bluuebunny/crossref_metadata_2025_split huggingface dataset:
In silico deconjugation of glucuronide conjugates enhances tandem mass spectra library annotation of human samples
Authors: Huber Carolin , Krauss Martin , Reinstadler Vera , Denicolò Sara , Mayer Gert , Schulze Tobias , Brack Werner , Oberacher Herbert 
Published: January 2022

AbstractMass spectral library annotation of liquid chromatography-high resolution tandem mass spectrometry (LC-HRMS/MS) data is a reliable approach for fast identification of organic contaminants and toxicants in complex environmental and biological matrices. While determining the exposure of humans or mammals, it is indispensable to include phase I and phase II metabolites (conjugates) along with the parent compounds, but often, tandem mass spectra for these are unavailable. In this study, we present and evaluate a strategy for annotating glucuronide conjugates in LC-HRMS/MS scans by applying a neutral loss search for detection, then truncating the spectra which we refer to as in silico deconjugation, and finally searching these against mass spectral libraries of the aglycones. The workflow was tested on a dataset of in vitro–generated glucuronides of reference standard mixtures and a dataset of 51 authentic urine samples collected from patients with known medication status, acquired on different instrumentations. A total number of 75 different glucuronidated molecular structures were identified by in silico deconjugation and spectral library annotation. We also identified specific molecular structures (sulfonamides, ether bonds, di-glucuronides), which resulted in slightly different fragmentation patterns between the glucuronide and the unconjugated compound. This led to a decreased spectral matching score and in some cases to a false-negative identification. Still, by applying this method, we revealed a reliable annotation of most common glucuronides, leading to a new strategy reducing the need for deconjugation steps or for recording many reference glucuronide spectra for screening approaches.
Graphical Abstract
Visual deterioration in patients with photoreceptor loss after retinal reattachment surgery
Authors: Rasool Sana , Kaushik Megha , Chaudhary Rishika , Blachford Karen , Berry Martin , Scott Robert A. H. , Logan Ann , Blanch Richard J. 
Published: January 2022

Abstract
Purpose
Assess the relationship between photoreceptor degeneration and visual function after retinal reattachment surgery (RRS) in a prospective cohort.

Methods
Patients with rhegmatogenous retinal detachment (RRD) were reviewed before and 6 months after vitreoretinal surgery. Optical coherence tomographical thickness of the outer nuclear layer (ONL), outer retinal segment (ORS), retinal pigmented epithelium to ellipsoid zone (RPE-EZ) and external limiting membrane to EZ (ELM-EZ) were recorded 6 months post-operatively. These were compared to best corrected visual acuity (BCVA) and retinal sensitivity (Humphrey visual field).

Results
Thirteen macula-off and 8 macula-on RRD patients were included. The mean ONL thickness was higher after macula-on RRD compared to macula-off RRD (97.70 ± 3.62 μm vs. 73.10 ± 4.98 μm). In all RRD eyes, every 1 μm decrease in ONL thickness correlated with a 0.052 dB decrease and in retinal sensitivity and every 1 μm decrease in ORS thickness was associated with a 0.062 dB reduction in retinal sensitivity. ORS, ELM-EZ and RPE-EZ thickness did not correlate with BCVA post-RRS.

Conclusion
There was greater ONL and ORS thinning following macula-off compared to macula-on RRD. Correlations between ONL and ORS thinning with decreased retinal sensitivity may be explained by RRD-induced photoreceptor death.
Hydrochemical-geophysical study of saline paleo-water contamination in alluvial aquifers
Authors: Pilla Giorgio , Torrese Patrizio 
Published: January 2022

