Miracle-dz/UniFAR-FTUs huggingface dataset:
Rhizobium induces DNA damage in Caenorhabditis elegans intestinal cells

Significance An incredible diversity of microbial species inhabit the Earth. Many new interactions of bacteria with animals are only beginning to surface. We show that feeding a worm, Caenorhabditis elegans, with Rhizobium bacteria causes failed nuclear divisions in intestinal cells. C. elegans mutations compromising DNA damage repair pathways and exogenous reactive oxygen species cause similar failure in intestinal nuclear divisions, suggesting that Rhizobium may produce reactive oxygen species. In accordance, free radical scavenger chemicals suppress the response to Rhizobium. We propose that Rhizobium induces reactive oxygen species in its encounter with C. elegans. Our findings provide an insight into the interactions between microbes and animal cells. In their natural habitat of rotting fruit, the nematode Caenorhabditis elegans feeds on the complex bacterial communities that thrive in this rich growth medium. Hundreds of diverse bacterial strains cultured from such rotting fruit allow C. elegans growth and reproduction when tested individually. In screens for C. elegans responses to single bacterial strains associated with nematodes in fruit, we found that Rhizobium causes a genome instability phenotype; we observed abnormally long or fragmented intestinal nuclei due to aberrant nuclear division, or defective karyokinesis. The karyokinesis defects were restricted to intestinal cells and required close proximity between bacteria and the worm. A genetic screen for C. elegans mutations that cause the same intestinal karyokinesis defect followed by genome sequencing of the isolated mutant strains identified mutations that disrupt DNA damage repair pathways, suggesting that Rhizobium may cause DNA damage in C. elegans intestinal cells. We hypothesized that such DNA damage is caused by reactive oxygen species produced by Rhizobium and found that hydrogen peroxide added to benign Escherichia coli can cause the same intestinal karyokinesis defects in WT C. elegans. Supporting this model, free radical scavengers suppressed the Rhizobium-induced C. elegans DNA damage. Thus, Rhizobium may signal to eukaryotic hosts via reactive oxygen species, and the host may respond with DNA damage repair pathways.
“We write as little as we have to”: charting practices and documenting disclosure in response to HIV criminalization in Canada

ABSTRACT The criminalization of HIV nondisclosure is reshaping the landscape of support and care for people living with HIV/AIDS (PLWHA). Focusing on Canada, this article examines how criminalization is reshaping the relationships between frontline AIDS Service Organization (ASO) workers and their HIV-positive service users. Using data gleaned through semi-structured interviews with N = 62 frontline ASO staff members across Canada that were coded using thematic analysis, we describe how ASO workers are rethinking and altering their notetaking practices in light of fears about criminalization and how their charts may be used by legal actors. Specifically, we identified three main themes. First, awareness that their notes can be subpoenaed and used against their clients in criminal proceedings is leading ASO staff to keep less detailed records of their conversations with PLWHA, although there were variations by the type of position held. Participants with professional obligations (doctors, nurses, social workers) reported that they continue to keep more detailed charting records than other frontline ASO staff (peer counselors, educators, etc.). Second, participants acknowledged that criminalization threatens the trust dynamic in the therapeutic relationship and that by taking less detailed notes they risk the quality of care provided. Third, we found that evolving knowledge about risk and responsibility in light of criminalization is impacting the type of counsel ASO workers offer to PLWHA regarding how to document disclosure. The article concludes by reflecting on the challenges associated with navigating the “medico-legal borderland”, as ASO staff balance their commitments to serving PLWHA with the realities created by the harsh climate of criminalization. Greater political attention should be paid to the risks that criminalization poses to frontline HIV support work and efforts to support PLWHA, who already face significant stigma, without the additional stigma of the criminal label.
Design of Polyimide based Piezoelectric Micromachined Ultrasonic Transducer for Underwater Imaging Application

