bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterising the area under the curve loss function landscape
Authors: Niroomand Maximilian P , Cafolla Conor T , Morgan John W R , Wales David J 
Published: January 2022

Abstract
One of the most common metrics to evaluate neural network classifiers is the area under the receiver operating characteristic curve (AUC). However, optimisation of the AUC as the loss function during network training is not a standard procedure. Here we compare minimising the cross-entropy (CE) loss and optimising the AUC directly. In particular, we analyse the loss function landscape (LFL) of approximate AUC (appAUC) loss functions to discover the organisation of this solution space. We discuss various surrogates for AUC approximation and show their differences. We find that the characteristics of the appAUC landscape are significantly different from the CE landscape. The approximate AUC loss function improves testing AUC, and the appAUC landscape has substantially more minima, but these minima are less robust, with larger average Hessian eigenvalues. We provide a theoretical foundation to explain these results. To generalise our results, we lastly provide an overview of how the LFL can help to guide loss function analysis and selection.
Telogator: a method for reporting chromosome-specific telomere lengths from long reads
Authors: Stephens Zachary , Ferrer Alejandro , Boardman Lisa , Iyer Ravishankar K , Kocher Jean-Pierre A 
Published: January 2022

Abstract

Motivation
Telomeres are the repetitive sequences found at the ends of eukaryotic chromosomes and are often thought of as a ‘biological clock,’ with their average length shortening during division in most cells. In addition to their association with senescence, abnormal telomere lengths are well known to be associated with multiple cancers, short telomere syndromes and as risk factors for a broad range of diseases. While a majority of methods for measuring telomere length will report average lengths across all chromosomes, it is known that aberrations in specific chromosome arms are biomarkers for certain diseases. Due to their repetitive nature, characterizing telomeres at this resolution is prohibitive for short read sequencing approaches, and is challenging still even with longer reads.

Results
We present Telogator: a method for reporting chromosome-specific telomere length from long read sequencing data. We demonstrate Telogator’s sensitivity in detecting chromosome-specific telomere length in simulated data across a range of read lengths and error rates. Telogator is then applied to 10 germline samples, yielding a high correlation with short read methods in reporting average telomere length. In addition, we investigate common subtelomere rearrangements and identify the minimum read length required to anchor telomere/subtelomere boundaries in samples with these haplotypes.

Availability and implementation
Telogator is written in Python3 and is available at github.com/zstephens/telogator.

Supplementary information
Supplementary data are available at Bioinformatics online.
Magnetic Solid-Phase Extraction Based on Magnetite-Multiwalled Carbon Nanotubes of Non-Steroidal Anti-Inflammatories from Water Followed by LC–ESI–MS/MS
Authors: Hsen Ele Ben , Latrous Latifa 
Published: January 2022

Abstract
An analytical method based on liquid chromatography–electrospray ionization–tandem mass spectrometry detection (LC–ESI–MS/MS) has been developed for the determination of pharmaceutical compounds in water samples. Five non-steroidal anti-inflammatory drugs (NSAIDs) namely Naproxen, Ketoprofen, Piroxicam, Diflunisal and Celecoxib were investigated. Magnetic solid phase extraction (MSPE) was used for sample pre concentration of water samples and magnetic carbon nanotubes (Fe3O4-MWCNTs) were considered as solid phase extraction sorbent. Important parameters influencing the extraction efficiency such as nature and volume of eluent, sample pH and adsorbent mass were optimized. The developed MSPE method involved 75 mg of Fe3O4-MWCNTs sorbent, 5 mL of water sample at pH = 4 and 5 mL of 10% ammonia in methanol in the elution step. Under the optimized extraction conditions, linearity, detection and quantification limits and reproducibility were evaluated. The proposed method was successfully applied to the analysis of NSAIDs in surface waters, and mean recoveries of all the NSAIDs were above 90% with relative standard deviations &lt; 17%. The detection and quantification limits were comprised between 0.05–3.6 ng.mL−1 and 0.2–11.9 ng.mL−1, respectively.
Evidence of chronic kidney injury in patients not meeting KDIGO criteria for chronic kidney disease
Authors: Alvarez-Llamas Gloria , Santiago-Hernandez Aranzazu , Ruilope Luis M 
Published: January 2022