AbstractAn integrated hydrochemical and geophysical study of the saline paleo-water uprising into the alluvial aquifer of the Oltrepò Pavese plain sector (Po Plain, northern Italy) is presented. This study involved hydrochemical analysis of groundwater, assessment of well logs, and one-, two- and three-dimensional electrical geophysical surveys. The studied area was selected for its characteristic hydrogeological setting. The alluvial aquifer is strongly conditioned by the presence of a buried tectonic discontinuity along which the saline waters are mainly distributed. These waters rise along the discontinuities in the bedrock and flow into the overlying alluvial aquifer. Contamination from saline waters is not spatially and vertically homogeneous within the aquifer. The spatial distribution of Na–Cl waters suggests the existence of plumes of highly mineralized waters that locally reach the aquifer, diffuse and mix with freshwaters. The saline waters show a dilution during upward migration, which is due to mixing with the shallow fresh groundwater. Highly mineralized groundwater is identified even at very shallow depth in correspondence with each plume. On the other hand, there is a lower degree of contamination in those sectors of the aquifer that are further away from the structural discontinuities and this lesser contamination generally only involves the deeper parts of the aquifer.
Modulation Depth Discrimination by Cochlear Implant Users
Authors: Monaghan Jessica J. M. , Carlyon Robert P. , Deeks John M. 
Published: January 2022

AbstractCochlear implants (CIs) convey the amplitude envelope of speech by modulating high-rate pulse trains. However, not all of the envelope may be necessary to perceive amplitude modulations (AMs); the effective envelope depth may be limited by forward and backward masking from the envelope peaks. Three experiments used modulated pulse trains to measure which portions of the envelope can be effectively processed by CI users as a function of AM frequency. Experiment 1 used a three-interval forced-choice task to test the ability of CI users to discriminate less-modulated pulse trains from a fully modulated standard, without controlling for loudness. The stimuli in experiment 2 were identical, but a two-interval task was used in which participants were required to choose the less-modulated interval, ignoring loudness. Catch trials, in which judgements based on level or modulation depth would give opposing answers, were included. Experiment 3 employed novel stimuli whose modulation envelope could be modified below a variable point in the dynamic range, without changing the loudness of the stimulus. Overall, results showed that substantial portions of the envelope are not accurately encoded by CI users. In experiment 1, where loudness cues were available, participants on average were insensitive to changes in the bottom 30% of their dynamic range. In experiment 2, where loudness was controlled, participants appeared insensitive to changes in the bottom 50% of the dynamic range. In experiment 3, participants were insensitive to changes in the bottom 80% of the dynamic range. We discuss potential reasons for this insensitivity and implications for CI speech-processing strategies.
Laparoscopic Nissen fundoplication versus 90° and 180° fundoplication for gastroesophageal reflux disease
Authors: Hoffsten Johanna , Forsell Yvonne 
Published: January 2022

Summary
Background
Laparoscopic Nissen fundoplication (LNF) is standard care for surgical treatment of gastroesophageal reflux disease (GERD) in adults. The main disadvantage is the compression of the food passageway, affecting the ability to belch and vomit, and causing swallowing difficulties. Therefore, partial fundoplication methods encircling esophagus as little as 90° and 180° have been developed. Previous studies have been inconclusive. The aim was to assess the effectiveness of LNF compared to laparoscopic anterior 90° and 180° fundoplication.

Methods
Randomized controlled trials were searched for in MEDLINE, Embase, CINAHL, the Cochrane Library, and Web of Science, and in eligible studies’ reference lists and relevant reviews. Outcomes of interest were 5-year heartburn, medication use, dysphagia, reoperation, and satisfaction. Dichotomous data were calculated as risk ratios (RR). Subgroup analyses were performed to compare each comparator separately with LNF. The meta-analyses were conducted using a random-effects model with an inverse variance statistical method and a significance level of 0.05.

Results
Four eligible trials were included with 398 participants, of which half compared LNF with 90°. At 5 years there was higher risk of dysphagia for solids after LNF compared to 90° and 180° fundoplication (RR 1.68 [1.14, 2.49]). However, LNF was associated with a significantly lower risk of medication use compared to laparoscopic anterior 90° fundoplication (RR 0.23 [0.09, 0.58], subgroup analysis). No differences between treatments in terms of heartburn, reoperation, and satisfaction were found.

