bluuebunny/crossref_metadata_2025_split huggingface dataset:
SmMIP-tools: a computational toolset for processing and analysis of single-molecule molecular inversion probes-derived data
Authors: Medeiros Jessie J F , Capo-Chichi Jose-Mario , Shlush Liran I , Dick John E , Arruda Andrea , Minden Mark D , Abelson Sagi 
Published: February 2022

Abstract

Motivation
Single-molecule molecular inversion probes (smMIPs) provide an exceptionally cost-effective and modular approach for routine or large-cohort next-generation sequencing. However, processing the derived raw data to generate highly accurate variants calls remains challenging.

Results
We introduce SmMIP-tools, a comprehensive computational method that promotes the detection of single nucleotide variants and short insertions and deletions from smMIP-based sequencing. Our approach delivered near-perfect performance when benchmarked against a set of known mutations in controlled experiments involving DNA dilutions and outperformed other commonly used computational methods for mutation detection. Comparison against clinically approved diagnostic testing of leukaemia patients demonstrated the ability to detect both previously reported variants and a set of pathogenic mutations that did not pass detection by clinical testing. Collectively, our results indicate that increased performance can be achieved when tailoring data processing and analysis to its related technology. The feasibility of using our method in research and clinical settings to benefit from low-cost smMIP technology is demonstrated.

Availability and implementation
The source code for SmMIP-tools, its manual and additional scripts aimed to foster large-scale data processing and analysis are all available on github (https://github.com/abelson-lab/smMIP-tools). Raw sequencing data generated in this study have been submitted to the European Genome-Phenome Archive (EGA; https://ega-archive.org) and can be accessed under accession number EGAS00001005359.

Supplementary information
Supplementary data are available at Bioinformatics online.
Grey matter network markers identify individuals with prodromal Alzheimer’s disease who will show rapid clinical decline
Authors: Pelkmans Wiesje , Vromen Ellen M. , Dicks Ellen , Scheltens Philip , Teunissen Charlotte E. , Barkhof Frederik , van der Flier Wiesje M. , Tijms Betty M. ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: February 2022

AbstractIndividuals with prodromal Alzheimer’s disease show considerable variability in rates of cognitive decline, which hampers the ability to detect potential treatment effects in clinical trials. Prognostic markers to select those individuals who will decline rapidly within a trial time frame are needed. Brain network measures based on grey matter covariance patterns have been associated with future cognitive decline in Alzheimer’s disease. In this longitudinal cohort study, we investigated whether cut-offs for grey matter networks could be derived to detect fast disease progression at an individual level. We further tested whether detection was improved by adding other biomarkers known to be associated with future cognitive decline [i.e. CSF tau phosphorylated at threonine 181 (p-tau181) levels and hippocampal volume]. We selected individuals with mild cognitive impairment and abnormal CSF amyloid β1–42 levels from the Amsterdam Dementia Cohort and the Alzheimer’s Disease Neuroimaging Initiative, when they had available baseline structural MRI and clinical follow-up. The outcome was progression to dementia within 2 years. We determined prognostic cut-offs for grey matter network properties (gamma, lambda and small-world coefficient) using time-dependent receiver operating characteristic analysis in the Amsterdam Dementia Cohort. We tested the generalization of cut-offs in the Alzheimer’s Disease Neuroimaging Initiative, using logistic regression analysis and classification statistics. We further tested whether combining these with CSF p-tau181 and hippocampal volume improved the detection of fast decliners. We observed that within 2 years, 24.6% (Amsterdam Dementia Cohort, n = 244) and 34.0% (Alzheimer’s Disease Neuroimaging Initiative, n = 247) of prodromal Alzheimer’s disease patients progressed to dementia. Using the grey matter network cut-offs for progression, we could detect fast progressors with 65% accuracy in the Alzheimer’s Disease Neuroimaging Initiative. Combining grey matter network measures with CSF p-tau and hippocampal volume resulted in the best model fit for classification of rapid decliners, increasing detecting accuracy to 72%. These data suggest that single-subject grey matter connectivity networks indicative of a more random network organization can contribute to identifying prodromal Alzheimer’s disease individuals who will show rapid disease progression. Moreover, we found that combined with p-tau and hippocampal volume this resulted in the highest accuracy. This could facilitate clinical trials by increasing chances to detect effects on clinical outcome measures.
Enhancing well-being and social connectedness of rural communities through community shops
Authors: Finegan Trish , Cawley Buckley Morgan 
Published: February 2022

