cine cardiac magnetic resonance (CMR) imaging enables the assessment of regional myocardial function and is important for understanding and analyzing cardiovascular disease. However, 3D cardiac motion estimation is challenging because the acquired cine CMR images are usually 2D slices which limit the accurate estimation of through-plane motion. To address this problem, we propose a novel multi-view motion estimation network (MulViMotion), which integrates 2D cine CMR images acquired in short-axis and long-axis planes to learn a consistent 3D motion field of the heart. In the proposed method, a hybrid 2D/3D network is built to generate dense 3D motion fields by learning fused representations from multi-view images. To ensure that the motion estimation is consistent in 3D, a shape regularization module is introduced during training, where shape information from multi-view images is exploited to provide weak supervision to 3D motion estimation. We extensively evaluate the proposed method on 2D cine CMR images from 580 subjects of the UK Biobank study for 3D motion tracking of the left ventricular myocardium. Experimental results show that the proposed method quantitatively and qualitatively outperforms competing methods.
Critical Role of Notch‐1 in Mechanistic Target of Rapamycin Hyperactivity and Vascular Inflammation in Patients With Takayasu Arteritis

Takayasu arteritis (TA) is a major type of large vessel vasculitis characterized by progressive inflammation in vascular layers. In our recent study we identified a central role of mechanistic target of rapamycin (mTOR) hyperactivity in proinflammatory T cell differentiation in TA. This study was undertaken to explore potential mechanisms underpinning T cell–intrinsic mTOR hyperactivity and vascular inflammation in TA, with a focus on Notch‐1.
Mask‐induced skin changes during COVID pandemic: A cross‐sectional web‐based survey among physicians in a tertiary care teaching hospital

The COVID pandemic has affected the human race both physically and mentally. Mask use remains the standard way of preventing the spread of this virus. The continuous mask use has led to the emergence of various dermatoses like acne, pigmentation, and seborrhea in mask contact areas. The present survey has been undertaken to describe the various dermatoses encountered in the medical fraternity especially doctors, who are frequently exposed to prolonged mask use.
Effect of platelet-rich plasma injections for chronic nonspecific low back pain

Abstract Background: Patient with chronic nonspecific low back pain is weakened ligament, and prolotherapy is the effective treatment but their use remains controversial. These ligaments can be strengthened by platelet-rich plasma injection. We hypothesized that the effectiveness of platelet-rich plasma injection and prolotherapy may decrease pain and improved disability of patient with chronic low back pain Methods: This study was a prospective, double-blind, randomized controlled trial and was conducted for 3 years for patient enroll and follow-up. Thirty-four patients with chronic nonspecific low back pain (duration of at least 3 months) refectory to conventional management were randomized to platelet-rich plasma injection and lidocaine injection. Patients were treated with weekly platelet-rich plasma or lidocaine injections at the lumbopelvic ligaments for 2 weeks and then weekly prolotherapy with 15% glucose for 2 weeks and followed up 6 months. Visual analog scale, Oswestry Disability Index, and Roland–Morris Disability Questionnaire were evaluated at initial, 4 weeks, 3 months, and 6 months. Four patients did not complete this trial. Three were in the platelet-rich plasma injection and 1 was in the lidocaine injection. Results: The intensity of pain was significantly decreased in platelet-rich plasma injections at 6 months as compared lidocaine injections; between-group differences were 0.9 (95% confidence interval 0.10–1.75 [P = .027]). All participants were significantly decreased pain and disability index at 4 weeks, 3 months, and 6 months but there were no significant differences between groups except for visual analog scale at 6 months. The baseline parameters were no significant differences in both groups. Conclusions: In chronic nonspecific low back pain, the platelet-rich plasma injection in combination with prolotherapy is an effective intervention and either lidocaine or platelet-rich plasma injection significantly reduced disability. And injection at the lumbopelvic ligaments using the platelet-rich plasma and prolotherapy is also an effective treatment for pain.
Genomics and ecological modelling clarify species integrity in a confusing group of butterflies

Recent advances in both genomics and ecological modelling present new, multidisciplinary opportunities for resolving species boundaries and understanding the mechanisms that maintain their integrity in regions of contact. Here, we use a combination of high‐throughput DNA sequencing and ecological niche modelling to resolve species boundaries and niche divergence within the Speyeria atlantis‐hesperis (Lepidoptera: Nymphalidae) complex, a confusing group of North American butterflies. This complex is notorious for its muddled species delimitations, morphological ambiguity, and extensive mitonuclear discordance. Our admixture and multispecies coalescent‐based analyses of single nucleotide polymorphisms identified substantial divergences between S. atlantis and S. hesperis in areas of contact, as well as between distinct northern and southern lineages within S. hesperis. Our results also provide evidence of past introgression relating to another species, S. zerene, which previous work has shown to be more distantly related to the S. atlantis‐hesperis complex. We then used ecological models to predict habitat suitability for each of the three recovered genomic lineages in the S. atlantis‐hesperis complex and assessed their pairwise niche divergence. These analyses resolved that these three lineages are significantly diverged in their respective niches and are not separated by discontinuities in suitable habitat that might present barriers to gene flow. We therefore infer that ecologically‐mediated selection resulting in disparate habitat associations is a principal mechanism reinforcing their genomic integrity. Overall, our results unambiguously support significant evolutionary and ecological divergence between the northern and southern lineages of S. hesperis, sufficient to recognize the southern evolutionary lineage as a distinct species, called S. nausicaa based on taxonomic priority.
Joint modeling of survival and backwards recurrence outcomes: an analysis of factors associated with fertility treatment

