bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circulating micro-RNAs Differentially Expressed in Korean Alzheimer’s Patients With Brain Aβ Accumulation Activate Amyloidogenesis
Authors: Mankhong Sakulrat , Kim Sujin , Moon Sohee , Choi Seong-Hye , Kwak Hyo-Bum , Park Dong-Ho , Shah Pratik , Lee Phil Hyu , Yang Seong Wook , Kang Ju-Hee 
Published: May 2022

AbstractBackgroundRoles for extracellular vesicles (EVs) enriched with micro-RNAs (miRNAs) have been proposed in Alzheimer’s disease (AD) pathogenesis, leading to the discovery of blood miRNAs as AD biomarkers. However, the diagnostic utility of specific miRNAs is not consistent. This study aimed to discover blood miRNAs that are differentially expressed in Korean AD patients, evaluate their clinical performance, and investigate their role in amyloidogenesis.MethodsWe discovered miRNAs differentially expressed in AD (N = 8) from cognitively normal participants (CN, N = 7) or Parkinson’s disease (PD) patients (N = 8). We evaluated the clinical performance of these miRNAs in plasma of subgroup (N = 99) and in plasma EVs isolated from the total cohort (N = 251). The effects of miRNAs on amyloidogenesis and on the regulation of their target genes were investigated in vitro.ResultsAmong 17 upregulated and one downregulated miRNAs in AD (&gt;twofold), miR-122-5p, miR-210-3p, and miR-590-5p were differentially expressed compared with CN or PD. However, the diagnostic performance of the selected plasma or EV miRNAs in total participants were limited (area under the curve &lt; 0.8). Nevertheless, levels of 3 miRNAs in plasma or plasma EVs of participants who were amyloid positron emission tomography (Aβ-PET) positive were significantly higher than those from the Aβ-PET negative participants (p &lt; .05). The selected miRNAs induced Aβ production (p &lt; .05) through activation of β-cleavage of amyloid precursor protein (CTF-β; p &lt; .01), and downregulated their target genes (ADAM metallopeptidase domain 10, Brain-derived neurotrophic factor, and Jagged canonical notch ligand 1; p &lt; .05), which was further supported by pathway enrichment analysis of target genes of the miRNAs.ConclusionIn conclusion, despite of the limited diagnostic utility of selected miRNAs as plasma or plasma EV biomarkers, the discovered miRNAs may play a role in amyloidogenesis during AD onset and progression.
Nursing Home Palliative Care During the Pandemic: Directions for the Future
Authors: Ninteau Kacy , Bishop Christine E 
Published: May 2022

Abstract

Background and Objectives
Palliative care addresses physical, emotional, psychological, and spiritual suffering that accompanies serious illness. Emphasis on symptom management and goals of care is especially valuable for seriously ill nursing home residents. We investigated barriers to nursing home palliative care provision highlighted by the coronavirus disease 2019 (COVID-19) pandemic and the solutions nursing home staff used to provide care in the face of those barriers.

Research Design and Methods
For this descriptive qualitative study, seven Massachusetts nursing home directors of nursing were interviewed remotely about palliative care provision before and during the COVID-19 pandemic. Interview data were analyzed using thematic analysis.

Results
Before the pandemic, palliative care was delivered primarily by nursing home staff depending on formal and informal consultations from palliative care specialists affiliated with hospice providers. When COVID-19 lockdowns precluded these consultations, nursing staff did their best to provide palliative care, but were often overwhelmed by shortfalls in resources, resident decline brought on by isolation and COVID-19 itself, and a sense that their expertise was lacking. Advance care planning conversations focused on hospitalization decisions and options for care given resource constraints. Nevertheless, nursing staff discovered previously untapped capacity to provide palliative care on-site as part of standard care, building trust of residents and families.

Discussion and Implications
Nursing staff rose to the palliative care challenge during the COVID-19 pandemic, albeit with great effort. Consistent with prepandemic analysis, we conclude that nursing home payment and quality standards should support development of in-house staff capacity to deliver palliative care while expanding access to the formal consultations and family involvement that were restricted by the pandemic. Future research should be directed to evaluating initiatives that pursue these aims.
Inequalities in Health Impact of Alternative Reimbursement Pathways for Nirsevimab in the United States
Authors: Gomez Gabriela B , Nelson Christopher B , Rizzo Christopher , Shepard Donald S , Chaves Sandra S 
Published: May 2022