Abstract
This article evaluates the impact of a community development initiative to establish a network of community shops across County Kilkenny, Ireland. Specifically, this research investigates the impact of this initiative on community well-being in two localities. Data were gathered through multi-site semi-structured interviews with community workers and members. Respondents self-reported a perceptible improvement in individual and community well-being. The primary drivers of this process are identified as social connectedness, intergenerational contacts and emotional support. This research is an important early contribution to a relatively small body of research literature on community shops, particularly in Ireland. Furthermore, as community shops are increasingly recognized as effective resources in community development strategies, it is now critical to conduct analytical and qualitative work on their impact from the perspective of community member’s lived experience.
Navigating through the storm: conservancies as local institutions for regional resilience in Zambezi, Namibia
Authors: Hulke Carolin , Kalvelage Linus , Kairu Jim , Revilla Diez Javier , Rutina Lucas 
Published: February 2022

Abstract
The COVID-19 pandemic has disrupted global production networks and challenged the resilience of regional economies to external shocks. The tourism sector was severely affected by the travel bans imposed, as were regions characterised by tourism development, such as Zambezi in northern Namibia. Nonetheless, with the support of the national government, conservancies, as local governance institutions, partly maintained the distribution of value from tourism throughout the pandemic and strengthened agriculture-tourism linkages to achieve long-term transformation. These findings suggest that local institutions are able to create regional resilience through their capacity to drive adaptation and adaptability in a diversified regional economy.
The association between time to extracorporeal cardiopulmonary resuscitation and outcome in patients with out-of-hospital cardiac arrest
Authors: Kawakami Shoji , Tahara Yoshio , Koga Hidenobu , Noguchi Teruo , Inoue Shujiro , Yasuda Satoshi 
Published: February 2022

Abstract

Aims
Extracorporeal cardiopulmonary resuscitation (ECPR) is considered for potentially reversible out-of-hospital cardiac arrest (OHCA). However, the association between time to ECPR and outcome has not been well established.

Methods and results
Between June 2014 and December 2017, we enrolled 34 754 OHCA patients in a multicentre, prospective fashion [Japanese Association for Acute Medicine (JAAM)-OHCA registry]. After the application of exclusion criteria, 695 OHCA patients who underwent ECPR for cardiac causes were eligible for this study. We investigated the association between the call-to-ECPR interval and favourable neurological outcome (cerebral performance category 1 or 2) at 30 days. Seventy-seven patients (11%) had a favourable neurological outcome at 30 days. The call-to-ECPR intervals in these patients were significantly shorter than in those with an unfavourable neurological outcome [49 (41–58) vs. 58 (48–68) min, respectively, P &lt; 0.001]. A longer call-to-ECPR interval was associated with a smaller proportion of patients undergoing percutaneous coronary intervention (PCI) (P = 0.034) or target temperature management (TTM) (P &lt; 0.001). Stepwise multivariable logistic regression analysis revealed that the call-to-ECPR interval was an independent predictor of favourable neurological outcome [odds ratio (OR) 0.96, 95% confidence interval (CI) 0.94–0.99, P = 0.001], as were age, male gender, initial shockable rhythm, transient return of spontaneous circulation in the prehospital setting, arterial pH at hospital arrival, PCI (OR 2.30, 95% CI 1.14–4.66, P = 0.019), and TTM (OR 2.28, 95% CI 1.13–4.62, P = 0.019).

Conclusion
A shorter call-to-ECPR interval and implementation of PCI and TTM predicted a favourable neurological outcome at 30 days in OHCA patients who underwent ECPR for cardiac causes.
Can Population III stars be major origins of both merging binary black holes and extremely metal poor stars?
Authors: Tanikawa Ataru , Chiaki Gen , Kinugawa Tomoya , Suwa Yudai , Tominaga Nozomu 
Published: February 2022