The increase in methods focused on various types of survival outcomes has allowed practitioners to analyze data that are difficult or expensive to prospectively observe. Still, there are populations that are challenging to study. For example, obtaining a representative sample of couples attempting to become pregnant is difficult due to the dynamic nature of the population. This has led to an increase in the use of cross-sectional designs yielding backwards recurrent survival outcomes. In this paper, we consider the analysis of a survival outcome where subjects are observed if they are at-risk for a separate dependent survival outcome. The motivation for this problem is to determine which factors are associated with time-to-fertility-treatment (TTFT) among women currently attempting pregnancy in a cross-sectional sample. We propose appending a marginal accelerated failure time (AFT) model on TTFT with a conditional model on time-to-pregnancy (TTP) given TTFT to account for their dependence and avoid biases. We address challenges that arise due to the censoring of TTFT and the resulting increased computational complexity. The performance is validated via comprehensive simulation studies. We apply our approach to data from the National Survey of Family Growth to estimate the association insurance type has on TTFT, and estimate the impact of fertility treatment on TTP.
Cross-neutralizing activity against Omicron could be obtained in SARS-CoV-2 convalescent patients who received two doses of mRNA vaccination

The SARS-CoV-2 variant Omicron is now under investigation. We evaluated cross-neutralizing activity against Omicron in COVID-19 convalescent patients who had received two doses of an mRNA vaccination. Surprisingly and interestingly, after the second vaccination, the subject neutralizing antibody titers including that against Omicron all became seropositive, and significant fold-increases were seen regardless of the subject disease severity. Our findings thus demonstrate that at least two doses of mRNA vaccination to SARS-CoV-2 convalescent patients can induce cross-neutralizing activity against Omicron.
On the real possibility of “super” hydrogen intercalation into graphite nanofibers

Abstract In this work, data of Rodriguez-Baker et al. and some others were analyzed and interpreted in relation to the long-term, i.e., about 25 years, problem of “super” storage (intercalation) of “reversible” (at 300 K) hydrogen (∼38 ± 10 wt.%, i.e., the atomic ratio (H/C) ≈ 7 ± 3)), along with “irreversible” hydrogen (∼11 ± 3 wt.% ((H/C) ≈ 1.5 ± 0.4)) into graphite nanofibers (GNFs). For a more in-depth study of the a problem, an effective methodology of processing and analyzing the thermal desorption spectra of hydrogen and the related thermogravimetric data was modified and used. It was shown that the above noted extraordinary data on the “super” storage of hydrogen in GNFs are neither an error nor a hoax, as most researchers believed. The necessary conditions were determined to reproduce this extraordinary data. It has also been shown that the Rodriguez-Baker team can reproduce “normal,” i.e., typical results obtained by other researchers on hydrogen storage in GNFs.
Acceptance (for Some): In-Group Stigmatization within the LGBTQ+ Community

ABSTRACT Social stigma can have negative mental and physical health repercussions for those who experience it. The LGBTQ+ community is one group demonstrative of this finding. Much of the research on stigmatization and the LGBTQ+ community focuses on stigmatization toward this group from broader society. Social psychology research has demonstrated the prevalence of in-group stigmatization within the community. For this study, 22 participants who identify as members of the LGBTQ+ community were interviewed. Findings illustrate both enacted and perceived stigmatization that participants experience within the community related to behavioral, bisexual, and, Trans stigmatization, and demonstrate remaining work regarding how communities communicate about themselves, among their members, and the complex relationships that constitute them.
Investigating the Influence of Spatiotemporal Gait Characteristics on Shoe Wear Rate

OCCUPATIONAL APPLICATIONS We investigated the association between shoe wear rate and several metrics describing an individual’s spatiotemporal gait characteristics (cadence, step length, and preferred walking speed). No associations were found, indicating that alternative metrics should be investigated to predict the individualized rate at which workers wear down shoe tread. TECHNICAL ABSTRACT Background Shoe wear has been associated with increased slips and falls in the workplace. People wear down shoe tread at different rates; therefore, individualized shoe replacement timelines could improve resource targeting for organizations that use time as a basis for shoe replacement. Previous work has found that the shoe-floor kinetics, such as the friction requirements of walking, correlate with shoe wear rate. The use of easily measured metrics such as cadence, step length, or preferred walking speed to predict wear has not yet been investigated despite their relationship with friction requirements. Purpose This study seeks to determine the association between shoe wear rate and gait spatiotemporal characteristics. Methods Thirteen participants completed a longitudinal shoe wear study that consisted of a gait assessment followed by prolonged shoe wear in two pairs of slip-resistant shoes. The gait assessment was comprised of dry level-ground walking trials; kinematic and kinetic data were collected through optical motion capture and force plates. The participants’ mean cadence, step length, and preferred walking speed were calculated. The participants then wore their shoes at work; the shoe wear rate was determined by measuring the periodic volumetric tread loss during this wear-at-work portion of the study. Results Three linear regression models found no significant association between the chosen gait metrics and the shoe wear rate. Conclusions The lack of an association between the spatiotemporal gait characteristics and shoe wear rate indicates that these factors may not explain the differences in wear rate between participants. This negative finding suggests that other measures such as the required coefficient of friction are better for individualizing footwear replacement guidelines.
Acute Pain, Neck Extensor Endurance, and Kinematic Changes Resulting from Sustained Neck Flexion during Smartphone Use