Micromachined ultrasonic transducer has been used in many application for example non-destructive test, medical diagnostic and underwater application. One of the underwater application is underwater acoustic imaging system. Underwater acoustic imaging system needs a transducer with wide bandwidth to perform high resolution image. In previous paper, Capacitance Micromachined Ultrasonic Transducer (CMUT) and Piezoelectric Micromachined Ultrasonic Transducer (PMUT) was studied in acoustic imaging. In this paper, PMUT was designed and studied their receiving sensitivity. The target operating frequency is in between 300 kHz to 700 kHz for underwater acoustic imaging. Simulation using Comsol 5.0 was used to determine the PVDF thickness, pitch element and substrate's material, Polyimide and Silicon for desired frequency and high receiving sensitivity. In this paper, Polyimide was used as substrate rather than previous paper was used Silicon as substrate. The positive and ground electrode with lateral structure was fabricated onto Polyimide substrate. The polyvinylidene difluoride, (PVDF) used as sensing element was placed on top of electrodes to obtain polarization and with lateral structure of electrodes, PMUT will induced the d33 mode polarization. The Pulse-echo method was used in experiments to determine the receiving sensitivity. PMUT was obtained receiving sensitivity at -80.84 dB rev 1V/uPa with resonance frequency, 525 kHz. Low frequency for PMUT was obtained at 450 kHz and high frequency for PMUT was obtained at 650 kHz. Bandwidth for PMUT is 38.1%.
Temporal Changes in Anthropometric Parameters and Lipid Profile according to Body Mass Index among an Adult Iranian Urban Population

Aims: To examine changes in anthropometric parameters and lipid profiles over a period of 3.6 years in an Iranian adult population according to body mass index (BMI) groups. Methods: Between 1998 and 2001 (phase 1) and 2002 and 2005 (phase 2), 5,618 nondiabetic Iranian adults aged ≧20 years were examined. Analysis of covariance was used to delineate trends in anthropometric parameters as well as total and low- and high-density lipoprotein cholesterol (TC, LDL-C and HDL-C, respectively) across BMI groups. Results: Although BMI increased in women, this increase was not significant in obese persons. Among the men, however, a significant increase in BMI was observed only in lean persons. Waist circumference (WC) increased across all BMI groups in both sexes. A significant decrease was observed in TC [men: –0.83 mmol/l, 95% confidence interval (CI) –1.27 to –0.40; women: –0.78 mmol/l, CI –0.97 to –0.60] and LDL-C (men: –0.63 mmol/l, CI –1.13 to –0.13; women: –0.51 mmol/l, CI –0.78 to –0.24). A significant decrease in mean HDL-C was observed only among men (–0.09 mmol/l, CI –0.13 to –0.04), with no difference among BMI groups (p = 0.3). There were no significant decreases in TC/HDL-C and LDL-C/HDL-C ratios in men or women. Conclusions: Despite an increase in WC, favorable trends were observed in TC and LDL-C levels. The favorable trend in TC levels was counterbalanced by changes in HDL-C, as reflected by the absence of a significant decrease in TC/HDL-C or LDL-C/HDL-C.
Gonadal Functioning and Perceptions of Infertility Risk Among Adult Survivors of Childhood Cancer: A Report From the St Jude Lifetime Cohort Study.

PURPOSE To describe perceptions of infertility risk among adult survivors of childhood cancer, to test the concordance of survivors' risk perceptions and their adult fertility status, and to identify explanatory factors (sociodemographic factors, gonadotoxic treatments, reproductive history, sexual dysfunction) associated with these outcomes. PATIENTS AND METHODS Adult childhood cancer survivors (N = 1,067; without children or a history of pregnancies) completed questionnaires that asked about infertility risk perceptions and participated in physical evaluations, including biomarkers of gonadal functioning (eg, semen analysis, blood hormone levels, menses). Multivariable regression models tested associations between explanatory factors and risk perceptions as well as concordance of perceptions and fertility status. RESULTS Most childhood cancer survivors (61.9%) perceived themselves at increased risk for infertility, which was significantly associated with sociodemographic factors (older age, white ethnicity, being married/partnered, higher education), gonadotoxic treatments, fertility concerns, previous unsuccessful attempts to conceive, and sexual dysfunction (all P < .05). Laboratory-evaluated impaired gonadal function was found in 24.3% of female and 55.6% of male survivors, but concordance with survivors' risk perceptions was low (Cohen's κ < .19). Most survivors with discordant perceptions overestimated risk (ie, perceived being at risk, though fertility status seemed normal; 19.7% of male and 43.6% of female survivors), whereas a minority underestimated risk (ie, perceived no risk but were impaired/infertile; 16.3% of male and 5.3% of female survivors). Factors related to discordance included sociodemographics, gonadotoxic treatments, fertility concerns, and sexual dysfunction (all P < .05). CONCLUSION Although childfree survivors may correctly consider themselves at risk for infertility on the basis of their previous treatments, such risk perceptions were discordant from laboratory-evaluated fertility status among many survivors in adulthood. Thus, repeated fertility-related communication throughout survivorship is essential, because treatment-indicated risk does not equal fertility status after treatment. Offering fertility testing to those who were at risk and/or those with fertility-related concerns is recommended.
Functional protein representations from biological networks enable diverse cross-species inference

