Miracle-dz/UniFAR-FTUs huggingface dataset:
BAITING AND BANDING: EXPERT OPINION ON HOW BAIT TRAPPING MAY INFLUENCE THE OCCURRENCE OF HIGHLY PATHOGENIC AVIAN INFLUENZA (HPAI) AMONG DABBLING DUCKs

Abstract: A Eurasian lineage highly pathogenic avian influenza virus (HPAIV) of the clade 2.3. 4.4b (Goose/Guangdong lineage) was detected in migratory bird populations in North America in December 2021, and it, along with its reassortants, have since caused wild and domestic bird outbreaks across the continent. Relative to previous outbreaks, HPAIV cases among wild birds in 2022 exhibited wider geographic extent within North America and higher levels of mortality, suggesting the potential for population-level impacts. Given the possible conservation implications of HPAIV in wild birds, natural resource managers have sought guidance on actions that may mitigate negative effects of disease among North American bird populations, including modification of existing management practices. Banding of waterfowl is a critical tool for population management for several harvested species in North America, but some banding techniques, such as bait trapping, can lead to increased congregation of waterfowl, potentially altering HPAIV transmission. We used an expert opinion exercise to assess how bait trapping of dabbling ducks in Canada may influence HPAIV transmission and wild bird health. The expert group found that it is moderately likely that bait trapping of dabbling ducks in wetlands will significantly increase the transmission of HPAIV among individual ducks, but there is a low probability that this will result in significant population-level effects on North American dabbling ducks. Considering the lack of empirical work studying how capture and handling methods may change transmission of HPAIV among waterfowl, as well as the importance of bait trapping for waterfowl management in North America, future work should focus on filling knowledge gaps pertaining to the influence of baiting on HPAIV occurrence to better inform banding procedures and management decision making.
MRAβ: A multimodal MRI‐derived amyloid‐β biomarker for Alzheimer's disease

Florbetapir 18F (AV45), a highly sensitive and specific positron emission tomographic (PET) molecular biomarker binding to the amyloid‐β of Alzheimer's disease (AD), is constrained by radiation and cost. We sought to combat it by combining multimodal magnetic resonance imaging (MRI) images and a collaborative generative adversarial networks model (CollaGAN) to develop a multimodal MRI‐derived Amyloid‐β (MRAβ) biomarker. We collected multimodal MRI and PET AV45 data of 380 qualified participants from the ADNI dataset and 64 subjects from OASIS3 dataset. A five‐fold cross‐validation CollaGAN were applied to generate MRAβ. In the ADNI dataset, we found MRAβ could characterize the subject‐level AV45 spatial variations in both AD and mild cognitive impairment (MCI). Voxel‐wise two‐sample t‐tests demonstrated amyloid‐β depositions identified by MRAβ in AD and MCI were significantly higher than healthy controls (HCs) in widespread cortices (p < .05, corrected) and were much similar to those by AV45 (r > .92, p < .001). Moreover, a 3D ResNet classifier demonstrated that MRAβ was comparable to AV45 in discriminating AD from HC in both the ADNI and OASIS3 datasets, and in discriminate MCI from HC in ADNI. Finally, we found MRAβ could mimic cortical hyper‐AV45 in HCs who later converted to MCI (r = .79, p < .001) and was comparable to AV45 in discriminating them from stable HC (p > .05). In summary, our work illustrates that MRAβ synthesized by multimodal MRI could mimic the cerebral amyloid‐β depositions like AV45 and lends credence to the feasibility of advancing MRI toward molecular‐explainable biomarkers.
Circumsolar Radiation and Beam Irradiance Measurements for Focusing Collectors