OCCUPATIONAL APPLICATIONS The National Occupational Research Agenda for Musculoskeletal Health in the United States identified that with the changing nature of the traditional office environment, mobile devices are now frequently used for longer durations, warranting research on the impacts of mobile computing on musculoskeletal health. A recent study of office workers showed that those with “smartphone overuse” were six times more likely to report neck pain. Working in pain may also result in withdrawal and less proactive extra-role behaviors at work (such as making recommendations at work and willing to help colleagues). We found that 30-minutes of mobile device use resulted in pain reporting in the neck and upper back when the device was used with neck flexion. This musculoskeletal pain could lead to acute concerns during the workday and long-term problems over time. TECHNICAL ABSTRACT Background: People commonly use their phones with a flexed neck. Such use is concerning because epidemiological studies have demonstrated a direct relationship between prolonged neck flexion and neck pain, and mobile device use is associated with neck pain development. Purpose: Determine the repeatability of neck and upper back pain symptom development among young adults (ages 18-29) during 30-minutes of smartphone use with a flexed neck and compare neck flexion range of motion, neck extensor endurance, and posture among participants who develop neck and/or upper back pain during the task compared to those who do not develop pain. Methods: Participants (n = 40) came to the lab on two days separated by one week. They completed a 30-minute smartphone use trial with the device in their lap to elicit neck flexion. Participants were separated into pain groups based on a 10-mm change in their self-reported pain reports on a 100-mm visual analog scale (VAS). Pre-post tests and kinematics during the 30-minute trial were compared between individuals who did and did not consistently develop pain. Results: Seventy-five percent of the total study sample were categorized in the same pain category in the two trials using VAS score change. Of those participants, 66% developed neck pain during 30-minutes of smartphone use with sustained neck flexion. The most common symptom description was “aching. ” Pain developers had a lower cervical extensor test duration after 30-minutes of smartphone use than before smartphone use. Conclusions: Two-thirds of young adults developed consistent neck and/or upper back musculoskeletal pain that they described as aching after 30-minutes of smartphone use with sustained neck flexion. Since the nontraditional work environment may result in the use of these devices, employers will need to be aware of the potential consequences of sustained postures during mobile device use and develop methods to mitigate pain.
Identification of Signature Genes and Characterizations of Tumor Immune Microenvironment and Tumor Purity in Lung Adenocarcinoma Based on Machine Learning

The implication of the Estimation of Stromal and Immune cells in Malignant tumor tissues using expression data (ESTIMATE) method to determine the tumor microenvironment (TME) and tumor immune score including tumor purity represents an efficient method to identify and assess biomarkers for immunotherapy response in precision medicine. In this study we utilized a machine learning algorithm to analyze the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus database (GEO) lung adenocarcinoma (LUAD) transcriptome data to evaluate the association between TME and tumor purity. Furthermore, we investigated whether fewer TME components or a few dominant genes can infer tumor purity. The results indicated that the 29 immune infiltrating components determined by the ssGSEA method could screen the 5 TME components [chemokine C-C-Motif receptor (CCR), T-helper-cells, Check-point, Treg, and tumor-infiltrating lymphocytes (TIL)] that significantly contributed the most to tumor purity prediction through regression tree and random forest regression methods. The findings revealed that higher activity of these five immune infiltrating components significantly lowered the tumor purity. Moreover, 5 TME components contributed significantly to the improvement of Mean Square Error (MES); therefore, we selected these five sets' genes and analyzed survival data to establish a prognostic model. We screened out 11 prognostic-related genes and constructed a risk model comprising 11 genes with good predictive value for patients' prognosis. Furthermore, we obtained four genes (GIMAP6, CD80, IL16, and CCR2) that had predictive advantages for tumor purity using random forest classification and random forest regression. The comprehensive score of genes for tumor purity prediction (CSGTPP) was obtained by least absolute shrinkage and selection operator (LASSO) regression indicated that four genes could be successfully used to classify high and low CSGTPP samples and that tumor purity was negatively correlated with CSGTPP. Survival analysis revealed that the higher the CSGTPP, the better the prognosis of patients. The association between a cluster of differentiation 274 (CD274) and CSGTPP revealed a higher expression of CD274 in the high CSGTPP group. Collectively, we speculated that CSGTPP could serve as a predictor of the response to immunotherapy and a promising indicator of immunotherapy effect.