bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feature selection for kernel methods in systems biology
Authors: Brouard Céline , Mariette Jérôme , Flamary Rémi , Vialaneix Nathalie 
Published: March 2022

AbstractThe substantial development of high-throughput biotechnologies has rendered large-scale multi-omics datasets increasingly available. New challenges have emerged to process and integrate this large volume of information, often obtained from widely heterogeneous sources. Kernel methods have proven successful to handle the analysis of different types of datasets obtained on the same individuals. However, they usually suffer from a lack of interpretability since the original description of the individuals is lost due to the kernel embedding. We propose novel feature selection methods that are adapted to the kernel framework and go beyond the well-established work in supervised learning by addressing the more difficult tasks of unsupervised learning and kernel output learning. The method is expressed under the form of a non-convex optimization problem with a ℓ1 penalty, which is solved with a proximal gradient descent approach. It is tested on several systems biology datasets and shows good performances in selecting relevant and less redundant features compared to existing alternatives. It also proved relevant for identifying important governmental measures best explaining the time series of Covid-19 reproducing number evolution during the first months of 2020. The proposed feature selection method is embedded in the R package mixKernel version 0.8, published on CRAN. Installation instructions are available at http://mixkernel.clementine.wf/.
New progress in zeolite synthesis and catalysis
Authors: Xu Hao , Wu Peng 
Published: March 2022

AbstractThe rational design synthesis of zeolite catalysts with effective, environmentally benign and atom-economic routes is a major topic in the field of microporous materials, as it would avoid the high labor cost and inefficiency of traditional trial-and-error methods in developing new structures and dispel environmental concerns regarding the industrial mass production of zeolites. Catalytic applications of zeolite materials have expanded from conventional single functionalities, such as solid acids or selective oxidation catalysts to bi/multifunctionalities through combination with metals or metal oxides. This is a response to new requirements from petrochemical and fine chemical industries, such as precise control of product distribution, conversion of low-carbon resources for chemical production, and solutions to increasingly severe environmental problems related to CO2 and NOx. Thus, based on the systematic knowledge of zeolite chemistry and science that researchers have acquired in the past half-century and the development requirements, remarkable progress has been made in zeolite synthesis and catalysis in the past 10 years. This includes the manipulation of zeolitic monolayers derived from layered zeolites and germanosilicates to construct novel zeolite materials and effective and green zeolite syntheses as well as the synergistic interaction of zeolites and metal/metal oxides with different space distributions in the conversion of low-carbon resources. With many zeolite catalysts and catalytic processes being developed, our understanding of the close relationship between zeolite synthesis, structure and catalytic properties has deepened. Researchers are gradually approaching the goal of rationally designing zeolite catalysts with precisely controlled activity and selectivity for particular applications.
Quality of Conduct and Reporting of Propensity Score Methods in Studies Investigating the Effectiveness of Antimicrobial Therapy
Authors: Eikenboom Anna M , Le Cessie Saskia , Waernbaum Ingeborg , Groenwold Rolf H H , de Boer Mark G J 
Published: March 2022

Abstract

Background
Propensity score methods are becoming increasingly popular in infectious disease medicine to correct for confounding in observational studies. However, applying and reporting propensity score techniques correctly requires substantial knowledge of these methods. The quality of conduct and reporting of propensity score methods in studies investigating the effectiveness of antimicrobial therapy is yet undetermined.

Methods
A systematic review was performed to provide an overview of studies (2005–2020) on the effectiveness of antimicrobial therapy that used propensity score methods. A quality assessment tool and a standardized quality score were developed to evaluate a subset of studies in which antibacterial therapy was investigated in detail. The scale of this standardized score ranges between 0 (lowest quality) and 100 (excellent).

Results
A total of 437 studies were included. The absolute number of studies that investigated the effectiveness of antimicrobial therapy and that used propensity score methods increased 15-fold between the periods 2005–2009 and 2015–2019. Propensity score matching was the most frequently applied technique (65%), followed by propensity score–adjusted multivariable regression (25%). A subset of 108 studies was evaluated in detail. The median standardized quality score per year ranged between 53 and 61 (overall range: 33–88) and remained constant over the years.