Abstract Transferring knowledge between species is key for many biological applications, but is complicated by divergent and convergent evolution. Many current approaches for this problem leverage sequence and interaction network data to transfer knowledge across species, exemplified by network alignment methods. While these techniques do well, they are limited in scope, creating metrics to address one specific problem or task. We take a different approach by creating an environment where multiple knowledge transfer tasks can be performed using the same protein representations. Specifically, our kernel-based method, MUNK, integrates sequence and network structure to create functional protein representations, embedding proteins from different species in the same vector space. First we show proteins in different species that are close in MUNK-space are functionally similar. Next, we use these representations to share knowledge of synthetic lethal interactions between species. Importantly, we find that the results using MUNK-representations are at least as accurate as existing algorithms for these tasks. Finally, we generalize the notion of a phenolog (‘orthologous phenotype’) to use functionally similar proteins (i.e. those with similar representations). We demonstrate the utility of this broadened notion by using it to identify known phenologs and novel non-obvious ones supported by current research.
Concurrence and selection of sexual partners as predictors of condom use among Mexican indigenous migrant workers.

OBJECTIVE To identify if the selection of mixed sexual partners and the existence of concurrent partners are predictors of condom use in indigenous migrant agricultural workers from Colima, Mexico. METHODS Analytical cross-sectional study using an egocentric sexual network approach. Community interviewers applied a structured questionnaire to 192 indigenous migrant workers in a sugarcane agro-industrial context. Data were analyzed with binary logistic regression; odds ratios (OR) and 95% confidence intervals (CI 95%) were estimated. RESULTS In the logistic regression model, adjusted odds (OR; 95% CI) of steady condom use were lower within partnerships of the same indigenous ethnicity compared to other partnerships (0.30; 0.17-0.53), partnerships that were concurrent to other partnerships (0.27; 0.15-0.50), and partnerships that used illegal drugs during sex to other partnerships (0.23; 0.11-0.49). Those variables were actually associated with increased risk of unprotected sex (occasionally or never using condoms), and therefore exposures were unprotected. CONCLUSION Sexual partners of the same ethnicity, concurrent partnerships and partnerships that use illegal drugs favor the low frequency of constant condom use and, in turn, the vulnerability to STIs and HIV transmission in indigenous migrant agricultural workers.
Event-by-event non-rigid data-driven PET respiratory motion correction methods: comparison of principal component analysis and centroid of distribution

Respiratory motion is a major cause of degradation of PET image quality. Respiratory gating and motion correction can be performed to reduce the effects of respiratory motion; these methods require motion information, typically obtained from external tracking systems. Various groups have studied data-driven (DD) motion estimation methods. Recently, a DD respiratory motion estimation method was established by calculating the centroid of distribution (COD) of listmode events, which was then used with event-by-event respiratory motion correction (EBE-MC) and showed results comparable to those with an external motion tracking device. The EBE-MC method only corrected for rigid motion, so that non-rigid components still contributed to motion-induced blurring. A non-rigid respiratory motion correction (NRMC) was later developed to overcome this problem, but was only evaluated using signals from an external monitor. Thus, it is desirable to further develop DD motion estimation to achieve the best respiratory motion correction results. We evaluated two DD respiratory motion detection methods, COD and principal component analysis (PCA), by comparing the extracted motion trace to that acquired by the Anzai system in dynamic studies with two tracers. PCA was chosen as a preliminary study indicated that it produced stable results than other DD methods. We then developed and performed DD-EBE-NRMC using either COD- or PCA-derived respiratory motion information. DD correction results were compared with Anzai-based results. For all tested studies, both COD and PCA showed a good-to-excellent match with Anzai signals, with PCA showing a higher correlation with Anzai signals. The DD-EBE-NRMC results showed that both COD and PCA provide comparable image quality improvement to the Anzai-based correction. Although COD showed a lower correlation with Anzai than PCA, COD-based NRMC results are comparable to those of PCA, both of which showed great reduction in motion-induced blurring.
SUMO1 Modification Facilitates Avibirnavirus Replication by Stabilizing Polymerase VP1