ABSTRACT
Subjects not meeting KDIGO criteria for chronic kidney disease (CKD), i.e. normoalbuminuric (urinary albumin:creatinine ratio, UACR &lt;30 mg/g) individuals with an estimated glomerular filtration rate &gt;60 mL/min/1.73 m2, are considered at no increased cardiovascular or kidney risk associated with kidney disease, but the incidence of subclinical atherosclerosis, cardiovascular events and CKD progression is already increased in the high-normal UACR range (10–30 mg/g). Earlier intervention in this subclinical pre-CKD stage may diminish cardiorenal risk. However, tools to predict albuminuria development and to identify those subjects who will benefit most from intervention are limited. Recent data have identified urine molecular changes within the normoalbuminuria condition, consisting of an altered urinary peptidome, proteome and metabolome, which represent subclinical organ damage and processes such as inflammation, oxidative stress, tricarboxylic acids cycle deregulation, impaired fatty acids β-oxidation or defective tubular reabsorption.
Investigation of European modular façade system utilizing renewable energy
Authors: Li Yangluxi , Chen Lei 
Published: January 2022

Abstract
The purpose of this investigation is to summarize modular façade construction using renewable energy features in different aspects. Researches done so far primarily focusing on building envelop have shown various constructions of building enclosure without energy usage. This paper mainly focuses on modular façade renovation system programmes of European Horizon 2020 [34] and IEA ECBCS Annex 50 Prefabricated Systems for Low Energy Renovation of Residential Buildings in terms of construction, material, installation and thermal performance. Four aspects of construction, material, installation and thermal performance are adopted to evaluate these practices. Related website, paper and report from European commission constitute the database providing for review. Final results illustrate that all modular façade systems mentioned above could be classified into three layers: interior; module and exterior layer, taking charge of disparate functions. Both insulation and energy usage achieve the innovative envelop constructions manufacture. Integrating the renewable energy resources utilization technique into insulated building façade system is the core of this innovative projects achievement.
Fatal Intoxication by the Novel Cathinone 4-Fluoro-3-methyl-α-PVP
Authors: Hobbs Jennifer M , DeRienz Rebecca T , Baker Daniel D , Shuttleworth Morgan R , Pandey Maneesha 
Published: January 2022

Abstract
A 30 year old non-hispanic white male was found unresponsive at his workplace and admitted to the hospital in cardiac arrest. He was pronounced deceased shortly after arrival. At autopsy the pathologist noted a 176 pound, well-nourished, atraumatic, adult male with significant bilateral frothy pulmonary edema (right lung 930 g and left lung 1,130 g), cardiomegaly (430 g), dilated ventricles and slight cerebral edema. Upon completion of the systematic toxicological analysis scope for the Franklin County Coroner’s Office Toxicology Laboratory, no known drugs were found. Further review of the gas chromatography--mass spectrometry (GC--MS) full-scan library summary reports showed an unknown peak in both the blood and urine solid phase extracts. An analogue of α-pyrrolidinovalerophenone (α-PVP) was identified, and a GC--MS selected ion monitoring method was developed to identify and quantitate the presence of 4-fluoro-3-methyl-α-PVP. This method quantified the drug at 26 ng/mL in gray top femoral blood, 30 ng/mL in purple top heart blood and 20 ng/mL in red top vitreous humor. Qualitative presence was also observed in the urine but was not detected in the liver. The decedent’s cause of death was determined to be due to fluoro-methyl-PVP toxicity and the manner was ruled to be accidental. Investigational follow-up interviews corroborated drug use by the deceased with a preference of research chemicals and synthetic cannabinoids via the internet. No published literature is available currently, and to the author’s knowledge this is the first incident of a fatal death solely attributed to this substituted cathinone.
Improved binary gaining–sharing knowledge-based algorithm with mutation for fault section location in distribution networks
Authors: Xiong Guojiang , Yuan Xufeng , Mohamed Ali Wagdy , Chen Jun , Zhang Jing 
Published: January 2022