Abstract
Population (Pop) III stars, first stars, or metal-free stars are made of primordial gas. We have examined if they can be dominant origins of merging binary black holes (BHs) and extremely metal-poor (EMP) stars. The abundance pattern of EMP stars is helpful to trace back the properties of Pop III stars. We have confirmed previous arguments that the observed BH merger rate needs Pop III star formation efficiency 10 times larger than theoretically predicted values, while the cosmic reionization history still permits such a high Pop III star formation efficiency. On the other hand, we have newly found that the elemental abundance pattern of EMP stars only allows the Pop III initial mass function with the minimum mass of ∼15–27 M$_{\odot}$. In other words, the minimum mass must not deviate largely from the critical mass below and above which Pop III stars leave behind neutron stars and BHs, respectively. Pop III stars may still be a dominant origin of merging binary BHs but our study has reduced the allowed parameter space under the hypothesis that EMP stars are formed from primordial gas mixed with Pop III supernova ejecta.
Measurements of chromospheric Mg i emission lines of zero-age main-sequence stars
Authors: Yamashita Mai , Itoh Yoichi 
Published: February 2022

Abstract
The chromosphere is the active atmosphere in which energetic eruption events, such as flares, occur. Chromospheric activity is driven by the magnetic field generated by stellar rotation and convection. The relationship between chromospheric activity and the Rossby number, the ratio of the rotational period to the convective turnover time, has been extensively examined for many types of stars, by using narrow chromospheric emission lines, such as the Ca ii lines and the Mg ii H and K lines. However, the stars with small Rossby numbers, i.e., stars with rapid rotations and/or long convective turnover times, show constant strengths of such lines against the Rossby number. In this study, we investigate the infrared Mg i emission lines at 8807 Å of 47 zero-age main-sequence (ZAMS) stars in IC 2391 and IC 2602 using the archive data of the Anglo-Australian Telescope at the University College London Echelle Spectrograph. After subtracting the photospheric absorption component, the Mg i line is detected as an emission line for 45 ZAMS stars, the equivalent widths of which are between 0.02 Å and 0.52 Å. A total of 42 ZAMS stars show the narrower Mg i emission lines instead of the Ca ii infrared triplet emission lines, suggesting that they are formed at different depths. The ZAMS stars with smaller Rossby numbers show stronger Mg i emission lines. The Mg i emission line is not saturated even in the saturated regime of the Ca ii emission lines, i.e., Rossby number &lt;10−1.1. The Mg i emission line is considered to be a good indicator of chromospheric activity, particularly for active objects.
Welfare and Redistribution in Residential Electricity Markets with Solar Power
Authors: Feger Fabian , Pavanini Nicola , Radulescu Doina 
Published: February 2022

Abstract
An increasing number of households installing solar panels and consuming the energy thus produced raises two challenges for regulators: network financing and vertical equity. We propose alternative tariff and subsidy designs for policymakers to incentivize solar panel adoptions and guarantee that network costs are recovered, while trading off efficiency, equity, and welfare motives. We estimate a structural model of energy demand and solar panel adoption, using a unique matched dataset on energy consumption, prices, income, wealth, solar panel installations, and building characteristics for 165,000 households in Switzerland from 2008 to 2014. Our counterfactuals recommend the optimal solar panel installation cost subsidies and two-part energy tariffs to achieve a solar energy target. We show that, relative to installation cost subsidies, relying on marginal prices to incentivize solar panel adoptions is more cost efficient and progressive across the income distribution, but generates a larger aggregate welfare loss.
Personalized management for unmet needs with food allergy
Authors: Miura Yoko , Yanagida Noriyuki , Sato Sakura , Ebisawa Motohiro 
Published: February 2022

Purpose of review
Patients with food allergies are at risk of experiencing accidental allergic symptoms in real life. Low thresholds may be a risk factor for accidental allergic reactions. Therefore, the evaluation of this threshold is required for the management of food allergies. We have suggested a management approach to identify the threshold dose and the consumable dose, considering patient age and the severity of food allergies.

Recent findings
A younger age is a risk factor for accidental allergic reactions, and school-age children are likely to have a lower quality of life (QOL) than younger children. Additionally, patients with a low threshold may have difficulty in acquiring tolerance. We performed a stepwise oral food challenge (OFC) to evaluate the threshold and consumable doses for patients with food allergies. Performing a low-dose OFC for the first step would identify the dose that could be consumed at home safely and avoid the complete elimination of allergic foods. Identifying the threshold dose would be effective in managing the risk of accidental ingestion. For patients who react to low-dose OFC, low-dose oral immunotherapy (OIT) would be expected to prevent the experience of allergic reactions by accidental ingestion and consume medium doses safely.