Depending on the present atmospheric conditions a considerable part of the direct solar radiation can be scattered into the circumsolar region closely surrounding the solar disk. This forward scattered radiation, the circumsolar radiation, is widely detected by pyrheliometers, while concentrating solar collectors can only use a concentrator specific fraction of it. This lower response to circumsoalr radiation can lead to systematic overestimations of the collector performance. when thin clouds mask the sun, this overestimation can be greater than 10% although the direct normal irradiance (DNI) is often above 200 W/M2 in such case. The fraction of the measured DNI that is caused by circumsolar radiation varies depending on the day conditions. The average of this fraction depends also on the location. Thus, representativ site specific information on the circumsolar radiation is necessary for the accurate calcuation of the expected yield of a concentrating solar plant. Beam irradiance data for concentrating solar collectors should be accompanied with information on the circumsolar radiation. However, such information is not available for locations that are now of particular interest for concentrating solar power (CSP) or concentrating photovoltaics (CPV). As a first step to overcome this complication, a reference system consisting of the Sun and Aureole Measurement System (SAM), an Aeronet sun photometer and post processing software has been developed and is used at a small number of sites. In order to provide a sufficient database, an alternative method for the determination of the sunshape is presented using less expensive and maintenance intense equipment. This method makes use of a pair of pyrheliomters with different angular acceptance functions. By comparison of the measurements of the two pyrheliomters, the amount of circumsolar irradiance can be determined. The system was tested and verified using the reference system. As a result, the necessary information for CSP and CPV systems, and a basis for the development of of modeling methods for circumsolar radiation, can now be achieved.
Report of the 23rd nationwide follow‐up survey of primary liver cancer in Japan (2014–2015)

For the 23rd Nationwide Follow‐up Survey of Primary Liver Cancer in Japan, data from 20 889 newly registered patients and 42 274 previously registered follow‐up patients were compiled from 516 institutions over a 2‐year period from January 1, 2014 to December 31, 2015. Basic statistics compiled for patients newly registered in the 23rd survey were cause of death, past medical history, clinical diagnosis, imaging diagnosis, treatment‐related factors, pathological diagnosis, recurrence status, and autopsy findings. Compared with the previous 22nd survey, the population of patients with hepatocellular carcinoma (HCC) was older at the time of clinical diagnosis, had more female patients, had more patients with non‐B non‐C HCC, had smaller tumor diameter, and was more frequently treated with hepatectomy. Cumulative survival rates were calculated for HCC, intrahepatic cholangiocarcinoma, and combined hepatocellular cholangiocarcinoma (combined HCC and intrahepatic cholangiocarcinoma) by treatment type and background characteristics for patients newly registered between 2004 and 2015 whose final outcome was survival or death. The median overall survival and cumulative survival rates for HCC were calculated by dividing patients by combinations of background factors (number of tumors, tumor diameter, Child–Pugh grade, or albumin‐bilirubin grade) and by treatment type (hepatectomy, radiofrequency ablation therapy, transcatheter arterial chemoembolization, hepatic arterial infusion chemotherapy, and systemic therapy). The same values were also calculated according to registration date by dividing patients newly registered between 1978 and 2015 into five time period groups. The data obtained from this nationwide follow‐up survey are expected to contribute to advancing clinical research and treatment of primary liver cancer in the world.
JOINT RESEARCH CENTER FOR PANEL STUDIES DISCUSSION PAPER SERIES

The hedonic pricing approach is used to examine whether homeowners and/or renters alter their subjective assessments of earthquake risks after massive earthquakes. Using nation-wide household panel data coupled with earthquake hazard information and records of observed earthquakes, we find that there are some modifications of individuals’ assessments of earthquake risk in both cases. We have carefully taken into consideration the bias stemming from the use of objective risk variables as a proxy for individual risk assessments. Our results suggest that the price discount from locating within a quake-prone area is significantly larger soon after earthquake events than beforehand. We argue that the most likely interpretation for this result is that households tend to underestimate earthquake risk if there has not been a recent occurrence.
Clinical management of Kaposi sarcoma herpesvirus-associated diseases: an update on disease manifestations and treatment strategies

ABSTRACT Introduction Kaposi sarcoma herpes virus (KSHV) is associated with several diseases including Kaposi sarcoma, a form of multicentric Castleman’s disease, primary effusion lymphoma, and an inflammatory cytokine syndrome. These KSHV-associated diseases (KAD) can present with heterogenous signs and symptoms that are often associated with cytokine dysregulation that may result in multiorgan dysfunction. The inability to promptly diagnose and treat these conditions can result in long-term complications and mortality. Areas covered Existing epidemiological subtypes of existing KSHV-associated diseases, specifically Kaposi sarcoma as well as the incidence of several KSHV-associated disorders are described. We review the KSHV latent and lytic phases as they correlate with KSHV-associated diseases. Given the complicated presentations, we discuss the clinical manifestations, current diagnostic criteria, existing treatment algorithms for individual KAD, and when they occur concurrently. With emerging evidence on the virus and host interactions, we evaluate novel approaches for the treatment of KAD. An extensive literature search was conducted to support these findings. Expert opinion KSHV leads to complex and concurrent disease processes that are often underdiagnosed both in the United States and worldwide. New therapies that exist for many of these conditions focus on chemotherapy-sparing options that seek to target the underlying viral pathogenesis or immunotherapy strategies.
Analysis of Hepatitis D Virus in Minor Salivary Gland of Sjögren’s Disease