AbstractFault section location (FSL) plays a critical role in shortening blackout time and restoring power supply for distribution networks. This paper converts the FSL task into a binary optimization problem using the feeder terminal unit (FTU) information. The discrepancy between the reported overcurrent alarms and the expected overcurrent states of the FTUs is adopted as the objective function. It is a typical 0–1 combinatorial optimization problem with many local optima. An improved binary gaining–sharing knowledge-based algorithm (IBGSK) with mutation is proposed to effectively solve this challenging binary optimization problem. Since the original GSK cannot be applied in binary search space directly, and it is easy to get stuck in local optima, IBGSK encodes the individuals as binary vectors instead of real vectors. Moreover, an improved junior gaining and sharing phase and an improved senior gaining and sharing phase are designed to update individuals directly in binary search space. Furthermore, a binary mutation operator is presented and integrated into IBGSK to enhance its global search ability. The proposed algorithm is applied to two test systems, i.e. the IEEE 33-bus distribution network and the USA PG&E 69-bus distribution network. Simulation results indicate that IBGSK outperforms the other 12 advanced algorithms and the original GSK in solution quality, robustness, convergence speed, and statistics. It equilibrates the global search ability and the local search ability effectively. It can diagnose different fault scenarios with 100% and 99% success rates for these two test systems, respectively. Besides, the effect of mutation probability on IBGSK is also investigated, and the result suggests a moderate value. Overall, simulation results demonstrate that IBGSK shows highly promising potential for the FSL problem of distribution networks.
Gastrointestinal duplication masquerading as intussusception in an adult
Authors: Nguyen Patricia , Azar Robert , Starley Greg , Scharff Elana 
Published: January 2022

Abstract
Gastrointestinal duplication is a rare congenital condition that involves tissues anywhere along the alimentary tract. It may also be referred to as enteric duplication or alimentary tract duplication. It typically presents in children and is hardly found in adults because the presentation varies and the diagnosis is often incidental. Surgical resection is generally indicated to prevent future complications. We present a case of duplicated small bowel discovered during surgery in a young female with the initial diagnosis of small bowel intussusception on CT.
The Latent Structure of Negative Symptoms in the General Population in Adolescence and Emerging Adulthood
Authors: Havers Laura , Cardno Alastair , Freeman Daniel , Ronald Angelica 
Published: January 2022

AbstractNegative symptoms predict adverse outcomes within psychotic disorders, in individuals at high-risk for psychosis, and in young people in the community. There is considerable interest in the dimensional structure of negative symptoms in clinical samples, and accumulating evidence suggests a 5-factor structure. Little is known about the underlying structure of negative symptoms in young people despite the importance of this developmental stage for mental health. We used confirmatory factor analysis to test the structure of parent-reported negative symptoms at mean ages 16.32 (SD 0.68, N = 4974), 17.06 (SD 0.88, N = 1469) and 22.30 (SD 0.93, N = 5179) in a community sample. Given previously reported associations between total negative symptoms and genome-wide polygenic scores (GPS) for major depressive disorder (MDD) and schizophrenia in adolescence, we assessed associations between individual subdomains and these GPSs. A 5-factor model of flat affect, alogia, avolition, anhedonia, and asociality provided the best fit at each age and was invariant over time. The results of our linear regression analyses showed associations between MDD GPS with avolition, flat affect, anhedonia, and asociality, and between schizophrenia GPS with avolition and flat affect. We showed that a 5-factor structure of negative symptoms is present from ages 16 to 22 in the community. Avolition was most consistently associated with polygenic liability to MDD and schizophrenia, and alogia was least associated. These findings highlight the value of dissecting negative symptoms into psychometrically derived subdomains and may offer insights into early manifestation of genetic risk for MDD and schizophrenia.
California Children Presenting to an Emergency Department for Mental Health Emergencies
Authors: Shearer Emily , Wang N. Ewen 
Published: January 2022

Objectives
Pediatric emergency department (ED) mental health visits are increasing in the United States. At the same time, child/adolescent psychiatric services are limited. This study examines the trajectory of pediatric patients presenting with mental health emergencies to better understand availability of specialty care resources in regional networks.