Conclusions
The quality of conduct and reporting of propensity score methods in research on the effectiveness of antimicrobial therapy needs substantial improvement. The quality assessment instrument that was developed in this study may serve to help investigators improve the conduct and reporting of propensity score methods.
New-Onset Dementia Among Survivors of Pneumonia Associated With Severe Acute Respiratory Syndrome Coronavirus 2 Infection
Authors: Qureshi Adnan I , Baskett William I , Huang Wei , Naqvi S Hasan , Shyu Chi-Ren 
Published: March 2022

Abstract

Background
Case series without control groups suggest that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may result in cognitive deficits and dementia in the postinfectious period.

Methods
Adult pneumonia patients with SARS-CoV-2 infection (index hospitalization) and age-, gender-, and race/ethnicity-matched contemporary control pneumonia patients without SARS-CoV-2 infection were identified from 110 healthcare facilities in United States. The risk of new diagnosis of dementia following &gt;30 days after the index hospitalization event without any previous history of dementia was identified using logistic regression analysis to adjust for potential confounders.

Results
Among 10 403 patients with pneumonia associated with SARS-CoV-2 infection, 312 patients (3% [95% confidence interval {CI}, 2.7%–3.4%]) developed new-onset dementia over a median period of 182 days (quartile 1 = 113 days, quartile 3 = 277 days). After adjustment for age, gender, race/ethnicity, hypertension, diabetes mellitus, hyperlipidemia, nicotine dependence/tobacco use, alcohol use/abuse, atrial fibrillation, previous stroke, and congestive heart failure, the risk of new-onset dementia was significantly higher with pneumonia associated with SARS-CoV-2 infection compared with pneumonia unrelated to SARS-CoV-2 infection (odds ratio [OR], 1.3 [95% CI, 1.1–1.5]). The association remained significant after further adjustment for occurrence of stroke, septic shock, and intubation/mechanical ventilation during index hospitalization (OR, 1.3 [95% CI, 1.1–1.5]).

Conclusions
Approximately 3% of patients with pneumonia associated with SARS-CoV-2 infection developed new-onset dementia, which was significantly higher than the rate seen with other pneumonias.
Risk Factors Associated With Hospitalization and Death in COVID-19 Breakthrough Infections
Authors: Suleyman Geehan , Fadel Raef , Brar Indira , Kassab Rita , Khansa Rafa , Sturla Nicholas , Alsaadi Ayman , Latack Katie , Miller Joseph , Tibbetts Robert , Samuel Linoj , Alangaden George , Ramesh Mayur 
Published: March 2022

Abstract

Background
Characterizations of coronavirus disease 2019 (COVID-19) vaccine breakthrough infections are limited. We aim to characterize breakthrough infections and identify risk factors associated with outcomes.

Methods
This was a retrospective case series of consecutive fully vaccinated patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a multicenter academic center in Southeast Michigan, between December 30, 2020, and September 15, 2021.

Results
A total of 982 patients were identified; the mean age was 57.9 years, 565 (59%) were female, 774 (79%) were White, and 255 (26%) were health care workers (HCWs). The median number of comorbidities was 2; 225 (23%) were immunocompromised. BNT162b2 was administered to 737 (75%) individuals. The mean time to SARS-CoV-2 detection was 135 days. The majority were asymptomatic or exhibited mild to moderate disease, 154 (16%) required hospitalization, 127 (13%) had severeâ&#x80;&#x93;critical illness, and 19 (2%) died. Age (odds ratio [OR], 1.14; 95% CI, 1.04â&#x80;&#x93;1.07; Pâ&#x80;&#x85;&lt;â&#x80;&#x85;.001), cardiovascular disease (OR, 3.02; 95% CI, 1.55â&#x80;&#x93;5.89; Pâ&#x80;&#x85;=â&#x80;&#x85;.001), and immunocompromised status (OR, 2.57; 95% CI, 1.70â&#x80;&#x93;3.90; Pâ&#x80;&#x85;&lt;â&#x80;&#x85;.001) were independent risk factors for hospitalization. Additionally, age (OR, 1.06; 95% CI, 1.02â&#x80;&#x93;1.11; Pâ&#x80;&#x85;=â&#x80;&#x85;.006) was significantly associated with mortality. HCWs (OR, 0.15; 95% CI, 0.05â&#x80;&#x93;0.50; Pâ&#x80;&#x85;=â&#x80;&#x85;.002) were less likely to be hospitalized, and prior receipt of BNT162b2 was associated with lower odds of hospitalization (OR, 0.436; 95% CI, 0.303â&#x80;&#x93;0.626; Pâ&#x80;&#x85;&lt;â&#x80;&#x85;.001) and/or death (OR, 0.360; 95% CI, 0.145â&#x80;&#x93;0.898; Pâ&#x80;&#x85;=â&#x80;&#x85;.029).