Conclusion
The limited evidence fails to provide an unequivocal method of choice, but rather indicates a trade-off between reflux control and complications.
A hybrid extreme learning machine model with harris hawks optimisation algorithm: an optimised model for product demand forecasting applications
Authors: Chaudhuri Koushiki Dasgupta , Alkan Bugra 
Published: January 2022

AbstractAccurate and real-time product demand forecasting is the need of the hour in the world of supply chain management. Predicting future product demand from historical sales data is a highly non-linear problem, subject to various external and environmental factors. In this work, we propose an optimised forecasting model - an extreme learning machine (ELM) model coupled with the Harris Hawks optimisation (HHO) algorithm to forecast product demand in an e-commerce company. ELM is preferred over traditional neural networks mainly due to its fast computational speed, which allows efficient demand forecasting in real-time. Our ELM-HHO model performed significantly better than ARIMA models that are commonly used in industries to forecast product demand. The performance of the proposed ELM-HHO model was also compared with traditional ELM, ELM auto-tuned using Bayesian Optimisation (ELM-BO), Gated Recurrent Unit (GRU) based recurrent neural network and Long Short Term Memory (LSTM) recurrent neural network models. Different performance metrics, i.e., Root Mean Squared Error (RMSE), Mean Absolute Percentage Error (MAPE) and Mean Percentage Error (MPE) were used for the comparison of the selected models. Horizon forecasting at 3 days and 7 days ahead was also performed using the proposed approach. The results revealed that the proposed approach is superior to traditional product demand forecasting models in terms of prediction accuracy and it can be applied in real-time to predict future product demand based on the previous week’s sales data. In particular, considering RMSE of forecasting, the proposed ELM-HHO model performed 62.73% better than the statistical ARIMA(7,1,0) model, 40.73% better than the neural network based GRU model, 34.05% better than the neural network based LSTM model, 27.16% better than the traditional non-optimised ELM model with 100 hidden nodes and 11.63% better than the ELM-BO model in forecasting product demand for future 3 months. The novelty of the proposed approach lies in the way the fast computational speed of ELMs has been combined with the accuracy gained by tuning hyperparameters using HHO. An increased number of hyperparameters has been optimised in our methodology compared to available models. The majority of approaches to improve the accuracy of ELM so far have only focused on tuning the weights and the biases of the hidden layer. In our hybrid model, we tune the number of hidden nodes, the number of input time lags and even the type of activation function used in the hidden layer in addition to tuning the weights and the biases. This has resulted in a significant increase in accuracy over previous methods. Our work presents an original way of performing product demand forecasting in real-time in industry with highly accurate results which are much better than pre-existing demand forecasting models.
Co-designing and piloting an Integrated Digital Literacy and Language Toolkit for vulnerable migrant students in higher education
Authors: Smith Angela , Rubio-Rico Lourdes , McClelland Gabrielle Tracy , Monserrate-Gómez Sílvia , Font-Jiménez Isabel , de Molina-Fernández Inmaculada 
Published: January 2022

AbstractThis paper presents the process of co-design, co-production, piloting, evaluation and revision of an Integrated Digital Literacy and Language Toolkit for Vulnerable Migrant Students (VMs) in Higher Education (HE). The language element focuses on academic language skills of reading, writing, listening and speaking required for effective involvement in both the host society and HE learning; the acquisition and improvement of digital literacy skills enable VMs to successfully participate in, and contribute to, university and societal collaboration, creativity and content curation. The Toolkit resulted from the co -operation and collaboration of five EU universities and was based on the ASSURE instructional design model. The Toolkit offers a self- access, self- paced, non-linear, fully online set of ten stand-alone units which offer a range of materials and activities to develop those skills pertinent to VM academic language and digital literacy needs. Evaluation by a group of VMs resident in EU countries highlight the positive impact of the Toolkit and validates the instrument as fit for purpose. Noteworthy aspects include its usefulness in supporting student autonomy, improving digital capabilities and academic language mastery,a positive experience of a flexible learning experience along with access to open resources of international scope and dissemination under the Creative Commons licence.
Application of array comparative genomic hybridization (aCGH) for identification of chromosomal aberrations in the recurrent pregnancy loss
Authors: Kowalczyk Katarzyna , Smyk Marta , Bartnik-Głaska Magdalena , Plaskota Izabela , Wiśniowiecka-Kowalnik Barbara , Bernaciak Joanna , Chojnacka Marta , Paczkowska Magdalena , Niemiec Magdalena , Dutkiewicz Daria , Kozar Agata , Magdziak Róża , Krawczyk Wojciech , Pietras Grzegorz , Michalak Elżbieta , Klepacka Teresa , Obersztyn Ewa , Bal Jerzy , Nowakowska Beata Anna 
Published: January 2022