Hepatitis delta virus (HDV) has been detected in the minor salivary gland (MSG) tissue of Sjögren’s disease (SjD) patients in the absence of a hepatitis B virus (HBV) coinfection. Previous research has shown that HDV antigen (HDAg) expression can trigger an SjD-like phenotype in vivo, demonstrating a potential cause-and-effect relationship. We hypothesize that if HDV plays a role in the development of SjD, then HDV profiles may be correlated with disease manifestations. This retrospective study characterized HDV in a cohort of 48 SjD MSG samples collected between 2014 and 2021. Analyses of HDAg expression, including cell type and subcellular localization, in situ hybridization of HDV RNA, and comparative analyses with associated SjD and viral hepatitis clinical features, were conducted. HDAg was detected in MSG acinar, ductal, myoepithelial, and adipose cells and localized with the nuclei, cytoplasm, and mitochondria. In situ hybridization detected HDV genomic RNA localization in the MSG nuclei. A significant negative correlation was found between HDAg intensity and focal lymphocytic inflammation and in patients with both anti-SSA/Ro-52 and anti-SSA/Ro-60. In analyzing autoimmune disease comorbidities with SjD, it was found that SjD patients diagnosed with autoimmune thyroiditis and/or hypothyroidism were significantly more represented in the high HDAg intensity group compared to the negative and moderate HDAg intensity groups. No significant associations were detected between MSG-localized HDAg and liver enzymes or an evident HBV coinfection. This study has further confirmed that there is a nonhepatic reservoir for chronic HDV persistence in SjD-affected salivary gland tissue in a third independent SjD patient cohort. In addition, this study describes the unique colocalization of HDAg with mitochondria. The detection of HDV antigen and sequence within SjD-affected salivary gland tissue, and in the absence of an evident current or past HBV coinfection, warrants further investigation.
TRAF5 regulates intestinal mucosal Th1/Th17 cell immune responses via Runx1 in colitis mice

Inflammatory bowel disease (IBD) is a chronic gastrointestinal inflammatory disease associated with CD4+ Th1 and Th17 cell immune responses. Tumour necrosis factor‐associated factor 5 (TRAF5) deficiency has been shown to aggravate DSS‐induced colitis. However, the potential role of TRAF5 in regulating CD4+ T cell immune responses in the pathogenesis of IBD remains unclear. TRAF5−/− CD4+CD45RBhigh T cells and WT CD4+CD45RBhigh T cells were transferred to Rag2−/− mice via intravenous (i.v.) tail injection, respectively, to establish a chronic colitis model. Adeno‐associated virus (AAV)‐mediated gene knockout technique was used to knock out runt‐associated transcription factor 1 (Runx1) expression in vivo. Specific cytokines of Th1 and Th17 cells were detected by quantitative RT‐PCR, immunohistochemistry, ELISA, and flow cytometry. In T‐cell transfer colitis mice, the Rag2−/− mice reconstituted with TRAF5−/− CD4+CD45RBhigh T cells showed more severe intestinal inflammation than the WT control group, which was characterised by increased expression of INF‐γ, TNF‐α, IL‐17a. Furthermore, we found that the INF‐γ+CD4+, IL17a+CD4+, and INF‐γ+ IL17a+CD4+ T cells in the intestinal mucosa of Rag2−/− mice reconstituted with TRAF5−/− CD4+CD45RBhigh T cells were significantly higher than those of the WT control group by flow cytometry. Mechanistically, knockout Runx1 inhibited the differentiation of TRAF5−/− CD4+ T cells into Th1 and Th17 cells in the intestinal mucosa of T‐cell transfer colitis mice. TRAF5 regulates Th1 and Th17 cell differentiation and immune response through Runx1 to participate in the pathogenesis of colitis. Thus targeting TRAF5 in CD4+ T cells may be a novel treatment for IBD.
Factors Associated with Continued Breastfeeding Practice in Children Under 2 Years of Age Assisted by the Brazilian Conditional Cash Transfer Program, Bolsa Família