Conclusions
COVID-19 vaccines remain effective at attenuating disease severity. However, patients with breakthrough infections necessitating hospitalization may benefit from early treatment modalities and COVID-19-mitigating strategies, especially in areas with substantial or high transmission rates.
Resource allocation underlies parental decision-making during incubation in the Manx Shearwater
Authors: Gillies Natasha , Padget Oliver , Syposz Martyna , Bond Sarah , Guilford Tim 
Published: March 2022

Abstract
For many bird species, trade-offs in resource allocation become stark during incubation, when caring demands put into direct conflict their investment in reproduction versus survival. We demonstrate the critical importance of resource allocation, here measured indirectly as body mass, for incubation behavior in the Manx Shearwater (Puffinus puffinus), a biparentally-caring seabird. Using daily measurements of body mass from breeding pairs in combination with field observations and remotely collected behavioral data, we examined how changes in mass related to nest attendance and foraging behavior. We furthermore tested whether this differed between the sexes and between pairs of different breeding experience. We found that while body mass predicted the probability that incubating birds would choose to temporarily desert the nest, incubation shift duration was ultimately set by return of the foraging bird. The trip durations of foraging birds in turn were primarily dictated by their body mass reserves on departure from the nest. However, foragers appeared to account for the condition of the incubating partner by returning from sea earlier when their partner was in poor condition. This key finding suggests that decisions relating to resource allocation may be made cooperatively within the breeding pair during incubation. Our results contribute to understanding the mechanisms by which individuals regulate both their own and their partner’s incubation behavior, with implications for interacting with fine-scale resource availability.
La prévention et la prise en charge des complications aiguës de l’anémie falciforme
Authors: Beck Carolyn E , Trottier Evelyne D , Kirby-Allen Melanie , Pastore Yves 
Published: March 2022

RésuméL’anémie falciforme est une maladie multisystémique chronique qui exige des soins globaux. La falciformation des globules rouges entraîne une hémolyse et une occlusion vasculaire. L’anémie hémolytique, les syndromes douloureux et les atteintes organiques en sont des complications. En raison des profils d’immigration et d’une augmentation du dépistage néonatal, les professionnels de la santé pédiatrique du Canada doivent connaître l’anémie falciforme, tant dans les petits que les grands centres. Le présent document de principes porte sur les principes de prévention, de défense d’intérêts et de traitement rapide des complications aiguës courantes de l’anémie falciforme. Les lignes directrices comprennent l’état actuel du dépistage néonatal, les recommandations en matière de vaccination et de prophylaxie antibiotique et une introduction à l’hydroxyurée, un médicament qui réduit à la fois la morbidité et la mortalité chez les enfants atteints d’anémie falciforme. Des scénarios cliniques démontrent les principes de soins en cas de complications aiguës courantes : les épisodes vaso-occlusifs, le syndrome thoracique aigu, la fièvre, la séquestration splénique, les crises aplasiques et les accidents vasculaires cérébraux. Enfin, les principes de transfusion sanguine sont présentés, de même que les indications de transfusion simple ou d’exsanguinotransfusion.
Chest MRI with CT in the assessment of interstitial lung disease progression in patients with systemic sclerosis
Authors: Hochhegger Bruno , Lonzetti Lilian , Rubin Adalberto , de Mattos Juliane Nascimento , Verma Nupur , Mohammed Tan-Lucien H , Patel Pratik P , Marchiori Edson 
Published: March 2022

Abstract

Objective
To describe the performance of CT and MRI in the assessment of the progression of interstitial lung disease (ILD) associated with SSc and demonstrate the correlations of MRI with pulmonary function test (PFT) and CT scores.

Methods
This prospective single-centre observational study included patients with SSc diagnoses, and magnetic resonance (MR) images were assessed visually using the Scleroderma Lung Study (SLS) I system. Differences in the median scores were assessed with Student’s t-test and the Wilcoxon rank-sum test. Pearson’s and Spearman’s rank correlation coefficients were calculated to correlate imaging scores and PFT results. Using disease progression as the gold standard, we calculated the area under the curve (AUC) of the CT and MRI scores with Harrel’s c-index. The best thresholds for the prediction of disease progression were determined by receiver operating characteristic curve analysis with maximum Youden’s Index (P &lt; 0.05). The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the scores were calculated.