Abstract
The target populations and financing mechanisms for a new health technology may affect health inequalities in access and impact. We projected the distributional consequences of introducing nirsevimab for prevention of respiratory syncytial virus in a US birth cohort of infants through alternative reimbursement pathway scenarios. Using the RSV immunization impact model, we estimated that a vaccine-like reimbursement pathway would cover 32% more infants than a pharmaceutical pathway. The vaccine pathway would avert 30% more hospitalizations and 39% more emergency room visits overall, and 44% and 44%, respectively, in publicly insured infants. The vaccine pathway would benefit infants from poorer households.
Phenomics data processing: extracting dose–response curve parameters from high-resolution temperature courses and repeated field-based wheat height measurements
Authors: Roth Lukas , Piepho Hans-Peter , Hund Andreas 
Published: May 2022

Abstract
Temperature is a main driver of plant growth and development. New phenotyping tools enable quantifying the temperature response of hundreds of genotypes. Yet, for field-derived data, temperature response modelling bears flaws and pitfalls concerning the interpretation of derived parameters. In this study, climate data from five growing seasons with differing temperature distributions served as starting point for a growth simulation of wheat stem elongation, based on a four-parametric temperature response function (Wang–Engel) including all cardinal temperatures. In a novel approach, we re-extracted dose–responses from the simulation by combining high-resolution (hours) temperature courses with low-resolution (days) height data. The collection of such data is common in field phenotyping platforms. To take advantage of the lack of supra-optimal temperatures during the stem elongation, simpler (linear and asymptotic) models to predict temperature response parameters were investigated. The asymptotic model extracted the base temperature of growth and the maximum absolute growth rate with high precision, whereas simpler, linear models failed to do so. Additionally, the asymptotic model provided a proxy estimate for the optimum temperature. However, when including seasonally changing cardinal temperatures, the prediction accuracy of the asymptotic model was strongly reduced. In a field study with three winter wheat varieties, significant differences were found for all three asymptotic dose–response curve parameters. We conclude that the asymptotic model based on high-resolution temperature courses is suitable to extract meaningful parameters from field-based data.
The Utility of Myositis Specific Antibodies in Clinical Practice
Authors: Biddle Kathryn , Taylor Matthew D , Linstead Sarah E , Kiely Patrick D W 
Published: May 2022

Abstract

Background
Fifteen myositis-specific antibodies have been described and characterized over the past 40 years. Approximately two thirds of patients with idiopathic inflammatory myositis have a myositis-specific antibody and only rarely more than one. Assays to detect them are now widely available within clinical practice.

Content
We describe the original description and clinical phenotype of the myositis-specific antibodies, forming the antisynthetase syndrome group, anti-MDA-5 and rapidly progressive interstitial lung disease, anti-SRP/HMGCR and necrotizing myositis, anti-TIF-1γ/NXP-2 and malignancy, anti-SAE and esophageal disease, and anti-Mi-2 and classic dermatomyositis skin disease.

Summary
Clinical practice is likely to be refined, with diagnosis and classification of the idiopathic inflammatory myositides based primarily on myositis-specific antibody, rather than directed by muscle histology or the broader clinical characteristics of polymyositis and dermatomyositis. All patients newly presenting with idiopathic inflammatory myositis should be routinely screened for myositis-specific antibodies. A positive result will usefully provide diagnostic and prognostic information, guide selection of therapy, and prompt surveillance for potential organ involvement and other features, such as cancer, throughout the disease course.
Built by epidemiologists for epidemiologists: an internal COVID-19 dashboard for real-time situational awareness in New York City
Authors: Ngai Stephanie , Sell Jessica , Baig Samia , Iqbal Maryam , Eddy Meredith , Culp Gretchen , Montesano Matthew , McGibbon Emily , Johnson Kimberly , Devinney Katelynn , Baumgartner Jennifer , Huynh Mary , Mathes Robert , Van Wye Gretchen , Fine Annie D , Thompson Corinne N 
Published: May 2022

Abstract

Objective
New York City (NYC) experienced a large first wave of coronavirus disease 2019 (COVID-19) in the spring of 2020, but the Health Department lacked tools to easily visualize and analyze incoming surveillance data to inform response activities. To streamline ongoing surveillance, a group of infectious disease epidemiologists built an interactive dashboard using open-source software to monitor demographic, spatial, and temporal trends in COVID-19 epidemiology in NYC in near real-time for internal use by other surveillance and epidemiology experts.