ABSTRACT Breastfeeding is the first guarantee of the human right to adequate food and the benefits of continued breastfeeding up to 2 years of age are well established. This cross-sectional study sought to explore the association between socioeconomic, demographic, and nutritional factors and the practice of continued breastfeeding in children aged 6 to 24 months assisted by the Brazilian conditional cash transfer program, Bolsa Família. Our findings emphasize the role of unfavorable socioeconomic conditions in diminishing the practice of continued breastfeeding. They also suggest the importance of policy-level actions to promote and support breastfeeding and to combat early ultra-processed foods consumption.
Changes in Bone Quality after Treatment with Etelcalcetide

Visual Abstract Introduction Secondary hyperparathyroidism is associated with osteoporosis and fractures. Etelcalcetide is an intravenous calcimimetic for the control of hyperparathyroidism in patients on hemodialysis. Effects of etelcalcetide on the skeleton are unknown. Methods In a single-arm, open-label, 36-week prospective trial, we hypothesized that etelcalcetide improves bone quality and strength without damaging bone–tissue quality. Participants were 18 years or older, on hemodialysis ≥1 year, without calcimimetic exposure within 12 weeks of enrollment. We measured pretreatment and post-treatment areal bone mineral density by dual-energy X-ray absorptiometry, central skeleton trabecular microarchitecture by trabecular bone score, and peripheral skeleton volumetric bone density, geometry, microarchitecture, and estimated strength by high-resolution peripheral quantitative computed tomography. Bone–tissue quality was assessed using quadruple-label bone biopsy in a subset of patients. Paired t tests were used in our analysis. Results Twenty-two participants were enrolled; 13 completed follow-up (mean±SD age 51±14 years, 53% male, and 15% White). Five underwent bone biopsy (mean±SD age 52±16 years and 80% female). Over 36 weeks, parathyroid hormone levels declined 67%±9% (P < 0.001); areal bone mineral density at the spine, femoral neck, and total hip increased 3%±1%, 7%±2%, and 3%±1%, respectively (P < 0.05); spine trabecular bone score increased 10%±2% (P < 0.001); and radius stiffness and failure load trended to a 7%±4% (P = 0.05) and 6%±4% increase (P = 0.06), respectively. Bone biopsy demonstrated a decreased bone formation rate (mean difference −25±4 µm3/µm2 per year; P < 0.01). Conclusions Treatment with etelcalcetide for 36 weeks was associated with improvements in central skeleton areal bone mineral density and trabecular quality and lowered bone turnover without affecting bone material properties. Clinical Trial registry name and registration number: The Effect of Etelcalcetide on CKD-MBD (Parsabiv-MBD), NCT03960437
Mindfulness Enhances Cognitive Functioning: A Meta-Analysis of 111 Randomized Controlled Trials.

Background In theory, habitually exercising mindfulness skills can improve cognitive functioning abilities. However, no comprehensive quantitative reviews of the efficacy of MBIs on global and unique cognitive subdomains exist to date. Method: This meta-analysis examined the effects of MBIs on global cognition and 15 cognitive subdomains. Inclusion criteria: meditation naïve participants; participants randomly assigned to MBIs or no-treatment, waitlist, or active control; outcome measures included at least one behavioral cognitive assessment or subjective cognitive functioning measure; teaching mindfulness skills was the primary treatment focus. Exclusion criteria: inadequate data to calculate effect sizes; MBIs included only one session; control condition that contained any MBI form. Robust variance estimation and moderator analyses controlling for presence of reported treatment fidelity were conducted. Results: One-hundred-and-eleven RCTs (n = 9,538) met eligibility criteria. MBIs had small-to-moderate significant effects on global cognition, executive attention, WM accuracy, inhibition accuracy, shifting accuracy, sustained attention, and subjective cognitive functioning (vs. waitlist/no-treatment, average g = 0.257-0.643; vs. active controls, average g = 0.192-0.394). MBIs did not impact executive functioning (EF) latency indices, verbal fluency, processing speed, episodic memory, and cognitive error. Treatment effects were stronger for those with elevated psychiatric symptoms compared to healthy controls, and medical samples, studies with complete-case (vs. intention-to-treat) analysis, face-to-face (vs. self-guided) delivery, and use of non-standard mindfulness-based stress reduction or mindfulness-based cognitive therapy (vs. standard MBI). Conclusion: MBIs consistently yielded small-to-moderate yet practically meaningful effect sizes on global cognition and six cognitive subdomains that captured accuracy vs. latency-based indices of EF and sustained accuracy.
PTEN deficiency exposes a requirement for an ARF GTPase module for integrin‐dependent invasion in ovarian cancer