Summary
For food allergy patients and their caregivers, identifying the consumable dose would help manage the diet and eliminate their anxiety. Low-dose OFC and low-dose OIT are effective and well tolerated, which would improve their QOL. Considering the severity of food allergy and age, determining a safe threshold with no reactions would meet the unmet needs of patients with food allergy.
3D Radiological Outcomes and Quality of Life of Patients With Moderate Idiopathic Scoliosis Treated With Anterior Vertebral Growth Modulation Versus Bracing: Two-Year Follow-up
Authors: Duarte Matias Pereira , Aubin Carl-Eric , Cobetto Nikita , Roy-Beaudry Marjolaine , Bellefleur Christian , Turgeon Isabelle , Labelle Hubert , Guy Aymeric , Barchi Soraya , Parent Stefan 
Published: February 2022

Study Design.
Observational cohort study.

Objective.
To test the hypothesis that anterior vertebral body growth modulation (AVBGM) achieves 3D deformity correction after 2-year follow-up while brace treatment limits curve progression for moderate idiopathic scoliosis (30–50°).

Summary of Background Data.
For idiopathic scoliosis, bracing and AVBGM have overlapping indications in skeletally immature patients with moderate scoliosis curve angles, creating a grey zone in clinical practice between them. The relative 3D deformity control performance over a 2-year period between these fusionless treatments is still uncertain.

Methods.
A retrospective review of a prospective idiopathic scoliosis patients database, recruited between 2013 and 2018 was performed. Inclusion criteria were skeletally immature patients (Risser 0–2), with Cobb angles between 30° and 50° and a 2-year follow-up after bracing or AVBGM. 3D radiological parameters and health related quality of life (HRQoL) scores were evaluated. Unpaired t test was used.

Results.
Thirty nine patients (12.7 ± 1.3 y.o.) with Cobb angles more than or equal to 30° treated with brace and 41 patients (11.8 ± 1.2 y.o.) with presenting Cobb angles less than or equal to 50° who received AVBGM were reviewed. The statistical analysis of 3D deformity measurements showed that at 2-year follow-up, only the 3D spine length and both sides apical vertebral heights changed significantly with brace treatment. While AVBGM treatment achieved statistically significant correction differences in thoracic and lumbar Cobb angles, TrueKyphosis, 3D spine length, and selective left apical vertebral height (P< 0.05). 35% of brace patients had a curve progression of more than 5° at final follow-up while it was 0% for AVBGM. HRQoL assessment showed no statistically significant differences between pre and post SRS-22 total scores for each group (P > 0.05).

Conclusion.
Even though these two cohorts are not fully comparable, bracing seems to control progression for a significant portion of patients with moderate scoliosis curves, while AVBGM significantly corrected and maintained 3D deformity parameters at 2-year follow-up.
Compromised Integrity, Burnout, and Intent to Leave the Job in Critical Care Nurses and Physicians
Authors: LeClaire Michele , Poplau Sara , Linzer Mark , Brown Roger , Sinsky Christine 
Published: February 2022

OBJECTIVES:
To describe relationships between compromised integrity (CI), burnout, and intent-to-leave (ITL) practice in critical care (CC) and noncritical care (non-CC) nurses and physicians.

DESIGN:
CC nurses (RNs) and physicians (MDs) from the American Medical Association Coping with COVID survey were matched by gender, race, years in practice, and role with non-CC clinicians to determine likelihood of ITL in relation to burnout and CI.

SETTING:
U.S. Healthcare organizations; July—December 2020.

SUBJECTS:
One hundred sixty-five CC RNs and 148 CC MDs (n = 313) matched with 165 non-CC RNs and 148 non-CC MDs from 83 healthcare organizations.

MEASUREMENTS AND MAIN RESULTS:
Burnout was measured with a single, validated question that mainly reflects emotional exhaustion (EE), and CI was determined by asking if respondents worried about doing things that compromised their integrity moderately or to a great extent. ITL included those moderately, likely, or definitely, intending to leave. Burnout correlated strongly with CI (tetrachoric r = 0.704 [0.606–0.803]; P < 0.001). Of 626 subjects, 59% experienced burnout, 24% CI, and 33% ITL. CC RNs experienced burnout more often (76%) than non-CC RNs (62%; P < 0.01) and CC MDs (51%; P < 0.001). CI was more frequent in CC RNs (44%) than non-CC RNs (23%) and CC MDs (16%; P < 0.001). In multivariate regressions, CC clinicians experiencing burnout had 50% greater odds of ITL than non-CC clinicians experiencing burnout; odds of ITL were substantially higher (odds ratio, 2.8–3.2) in those with CI regardless of location or burnout. In the ICU, those feeling valued by their organization had one-third the odds of ITL.