AbstractSpontaneous abortion occurs in 8–20% of recognized pregnancies and usually takes place in the first trimester (7–11 weeks). There are many causes of pregnancy loss, but the most important (about 75%) is the presence of chromosomal aberrations. We present the results of oligonucleotide array application in a cohort of 62 miscarriage cases. The inclusion criteria for the study were the loss after 8th week of pregnancy and the appearance of recurrent miscarriages. DNA was extracted from trophoblast or fetal skin fibroblasts. In the 62 tested materials from recurrent miscarriages, the detection rate was 56.5% (35/62). The most commonly found were aneuploidies (65%) (chromosomal trisomy 14, 16, 18, 21, and 22), Turner syndrome, and triploidy (17.1%). Other chromosomal abnormalities included pathogenic and likely pathogenic structural aberrations: 1) pathogenic: deletion 7p22.3p12.3 and duplication 9p24.3p13.2 inherited from the normal father, deletion 3q13.31q22.2 and deletion 3q22.3q23 of unknown inheritance and duplication of 17p12 inherited from father with foot malformation; 2) likely pathogenic variants: deletion 17p13.1 inherited from normal mother, deletion 5q14.3 of unknown inheritance and de novo deletion 1q21.1q21.2. Among these aberrations, six CNVs (copy number variants) were responsible for the miscarriage: deletion 7p22.3p12.3 and duplication 9p24.3p13.2, deletion 3q13.31q22.2 and deletion 3q22.3q23, and deletion 17p13.1 and deletion 1q21.1q21.2. Other two findings were classified as incidental findings (deletion 5q14.3 and 17p12 duplication). Our research shows that 17% of the aberrations (6/35 abnormal results) that cannot be identified by the routine kariotype analysis are structural aberrations containing genes important for fetal development, the mutations of which may cause spontaneous abortion.
Effects of an Online Acceptance and Commitment Therapy Intervention on Children’s Quality of Life
Authors: Sairanen Essi , Lappalainen Raimo , Lappalainen Päivi , Hiltunen Arto 
Published: January 2022

AbstractThe present study examined if an Acceptance and Commitment Therapy (ACT)–based online intervention for parents had indirect effects on their children’s quality of life mediated by changes in parental well-being, psychological flexibility and mindfulness skills. Participants were 74 adults, who either received an ACT-based guided online intervention or were allocated to the wait list control group, and their children (n = 66) who had type 1 diabetes or functional disabilities. Structural equation modeling (SEM) and a bias-corrected bootstrap approach were applied to examine the indirect effects of the treatment on children’s quality of life through changes in parents’ well-being and psychological processes involving psychological flexibility, cognitive defusion, and mindfulness skills. Children’s quality of life was assessed both by self-reports and parents’ evaluations. Significant indirect effects on children’s quality of life were found through improvements in parental well-being and mindfulness skills. The intervention had significant indirect effects on parents’ evaluations of their children’s quality of life concerning family and other social relationships, as well as on physical well-being. In regard to children’s self-reported quality of life, the intervention had significant indirect effects on self-esteem, family relations, emotional well-being, and functioning at school/kindergarten. The results indicate that it is beneficial for children’s quality of life to improve parents’ ability to describe their experiences, being non-reactive to one’s inner experiences and acting with awareness as well as cognitive defusion.
Long-Term Follow-Up of Newborns with 22q11 Deletion Syndrome and Low TRECs
Authors: Framme Jenny Lingman , Lundqvist Christina , Lundell Anna-Carin , van Schouwenburg Pauline A. , Lemarquis Andri L. , Thörn Karolina , Lindgren Susanne , Gudmundsdottir Judith , Lundberg Vanja , Degerman Sofie , Zetterström Rolf H. , Borte Stephan , Hammarström Lennart , Telemo Esbjörn , Hultdin Magnus , van der Burg Mirjam , Fasth Anders , Oskarsdóttir Sólveig , Ekwall Olov 
Published: January 2022

Abstract
Background
Population-based neonatal screening using T-cell receptor excision circles (TRECs) identifies infants with profound T lymphopenia, as seen in cases of severe combined immunodeficiency, and in a subgroup of infants with 22q11 deletion syndrome (22q11DS).