Results
The AUCs for MRI and CT scores were 0.86 (0.72–0.98; P = 0.04) and 0.83 (0.70–0.99; P = 0.05), respectively. CT and MRI scores correlated with Forced vital capacity (%FVC) (MRI: r = −0.54, P = 0.0045; CT: r = −0.44; P = 0.137) and diffusing capacity of the lung for carbon monoxide (MRI: r = −0.39, P = 0.007; CT r = −0.36, P = 0.006). The sensitivity, specificity, PPV and NPV were 85%, 87.5%, 88.34% and 86.11% (MRI score) and 84.21%, 82.35%, 84.14% and 82.4% (CT score), respectively.

Conclusions
MRI scores from patients with SSc may be an alternative modality for the assessment of ILD progression in patients with SSc.
The Association Between Executive Functioning and Personal Recovery in People With Psychotic Disorders
Authors: van Aken B C , Wierdsma A I , Voskes Y , Pijnenborg G H M , van Weeghel J , Mulder C L 
Published: March 2022

Abstract

Background
Recovery in psychotic disorder patients is a multidimensional concept that can include personal, symptomatic, societal, and functional recovery. Little is known about the associations between personal recovery (PR) and functional recovery (FR). FR involves a person’s ability to recover or compensate for impaired cognition, such as executive functions, and the loss of skills.

Method
In this cross-sectional study (the UP’S study), we used measures of executive functioning and personal recovery to assess a cohort of people with a psychotic disorder. PR was measured using the Recovering Quality of Life (ReQOL) and Individual Recovery Outcomes (I.ROC). FR was assessed using two forms of assessment. The Behavioral Rating Inventory of Executive Functioning Adult version (BRIEF-A) was used for self-rated executive functioning, and the Tower of London (TOL) for performance-based executive functioning. Regression models were calculated between executive functioning (BRIEF-A and TOL) and PR (ReQOL and I.ROC). Model selection was based on the Wald test.

Results
The study included data on 260 participants. While total scores of BRIEF-A had a small negative association with those of the ReQOL (β = −0.28, P &gt; .001) and the I.ROC (β = −0.41, P &gt; .001), TOL scores were not significantly associated with the ReQOL scores (β = 0.03, P = .76) and the I.ROC scores (β = 0.17, P = 0.17).

Conclusion
Self-reported EF, which measures the accomplishment of goal pursuit in real life was associated with PR. However, processing efficiency and cognitive control as measured by performance-based EF were not.
Frontal Electroencephalography Findings in Critically Ill COVID-19 Patients
Authors: Chang Brian A. , Cassim Tuan Z. , Mittel Aaron M. , Brambrink Ansgar M. , García Paul S. 
Published: March 2022

Background:
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) negatively impacts the central nervous system, and studies using a full montage of electroencephalogram (EEG) electrodes have reported nonspecific EEG patterns associated with coronavirus disease 2019 (COVID-19) infection. The use of this technology is resource-intensive and limited in its implementation. In this descriptive pilot study, we report neurophysiological patterns and the potential prognostic capability of an abbreviated frontal EEG electrode montage in critically ill COVID-19 patients.

Materials and Methods:
Patients receiving mechanical ventilation for SARS-CoV-2 respiratory failure were monitored with Sedline Root Devices using EEG electrodes were placed over the forehead. Qualitative EEG assessments were conducted daily. The primary outcome was mortality, and secondary outcomes were duration of endotracheal intubation and lengths of intensive care and hospitalization stay.

Results:
Twenty-six patients were included in the study, and EEG discontinuity was identified in 22 (84.6%) patients. The limited sample size and patient heterogeneity precluded statistical analysis, but certain patterns were suggested by trends in the data. Survival was 100% (4/4) for those patients in which a discontinuous EEG pattern was not observed. The majority of patients (87.5%, 7/8) demonstrating activity in the low-moderate frequency range (7 to 17 Hz) survived compared with 61.1% (11/18) of those without this observation.

Conclusions:
The majority of COVID-19 patients showed signs of EEG discontinuity during monitoring with an abbreviated electrode montage. The trends towards worse survival among those with EEG discontinuity support the need for additional studies to investigate these associations in COVID-19 patients.
Pediatric Supracondylar Humerus Fracture AAOS Appropriate Use Criteria: Does Treatment at a Pediatric Level I Trauma Center Comply?
Authors: Douleh Diana G. , Carry Patrick , Sanders Julia S. , Rhodes Jason T. 
Published: March 2022

Background:
The primary purpose of this analysis was to compare supracondylar humerus fracture (SCHF) treatment patterns at a single quaternary pediatric hospital relative to the American Academy of Orthopedic Surgeons (AAOS) appropriate use treatment recommendation(s).