Materials and methods
Existing surveillance databases and systems were leveraged to create daily analytic datasets of COVID-19 case and testing information, aggregated by week and key demographics. The dashboard was developed iteratively using R, and includes interactive graphs, tables, and maps summarizing recent COVID-19 epidemiologic trends. Additional data and interactive features were incorporated to provide further information on the spread of COVID-19 in NYC.

Results
The dashboard allows key staff to quickly review situational data, identify concerning trends, and easily maintain granular situational awareness of COVID-19 epidemiology in NYC.

Discussion
The dashboard is used to inform weekly surveillance summaries and alleviated the burden of manual report production on infectious disease epidemiologists. The system was built by and for epidemiologists, which is critical to its utility and functionality. Interactivity allows users to understand broad and granular data, and flexibility in dashboard development means new metrics and visualizations can be developed as needed.

Conclusions
Additional investment and development of public health informatics tools, along with standardized frameworks for local health jurisdictions to analyze and visualize data in emergencies, are warranted.
A case of post-operative stenosis caused by colonic ischemia after low anterior resection for rectal cancer, followed by delayed colo-anal anastomosis
Authors: Uchiyama Shuichiro , Ikeda Naotaka , Oyama Tomohiro , Eguchi Mayumi , Ito Ayaka , Sato Rikiya , Toyosaki Ryoichi , Kitazono Masaki , Suenaga Toyokuni 
Published: May 2022

Abstract
Cases of delayed colo-anal anastomosis (DCAA) are currently reported instead of the colo-anal anastomosis with a protective loop ileostomy for rectal cancer. Post-operative colonic ischemia is considered as one of the serious complications of colorectal resection. Although indication of DCAA should be carefully selected, we experienced a case of post-operative stenosis caused by colonic ischemia after low anterior resection for rectal cancer, followed by this procedure.
Hamiltonian Monte Carlo reconstruction from peculiar velocities
Authors: Valade Aurélien , Hoffman Yehuda , Libeskind Noam I , Graziani Romain 
Published: May 2022

ABSTRACTThe problem of the reconstruction of the large-scale density and velocity fields from peculiar velocity surveys is addressed here within a Bayesian framework by means of Hamiltonian Monte Carlo (HMC) sampling. The HAmiltonian Monte carlo reconstruction of the Local EnvironmenT (hamlet) algorithm is designed to reconstruct the linear large-scale density and velocity fields in conjunction with the undoing of lognormal bias in the derived distances and velocities of peculiar velocity surveys, such as the Cosmicflows (CF) data. The hamlet code has been tested against CF mock catalogues consisting of up to 3 × 104 data points with mock errors akin to those of the Cosmicflows-3 (CF3) data, within the framework of the Lambda cold dark matter standard model of cosmology. The hamlet code outperforms previous applications of Gibbs sampling Markov chain Monte Carlo reconstruction from the CF3 data by two to four orders of magnitude in CPU time. The gain in performance is due to the inherent higher efficiency of the HMC algorithm and due to parallel computing on GPUs rather than CPUs. This gain will enable an increase in the reconstruction of the large-scale structure from the upcoming CF4 data and the setting of constrained initial conditions for cosmological high-resolution simulations.
Semi-analytic spectral fitting: simultaneously modelling the mass accumulation and chemical evolution in MaNGA spiral galaxies
Authors: Zhou Shuang , Merrifield Michael , Aragón-Salamanca Alfonso 
Published: May 2022

Abstract
We develop a novel semi-analytic spectral fitting approach to quantify the star-formation histories (SFHs) and chemical enrichment histories (ChEHs) of individual galaxies. We construct simple yet general chemical evolution models that account for gas inflow and outflow processes as well as star formation, to investigate the evolution of merger-free star-forming systems. These models are fitted directly to galaxies’ absorption-line spectra, while their emission lines are used to constrain current gas phase metallicity and star formation rate. We apply this method to spiral galaxies selected from the SDSS-IV MaNGA survey. By fitting the co-added absorption-line spectra for each galaxy, and using the emission-line constraints on present-day metallicity and star formation, we reconstruct both the SFHs and the ChEHs for all objects in the sample. We can use these reconstructions to obtain archaeological measures of derived correlations such as the mass–metallicity relation at any redshift, which compare favourably with direct observations. We find that both the SFHs and ChEHs have strong mass dependence: massive galaxies accumulate their stellar masses and become enriched earlier. This mass dependence causes the observed flattening of the mass–metallicity relation at lower redshifts. The model also reproduces the observed gas-to-stellar mass ratio and its mass dependence. Moreover, we are able to determine that more massive galaxies have earlier gas infall times and shorter infall time-scales, and that the early chemical enrichment of low-mass galaxies is suppressed by strong outflows, while outflows are not very significant in massive galaxies.
Unveiling the nature of the unidentified gamma-ray sources 4FGL J1908.6+0915e, HESS J1907+089/HOTS J1907+091, and 3HWC J1907+085 in the sky region of the magnetar SGR 1900+14
Authors: Hnatyk B , Hnatyk R , Zhdanov V , Voitsekhovskyi V 
Published: May 2022