Methods
This retrospective cohort study used a California Office of Statewide Health Planning and Development linked ED and Inpatient Discharge Dataset (2005–2015) to study pediatric patients (5–17 years) who presented to an ED with a primary mental health diagnosis. Outcomes were disposition: discharge, admission, or transfer.
Patients transferred were further analyzed for disposition. Regression models to identify characteristics associated with disposition were created.

Results
There were 384,339 pediatric patients presented for a primary mental health emergency from 2005 to 2015; 287,997 were discharged, 17,564 were admitted, and 78,725 were transferred. Among those not discharged, patients with public (odds ratio [OR], 1.28; P < 0.01) or self-pay insurance (OR, 5.64; P < 0.01), Black (OR, 2.15; P < 0.01), or Native American race (OR, 2.32; P < 0.01), and who presented to rural EDs (OR, 3.10; P < 0.01), nonteaching hospitals (OR, 3.06; P < 0.01), or hospitals in counties without dedicated child/adolescent psychiatric beds (OR, 5.59; P < 0.01) had higher odds of transfer.
Among those not discharged from the second hospital, Black patients (OR, 2.47; P < 0.03) and those who were transferred to a teaching hospital (OR, 1.9; P < 0.01) had higher odds of second transfer.

Conclusions
Pediatric patients with mental health emergencies experience different trajectories of care. Transfer protocols and regionalized networks may help streamline services and decrease inefficiencies in care.
Histopathological Features of Parathyroid Adenoma and 18F-Choline Uptake in PET/MR of Primary Hyperparathyroidism
Authors: Liberini Virginia , Morand Gregoire B. , Rupp Niels J. , Orita Erika , Deandreis Désirée , Broglie Däppen Martina , Hofbauer Marlena , Maurer Alexander , Husmann Lars , Mader Cäcilia E. , Grünig Hannes , Alharbi Abdullah A. , Messerli Michael , Huellner Martin W. 
Published: January 2022

Background
The aim of this study was to assess the relationship between the histopathological properties of hyperfunctioning parathyroids and parathyroid 18F-choline uptake.

Patients and Methods
A total of 31 parathyroid adenomas were retrospectively analyzed in patients with primary hyperparathyroidism and preoperative 18F-choline PET/MR. PET/MR parameters of parathyroid glands (SUVmax and target-to-background ratio in early-phase [EP] and late-phase [LP]), MRI volume, preoperative parathyroid hormone (PTH) serum concentration, and postoperative histopathology (predominant cell type and growth pattern of adenoma cells, location and size of adenoma) were assessed. The relationship of PET/MR parameters, PTH, and histological parameters was determined using linear regression, Spearman correlation and Kruskal-Wallis test.

Results
The median volume of parathyroid adenoma was 421.78 ± 142.46 mm3 (46.39–4412.69). Adenomas were predominantly composed of chief, water-clear, and oncocytic/oxyphilic cells in 27/31, 2/31, and 2/31 cases, respectively. The growth pattern was predominantly solid, follicular, and trabecular in 18/31, 8/31, and 5/31, respectively. The SUVmax was 6.71 ± 3.39 in EP and 6.91 ± 3.97 in LP. Follicular growth pattern had slightly higher EP SUVmax (trabecular: 4.12 ± 0.56; solid: 6.62 ± 3.19; follicular: 8.56 ± 3.96; P = 0.046). Spearman correlation showed strong positive correlation between volume and both EP and LP SUVmax (0.626; P = 0.0001 and 0.576; P = 0.0001, respectively). Linear regression analysis revealed significant correlation between PTH level and EP and LP SUVmax (both P = 0.001); in contrast, no correlation was found between PTH level and both cell type and growth pattern.

Conclusions
Our findings suggest that 18F-choline uptake of parathyroid adenomas might be associated both with the histological growth pattern and adenoma volume, but not with a specific cell type.
Compassionate use of recombinant human IL-7-hyFc as a salvage treatment for restoring lymphopenia in patients with recurrent glioblastoma
Authors: Ahn Stephen , Park Jae-Sung , Kim Heewon , Heo Minkyu , Sung Young Chul , Jeun Sin-Soo 
Published: January 2022