Methods:
Among all fractures included in the cohort (n=571), the observed treatment approach was evaluated relative to the AAOS “Appropriate” treatment recommendation(s). The proportion, and corresponding 95% confidence interval, of cases that agreed with the “Appropriate” treatment recommendation was estimated. Demographics and clinical characteristics among cases that were managed in accordance with the “Appropriate,” “May be Appropriate,” or “Rarely Appropriate” were compared.

Results:
All fractures were treated according to the “Appropriate,” “May be Appropriate,” or “Rarely Appropriate” AAOS treatment guidelines. The observed treatment among fractures included in the cohort agreed with AAOS “Appropriate” recommendations in 92.1% [95% confidence interval (CI): 89.6%-94.2%] of the cases. Fracture type differed significantly between patients treated according to AAOS “Appropriate” recommendations compared to those treated according to “May be Appropriate,” or “Rarely Appropriate” recommendation.

Conclusions:
The treatment approach implemented at a single level 1 trauma center was in concordance with the appropriate use criteria treatment recommendations in a significant majority of cases. Fractures not treated according to “Appopriate” recommendations were primarily type IIA injuries, and were treated with closed reduction and casting instead of the recommended closed reduction and percutaneous pinning.

Level of Evidence:
Level III.
Minimal Out-Toeing and Good Hip Scores of Severe SCFE Patients Treated With Modified Dunn Procedure and Contralateral Prophylactic Pinning at Minimal 5-year Follow up
Authors: Lerch Till D. , Boschung Adam , Leibold Christiane , Kalla Roger , Kerkeni Hassen , Baur Heiner , Eichelberger Patric , Steppacher Simon D. , Liechti Emanuel F. , Siebenrock Klaus A. , Tannast Moritz , Ziebarth Kai 
Published: March 2022

Background:
Slipped capital femoral epiphyses (SCFE) is associated with out-toeing of the foot and external rotation gait. But it is unknown if SCFE patients treated with the modified Dunn procedure have out-toeing at follow up.
Therefore, we used instrumented gait analysis and questioned (1) do severe SCFE patients treated with a modified Dunn procedure have symmetrical foot progression angle (FPA) compared with contralateral side and compared with asymptomatic volunteers (2) what is the prevalence of out-toeing gait and what are the outcome socres at follow up.

Methods:
Gait analysis of 22 patients (22 hips) treated with an unilateral modified Dunn procedure for severe SCFE (slip angle >60 degrees, 2002 to 2011) was retrospectively evaluated. Of 38 patients with minimal 5-year follow up, 2 hips (4%) had avascular necrosis of the femoral head and were excluded for gait analysis. Twenty-two patients were available for gait analysis at follow up (mean follow up of 9±2 y). Mean age at follow up was 22±3 years. Mean preoperative slip angle was 64±8 degrees (33% unstable slips) and decreased postoperatively (slip angle of 8±4 degrees). Gait analysis was performed with computer-based instrumented walkway system (GAITRite) to measure FPA with embedded pressure sensors. Patients were compared with control group of 18 healthy asymptomatic volunteers (36 feet, mean age 29±6 y).

Results:
(1) Mean FPA of SCFE patients (3.6±6.4 degrees) at follow up was not significantly different compared with their contralateral side (5.6±5.5 degrees) and compared with FPA of controls (4.0±4.5 degrees). (2) Of the 22 SCFE patients, most of them (19 hips, 86%) had normal FPA (−5 to 15 degrees), 2 patients had in-toeing (FPA<−5 degrees) and 1 had out-toeing (FPA >15 degrees) and was not significantly different compared with control group. (3) Mean modified Harris hip score (mHHS) was 93±11 points, mean Hip Disability and Osteoarthritis Outcome Score (HOOS) score was 91±10 points. Three patients (14%) had mHHS <80 points and walked with normal FPA. The 2 patients with in-toeing and one patient with out-toeing had mHHS >95 points.

Conclusions:
Patients with severe SCFE treated with modified Dunn procedure had mostly symmetrical FPA and good hip scores at long term follow up. This is in contrast to previous studies. Although 1 patient had out-toeing and 2 patients had in-toeing at follow up, they had good hip scores.

Level of Evidence:
Level III—retrospective comparative study.