CONCLUSIONS:
Burnout (EE) is high (>50%) among CC RNs and MDs, which may result in losses of CC clinicians while demand rises. Preventing CI independent of burnout may reduce turnover in all settings and especially in ICUs. Feeling valued may promote staff retention.
Stereotactic Body Radiotherapy and Systemic Dose Chemotherapy for Locally Advanced Lung Cancer
Authors: Kubicek Gregory J. , Khrizman Polina , Squillante Christian , Callahan Kevin , Xu Qianyi , Abouzgheib Wissam , Boujaoude Ziad , Patel Ashish , Hageboutros Alexander 
Published: February 2022

Purpose:
This is a single arm phase 2 study (Clinical trials.gov NCT02568033) to examine the role of stereotactic body radiotherapy (SBRT) along with full dose systemic chemotherapy in the treatment of unresectable stage 2 and stage 3 nonsmall cell lung cancer. Primary endpoints are disease free survival and toxicity.

Materials:
Patients were treated with SBRT to all sites of gross disease. Dosing consisted of 60 Gy in 3 fractions for peripheral lung tumors, 50 Gy in 5 fractions for central lung tumors, and 40 to 50 Gy in 5 fractions for hilar and mediastinal lymph nodes. Chemotherapy consisted of 4 cycles of pemetrexed and cisplatin or carboplatin and paclitaxel for nonsquamous histology and cisplatin and docetaxel or cisplatin and paclitaxel for squamous histology. SBRT was given in between the chemotherapy cycles. There was a 7 days break between chemotherapy and SBRT. Quality of life was measured using functional assessment of cancer therapy-lung.

Results:
Twenty two patients were enrolled and analyzed. Seventeen (77%) were stage III and 19 (86%) had lymph node involvement. Median follow-up for all patients was 23.1 months. Median overall survival is 27.2 months. Overall survival at 1 year was 82% and overall survival at 2 years was 53%. Median disease free survival is 16.0 months with a 2-year regional failure rate of 19% and 2-year distant failure rate of 47.2%. There were 6 grade 3 acute toxicities and 2 late grade 3 or higher toxicities including 1 grade 5 hemoptysis. Quality of life scores were unchanged compared with baseline.

Conclusion:
A combination of SBRT and full dose chemotherapy appears to be a safe and effective treatment for locally advanced NSCLC and warrants further investigation.
Short-Term Follow-Up of a Randomized Controlled Trial of 0.5% and 5% 5-Fluorouracil After Microneedling for Treatment of Facial Actinic Keratoses
Authors: Kalil Célia Luiza Petersen Vitello , Reinehr Clarissa Prieto Herman , Bakos Renato Marchiori 
Published: February 2022

INTRODUCTION
Topical 5-fluorouracil (5-FU) is used to treat actinic keratosis, although side effects limit treatment. Microneedling might be a tool for reducing treatment duration.

OBJECTIVE
To evaluate microneedling to promote 5-FU delivery at different concentrations (0.5% and 5%) for actinic keratoses (AKs) treatment.

METHODS
Forty-four patients with facial AKs subjected to 1.0 mm microneedling on 1 side of the face were randomized into 5% 5-FU or 0.5% 5-FU groups. Evaluations of efficacy and safety were conducted on days 21 and 111.

RESULTS
Forty-four patients aged 47 to 85 years were enrolled. Complete clearance of AKs was similar within groups for the side of the face treated with microneedling and 5-FU and the side treated with 5-FU alone in both the 5% and 0.5% 5-FU groups. Microneedling and 5% 5-FU was superior to microneedling and 0.5% 5-FU to reduce AKs (p = .025). Microneedling and 5% 5-FU resulted in fewer adverse effects than 5% 5-FU alone (p = .011).

CONCLUSION
Topical 5% and 0.5% 5-FU delivery for 3 days after microneedling was effective for treating facial AKs and equivalent to 5% and 0.5% 5-FU alone for 15 days after 3 months of follow-up. Microneedling may potentiate 5-FU treatment, reducing treatment time without losing efficacy.