AbstractPurposeLymphopenia is frequently observed and is associated with poor prognosis in glioblastoma (GBM) patients. Restoring lymphopenia in cancer patients has been suggested as a novel immunotherapeutic strategy. As interleukin-7 (IL-7) is necessary for proliferation of lymphocytes and to amplify the total lymphocyte count (TLC), IL-7 therapy has been tried for various cancers, although the results are inconclusive. Here, we describe the clinical results of recurrent GBM treated with long-acting engineered version of recombinant human IL-7 (rhIL-7-hyFc).MethodsThis prospective case series based on compassionate use was approved by the Ministry of Food and Drug Safety in South Korea. Patients with recurrent GBM were enrolled to Seoul St. Mary’s Hospital. Primary outcomes were the safety profile and elevated total lymphocyte count (TLC). Secondary outcomes were overall survival (OS) and progression-free survival (PFS). The duration of median follow-up was 372.6 days (range 98–864 days).ResultsAmong 18 patients enrolled, 10 received rhIL-7-hyFc with temozolomide, 5 received rhIL-7-hyFc with bevacizumab, 1 received rhIL-7-hyFc with PCV chemotherapy, and 2 received rhIL-7-hyFc alone. The mean TLC of enrolled patients after the first treatment with rhIL-7-hyFc was significantly increased from 1,131 cells/mm3(range 330-2,989) at baseline to 4,356 cells/mm3(range 661-22,661). Similar increase was observed in 16 of 18 patients (88.8%), only after the first treatment of rhIL-7-hyFc. TLCs of these patients were maintained higher while rhIL-7-hyFc was repeatedly administered. Most common adverse events were injection sites reactions (64.7%) including urticaria and itching sensation, however, there were no serious adverse events more than grade III. Median OS and PFS were 378 days (range 107-864 days) and 231 days (55-726 days), respectively.ConclusionOur study first reports that IL-7 immunotherapy can restore lymphopenia and maintain TLC with various salvageable chemotherapies in recurrent GBM patients without serious adverse toxicities. This outcome warrants further larger and randomized clinical trials to validate the clinical benefits of rhIL-7-hyFc for GBM patients.
Towards definitions of critical illness and critical care using concept analysis
Authors: Kayambankadzanja Raphael Kazidule , Schell Carl Otto , Wärnberg Martin Gerdin , Tamras Thomas , Mollazadegan Hedi , Holmberg Mats , Mølsted Alvesson Helle , Baker Tim 
Published: January 2022

AbstractObjectiveAs “critical illness” and “critical care” lack consensus definitions, this study aims to explore how the concepts’ are used, describe their defining attributes and propose potential definitions.DesignWe used the Walker and Avant stepwise approach to concept analysis. The uses and definitions of the concepts were identified through a scoping review of the literature and an online survey of 114 global clinical experts. Through content analysis of the data we extracted codes, categories and themes to determine the concepts’ defining attributes and we proposed potential definitions. To assist understanding, we present model, related and contrary cases concerning the concepts, we identified antecedents and consequences to the concepts, and defined empirical referents.ResultsThe defining attributes of critical illness were a high risk of imminent death; vital organ dysfunction; requirement for care to avoid death; and potential reversibility. The defining attributes of critical care were the identification, monitoring and treatment of critical illness; vital organ support; initial and sustained care; any care of critical illness; and specialized human and physical resources. Our proposed definition of critical illness is, “a state of ill health with vital organ dysfunction, a high risk of imminent death if care is not provided and the potential for reversibility”. Our proposed definition of critical care is, “the identification, monitoring and treatment of patients with critical illness through the initial and sustained support of vital organ functions.”ConclusionThe concepts critical illness and critical care lack consensus definitions and have varied uses. Through concept analysis of uses and definitions in the literature and among experts we have identified the defining attributes of the concepts and propose definitions that could aid clinical practice, research, and policy making.Strengths and Limitations of the StudyThis concept analysis is the first study to systematically describe the uses and definitions of the concepts critical illness and critical careThe study uses a scoping review of the literature and input from over one hundred clinical experts from diverse settings globally to identify the defining attributes and provide proposed definitions of the conceptsSome uses and definitions of the concepts in languages other than English, in unpublished grey literature and from clinical experts not included in the study may have been missedAs current usage of the concepts is diverse, the proposed definitions may not be universally accepted and are aimed to stimulate further discussion