SUMOylation is an extensively discussed posttranslational modification in diverse cellular biological pathways. However, there is limited understanding about SUMOylation of viral proteins of IBDV during infection. In the present study, we revealed a SUMO1 modification of VP1 protein, the RNA-dependent RNA polymerase of avibirnavirus infectious bursal disease virus (IBDV). The required site of VP1 SUMOylation comprised residues 404I and 406I of SUMO interaction motif 3, which was essential for maintaining its stability by inhibiting K48-linked ubiquitination. We also showed that IBDV with SUMOylation-deficient VP1 had decreased replication ability. These data demonstrated that the SUMOylation of IBDV VP1 played an important role in maintaining IBDV replication. ABSTRACT SUMOylation is a posttranslational modification that has crucial roles in diverse cellular biological pathways and in various viral life cycles. In this study, we found that the VP1 protein, the RNA-dependent RNA polymerase of avibirnavirus infectious bursal disease virus (IBDV), regulates virus replication by SUMOylation during infection. Our data demonstrated that the polymerase VP1 is efficiently modified by small ubiquitin-like modifier 1 (SUMO1) in avibirnavirus-infected cell lines. Mutation analysis showed that residues 404I and 406I within SUMO interaction motif 3 of VP1 constitute the critical site for SUMO1 modification. Protein stability assays showed that SUMO1 modification enhanced significantly the stability of polymerase VP1 by inhibiting K48-linked ubiquitination. A reverse genetic approach showed that only IBDV with I404C/T and I406C/F mutations of VP1 could be rescued successfully with decreased replication ability. Our data demonstrated that SUMO1 modification is essential to sustain the stability of polymerase VP1 during IBDV replication and provides a potential target for designing antiviral drugs targeting IBDV. IMPORTANCE SUMOylation is an extensively discussed posttranslational modification in diverse cellular biological pathways. However, there is limited understanding about SUMOylation of viral proteins of IBDV during infection. In the present study, we revealed a SUMO1 modification of VP1 protein, the RNA-dependent RNA polymerase of avibirnavirus infectious bursal disease virus (IBDV). The required site of VP1 SUMOylation comprised residues 404I and 406I of SUMO interaction motif 3, which was essential for maintaining its stability by inhibiting K48-linked ubiquitination. We also showed that IBDV with SUMOylation-deficient VP1 had decreased replication ability. These data demonstrated that the SUMOylation of IBDV VP1 played an important role in maintaining IBDV replication.
Rapid Response Team-Quality Champion Registered Nurse

Background: Operationalization of the rapid response team (RRT) and its quality champion (QC) nurses at a community hospital is unique and provides benefits not entirely captured by analysis of mortality data. Purpose: The purpose was to determine the perceived benefits of the RRT at the facility and behaviors and activities observed during actual RRT responses. Also examined was the timeliness of the RRT calls. Methods: This was a mixed-method study including qualitative (interviews, focus groups, and surveys) and quantitative (retrospective chart reviews) data collection. Results: Themes included teaching/education, foster development of critical thinking skills, expertise/resource, communication/facilitation/go-between, safety net/security, validation, and advocate/foster collaboration. RRT calls were made quickly after clinical deterioration. Conclusions: Benefits of the RRT-QC registered nurse were extensive. Observations showed support, education, and teamwork in an effort to improve outcomes and support clinicians.
Engineering Microfluidic Organoid-on-a-Chip Platforms