ABSTRACT
Supernova remnants (SNRs), star formation regions (SFRs), and pulsar wind nebulae (PWNe) are prime candidates for Galactic PeVatrons. The non-thermal high-energy (HE, ε &gt; 100 MeV) and very high-energy (VHE, ε &gt; 100 GeV) γ-ray emission from these sources should be a promising manifestation of acceleration processes. We investigate the possibility to explain the HE and VHE γ-ray emission from the sky region of the magnetar SGR 1900+14 as a signature of cosmic rays accelerated in above-mentioned sources. To this end, we simulate the γ-ray emission from the extended Fermi-LAT HE source 4FGL J1908.6+0915e, the extended VHE H.E.S.S. source candidate HOTS J1907+091, and the point-like HAWC TeV source 3HWC J1907+085, which are spatially coincident with the SNR G42.8+0.6, the magnetar SGR 1900+14, and the star-forming region W49A. The simulations are performed within the hadronic and leptonic models. We show that the observed γ-ray emission from the region of the magnetar SGR 1900+14 can, in principle, include contributions of different intensities from all three types of (potentially confused) sources. The considered in detail cases of a magnetar-connected but still undetected SNR and a PWN are the most promising ones, but with a serious requirement on the energy reserve of radiated CR particles – of the order of $10^{51}d_{\textrm {10kpc}}^{2}$ erg for sources at a distance of d ∼ 10 kpc. Such energy reserve can be provided by the magnetar-related hypernova and/or magnetar wind nebula remnant created by the newborn millisecond magnetar with the large supply of rotational energy Erot ∼ 1052 erg.
The UV 2175Å attenuation bump and its correlation with PAH emission at z ∼ 2
Authors: Shivaei Irene , Boogaard Leindert , Díaz-Santos Tanio , Battisti Andrew , da Cunha Elisabete , Brinchmann Jarle , Maseda Michael , Matthee Jorryt , Monreal-Ibero Ana , Nanayakkara Themiya , Popping Gergö , Vidal-García Alba , Weilbacher Peter M 
Published: May 2022

ABSTRACT
The UV bump is a broad absorption feature centred at 2175 Å that is seen in the attenuation/extinction curve of some galaxies, but its origin is not well known. Here, we use a sample of 86 star-forming galaxies at z = 1.7–2.7 with deep rest-frame UV spectroscopy from the MUSE HUDF Survey to study the connection between the strength of the observed UV 2175 Å bump and the Spitzer/MIPS 24 $\mu$m photometry, which at the redshift range of our sample probes mid-IR polycyclic aromatic hydrocarbon (PAH) emission at ∼6–8 μm. The sample has robust spectroscopic redshifts and consists of typical main-sequence galaxies with a wide range in stellar mass (log (M*/M⊙) ∼ 8.5–10.7) and star formation rates (SFRs; SFR$\sim 1\rm{-}100\, M_{\odot }\, {\rm yr}^{-1}$). Galaxies with MIPS detections have strong UV bumps, except for those with mass-weighted ages younger than ∼150 Myr. We find that the UV bump amplitude does not change with SFR at fixed stellar mass but increases with mass at fixed SFR. The UV bump amplitude and the PAH strength (defined as mid-IR emission normalized by SFR) are highly correlated and both also correlate strongly with stellar mass. We interpret these correlations as the result of the mass–metallicity relationship, such that at low metallicities PAH emission is weak due to a lower abundance of PAH molecules. The weak or complete absence of the 2175 Å bump feature on top of the underlying smooth attenuation curve at low mass/metallicities is then expected if the PAH carriers are the main source of the additional UV absorption.
Transcription feedback dynamics in the wake of cytoplasmic mRNA degradation shutdown
Authors: Chappleboim Alon , Joseph-Strauss Daphna , Gershon Omer , Friedman Nir 
Published: May 2022