Purpose
To investigate the long-term prognostic value of low levels of TRECs in newborns with 22q11DS.

Methods
Subjects with 22q11DS and low TRECs at birth (22q11Low, N=10), matched subjects with 22q11DS and normal TRECs (22q11Normal, N=10), and matched healthy controls (HC, N=10) were identified. At follow-up (median age 16 years), clinical and immunological characterizations, covering lymphocyte subsets, immunoglobulins, TRECs, T-cell receptor repertoires, and relative telomere length (RTL) measurements were performed.

Results
At follow-up, the 22q11Low group had lower numbers of naïve T-helper cells, naïve T-regulatory cells, naïve cytotoxic T cells, and persistently lower TRECs compared to healthy controls. Receptor repertoires showed skewed V-gene usage for naïve T-helper cells, whereas for naïve cytotoxic T cells, shorter RTL and a trend towards higher clonality were found. Multivariate discriminant analysis revealed a clear distinction between the three groups and a skewing towards Th17 differentiation of T-helper cells, particularly in the 22q11Low individuals. Perturbations of B-cell subsets were found in both the 22q11Low and 22q11Normal group compared to the HC group, with larger proportions of naïve B cells and lower levels of memory B cells, including switched memory B cells.

Conclusions
This long-term follow-up study shows that 22q11Low individuals have persistent immunologic aberrations and increased risk for immune dysregulation, indicating the necessity of lifelong monitoring.

Clinical Implications
This study elucidates the natural history of childhood immune function in newborns with 22q11DS and low TRECs, which may facilitate the development of programs for long-term monitoring and therapeutic choices.
Online Mindfulness Experience for Emotional Support to Healthcare staff in times of Covid-19
Authors: Castillo-Sánchez Gema , Sacristán-Martín Olga , Hernández María A. , Muñoz Irene , de la Torre Isabel , Franco-Martín Manuel 
Published: January 2022

AbstractDuring the first confinement in Spain, between the months of March to June 2020, Information and Communication Technologies strategies were implemented in order to support health workers in the Wellbeing of Mental Health. Faced with so much uncertainty about the pandemic, an Online Mindfulness course. The objective of the course was to support healthcare professionals in Castilla y León in managing stress, anxiety and other emotional disturbances generated by coping with a situation as uncertain and unexpected as a pandemic, in order to manage emotions and thoughts that can lead to suicidal ideation. The motivations for the demand, reasons or motivations in which the health professionals of Castilla y León decided to participate in the mindfulness course in the first wave of Covid-19 in Spain are described. The descriptive and inferential statistical analysis of the customer satisfaction survey applied at the end of the mindfulness course, to the health professionals who participated in a satisfaction survey (CSQ-8: Client Satisfaction Questionnaire). Professional were asked to complete a survey based on (CSQ-8: Client Satisfaction Questionnaire) whose Cronbach's alpha = 0.917 is why the instrument used with N = 130 participants has high reliability. The 66% answered with a highly satisfied that they would return to the mindfulness online course. The 93% of the people who answered the satisfaction survey were women, of which they are professionals in the nursing area, with a participation of around 62%. In relation to the online system used in the Mindfulness intervention, 74% expressed that they fully agreed that it has been easy to use the online system for the mindfulness intervention. Health Professionals responded with 58% high satisfaction and 36% satisfaction, making a total of 94% on the help received in the online mindfulness courses to solve their problems. There is no difference between the age groups of the professionals who have preferred the Mindfulness online course (p = 0.672).