In vitro cell culture models are emerging as promising tools to understand human development, disease progression, and provide reliable, rapid and cost-effective results for drug discovery and screening. In recent years, an increasing number of in vitro models with complex organization and controlled microenvironment have been developed to mimic the in vivo organ structure and function. The invention of organoids, self-organized organ-like cell aggregates that originate from multipotent stem cells, has allowed a whole new level of biomimicry to be achieved. Microfluidic organoid-on-a-chip platforms can facilitate better nutrient and gas exchange and recapitulate 3D tissue architecture and physiology. They have the potential to transform the landscape of drug development and testing. In this review, we discuss the challenges in the current organoid models and describe the recent progress in the field of organoid-on-a-chip.
Silencing of lncRNA AFAP1-AS1 Inhibits Cell Growth and Metastasis in Clear Cell Renal Cell Carcinoma

The lncRNA AFAP1-AS1, oriented from an antisense direction to the protein-coding gene AFAP1 in the opposite strand, was upregulated in a variety of tumors and associated with poor prognosis, including lung cancer, breast cancer, ovarian cancer, and so on. However, the biological role of AFAP1-AS1 in clear cell renal cell carcinoma (ccRCC) is still unknown. We observed that AFAP1-AS1 expression was significantly upregulated in ccRCC tissues and that patients with high-level expression of AFAP1-AS1 had a shorter overall survival. Knockdown of AFAP1-AS1 markedly suppressed the progression of proliferation, invasion, migration, and EMT in ccRCC cells. Downregulation of AFAP1-AS1 resulted in an increase in E-cadherin and a decrease in vimentin. Noticeably, we found that PTEN has a negative correlation with the lncRNA AFAP1-AS1 expression. Further studies verified that PTEN deficiency effectively attenuated the ability of AFAP1-AS1 in promoting ccRCC cell proliferation, invasion, migration, and EMT. Moreover, the similar biological response of silencing AFAP1-AS1 was observed in our ccRCC mice model. Knockdown of AFAP1-AS1 evidently suppressed tumor growth. Taken together, our results provide the evidences that silencing of AFAP1-AS1 inhibits cell proliferation, EMT, and metastasis through PTEN-dependent signaling, and our findings elucidate a novel potential therapeutic target or biomarker for the treatment of ccRCC.
Performance of Deep Learning Model in Detecting Operable Lung Cancer With Chest Radiographs

Purpose: The aim of this study was to evaluate the diagnostic performance of a trained deep convolutional neural network (DCNN) model for detecting operable lung cancer with chest radiographs (CXRs). Materials and Methods: The institutional review board approved this study. A deep learning model (DLM) based on DCNN was trained with 17,211 CXRs (5700 CT-confirmed lung nodules in 3500 CXRs and 13,711 normal CXRs), finally augmented to 600,000 images. For validation, a trained DLM was tested with 1483 CXRs with surgically resected lung cancer, marked and scored by 2 radiologists. Furthermore, diagnostic performances of DLM and 6 human observers were compared with 500 cases (200 visible T1 lung cancer on CXR and 300 normal CXRs) and analyzed using free-response receiver-operating characteristics curve (FROC) analysis. Results: The overall detection rate of DLM for resected lung cancers (27.2±14.6 mm) was a sensitivity of 76.8% (1139/1483) with a false positive per image (FPPI) of 0.3 and area under the FROC curve (AUC) of 0.732. In the comparison with human readers, DLM demonstrated a sensitivity of 86.5% at 0.1 FPPI and a sensitivity of 92% at 0.3 FPPI with AUC of 0.899 at an FPPI range of 0.03 to 0.44 for detecting visible T1 lung cancers, which were superior to the average of 6 human readers [mean sensitivity; 78% (range, 71.6% to 82.6%) at an FPPI of 0.1% and 85% (range, 80.2% to 89.2%) at an FPPI of 0.3, AUC of 0.819 (range, 0.754 to 0.862) at an FPPI of 0.03 to 0.44). Conclusions: A DLM has high diagnostic performance in detecting operable lung cancer with CXR, demonstrating a potential of playing a pivotal role for lung cancer screening.