AbstractIn the last decade, multiple studies demonstrated that cells maintain a balance of mRNA production and degradation, but the mechanisms by which cells implement this balance remain unknown. Here, we monitored cells’ total and recently-transcribed mRNA profiles immediately following an acute depletion of Xrn1—the main 5′-3′ mRNA exonuclease—which was previously implicated in balancing mRNA levels. We captured the detailed dynamics of the adaptation to rapid degradation of Xrn1 and observed a significant accumulation of mRNA, followed by a delayed global reduction in transcription and a gradual return to baseline mRNA levels. We found that this transcriptional response is not unique to Xrn1 depletion; rather, it is induced earlier when upstream factors in the 5′-3′ degradation pathway are perturbed. Our data suggest that the mRNA feedback mechanism monitors the accumulation of inputs to the 5′-3′ exonucleolytic pathway rather than its outputs.
AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms
Authors: Yang Yi , Mao Yufeng , Wang Ruoyu , Li Haoran , Liu Ye , Cheng Haijiao , Shi Zhenkun , Wang Yu , Wang Meng , Zheng Ping , Liao Xiaoping , Ma Hongwu 
Published: May 2022

Abstract
Advances in genetic manipulation and genome engineering techniques have enabled on-demand targeted deletion, insertion, and substitution of DNA sequences. One important step in these techniques is the design of editing sequences (e.g. primers, homologous arms) to precisely target and manipulate DNA sequences of interest. Experimental biologists can employ multiple tools in a stepwise manner to assist editing sequence design (ESD), but this requires various software involving non-standardized data exchange and input/output formats. Moreover, necessary quality control steps might be overlooked by non-expert users. This approach is low-throughput and can be error-prone, which illustrates the need for an automated ESD system. In this paper, we introduce AutoESD (https://autoesd.biodesign.ac.cn/), which designs editing sequences for all steps of genetic manipulation of many common homologous-recombination techniques based on screening-markers. Notably, multiple types of manipulations for different targets (CDS or intergenic region) can be processed in one submission. Moreover, AutoESD has an entirely cloud-based serverless architecture, offering high reliability, robustness and scalability which is capable of parallelly processing hundreds of design tasks each having thousands of targets in minutes. To our knowledge, AutoESD is the first cloud platform enabling precise, automated, and high-throughput ESD across species, at any genomic locus for all manipulation types.
Risk of intracranial hemorrhage with direct oral anticoagulants vs low molecular weight heparin in glioblastoma: A retrospective cohort study
Authors: Reed-Guy Lauren , Desai Arati S , Phillips Richard E , Croteau Desiree , Albright Karen , O’Neill Meghan , Brem Steven , O’Rourke Donald M , Amankulor Nduka M , Bagley Stephen J 
Published: May 2022

Abstract

Background
Glioblastoma (GBM) is associated with a high incidence of venous thromboembolism (VTE), but there are little data to guide anticoagulation in patients with GBM, in whom the risks of VTE must be balanced against the risk of intracranial hemorrhage (ICH).

Methods
We performed a single-institution retrospective cohort study of patients with GBM diagnosed with VTE from 2014 to 2021 who were treated with low molecular weight heparin (LMWH) or a direct oral anticoagulant (DOAC). The incidence of ICH was compared between the LMWH and DOAC groups. The primary outcome was clinically relevant ICH within the first 30 days of anticoagulation, defined as any ICH that was fatal, symptomatic, required surgical intervention, and/or led to cessation of anticoagulation. Secondary outcomes included clinically relevant ICH within 6 months, fatal ICH within 30 days and 6 months, and any bleeding within 30 days and 6 months.

Results
One hundred twenty-one patients were identified in the cohort for 30-day outcome analyses (DOAC, n = 33; LMWH, n = 88). For 6-month outcome analyses, the cohort included only patients who were maintained on their initial anticoagulant (DOAC, n = 32; LMWH, n = 75). The incidence of clinically relevant ICH at 30 days was 0% in the DOAC group and 9% in the LMWH group (P = .11). The cumulative incidence of clinically relevant ICH at 6 months was 0% in the DOAC group and 24% in the LMWH group (P = .001), with 4 fatal ICHs in the LMWH group.

Conclusions
DOACs are associated with a lower incidence of clinically relevant ICH in patients with GBM-associated VTE compared to LMWH.