Dysregulation of the PI3K/AKT pathway is a common occurrence in high‐grade serous ovarian carcinoma (HGSOC), with the loss of the tumour suppressor PTEN in HGSOC being associated with poor prognosis. The cellular mechanisms of how PTEN loss contributes to HGSOC are largely unknown. We here utilise time‐lapse imaging of HGSOC spheroids coupled to a machine learning approach to classify the phenotype of PTEN loss. PTEN deficiency induces PI(3,4,5)P3‐rich and ‐dependent membrane protrusions into the extracellular matrix (ECM), resulting in a collective invasion phenotype. We identify the small GTPase ARF6 as a crucial vulnerability of HGSOC cells upon PTEN loss. Through a functional proteomic CRISPR screen of ARF6 interactors, we identify the ARF GTPase‐activating protein (GAP) AGAP1 and the ECM receptor β1‐integrin (ITGB1) as key ARF6 interactors in HGSOC regulating PTEN loss‐associated invasion. ARF6 functions to promote invasion by controlling the recycling of internalised, active β1‐integrin to maintain invasive activity into the ECM. The expression of the CYTH2‐ARF6‐AGAP1 complex in HGSOC patients is inversely associated with outcome, allowing the identification of patient groups with improved versus poor outcome. ARF6 may represent a therapeutic vulnerability in PTEN‐depleted HGSOC.
Concise Report

Safety of resuming tumour necrosis factor inhibitors in patients who developed tuberculosis as a complication of previous TNF inhibitors Abstract Objectives. There is no consensus on whether restarting TNF inhibitors (TNFis) after treatment of an active tuberculosis (TB) infection caused by previous TNFi exposure is safe. In this study we sought to determine the safety of resuming TNFis in patients following TB treatment. Methods. The medical records of all patients (n = 683) that received TNFi treatment at a single rheuma-tology clinic between June 2003 and December 2012 were retrospectively reviewed. Among them, data from patients who developed active TB infection were collected and patient outcomes were evaluated for those who resumed TNFis after TB treatment. Results. Of 683 patients, 13 patients developed an active TB infection during TNFi treatment (4 on etanercept, 4 on adalimumab and 5 on infliximab). The median duration of TNFi treatment before TB infection was 20 months. TNFi treatment was reinitiated in six patients: four within 2 months after TB treatment and two after completion of TB treatment. Four patients reinitiated with the same TNFi, whereas two patients started with another TNFi. During a mean follow-up of 30.6 months, all six patients successfully completed TB treatment with no TB infection relapses. Conclusion. Our results suggest that resuming TNFi therapy in patients following adequate TB treatment is safe, even before completion of TB treatment.
THE 2023 RELEASE OF Cloudy

We describe the 2023 release of the spectral synthesis code Cloudy. Since the previous major release, migrations of our online services motivated us to adopt git as our version control system. This change alone led us to adopt an annual release scheme, accompanied by a short release paper, the present being the inaugural. Significant changes to our atomic and molecular data have improved the accuracy of Cloudy predictions: we have upgraded our instance of the Chianti database from version 7 to 10; our H- and He-like collisional rates to improved theoretical values; our molecular data to the most recent LAMDA database, and several chemical reaction rates to their most recent UDfA and KiDA values. Finally, we describe our progress on upgrading Cloudy's capabilities to meet the requirements of the X-ray microcalorimeters aboard the upcoming XRISM and Athena missions, and outline future developments that will make Cloudy of use to the X-ray community.