bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis methods for measuring fNIRS responses generated by a block-design paradigm
Authors: Luke Robert , Larson Eric , Shader Maureen J , Innes-Brown Hamish , Van Yper Lindsey , Lee Adrian KC , Sowman Paul F , McAlpine David 
Published: December 2020

OverviewSignificancefNIRS is an increasingly popular tool in auditory research, but the range of analysis procedures employed across studies complicates interpretation of data.AimTo assess the impact of different analysis procedures on the morphology, detection, and lateralization of auditory responses in fNIRS. Specifically, whether averaging or GLM-based analyses generate different experimental conclusions, when applied to a block-protocol design. The impact of parameter selection of GLMs on detecting auditory-evoked responses was also quantified.Approach17 listeners were exposed to three commonly employed auditory stimuli: noise, speech, and silence. A block design was employed, comprising sounds of 5-s duration, and 10–20 s silent intervals.ResultsBoth analysis procedures generated similar response morphologies and amplitude estimates, and both also indicated responses to speech to be significantly greater than to noise and silence. Neither approach indicated a significant effect of brain hemisphere on responses to speech. Methods to correct for systemic hemodynamic responses using short channels improved detection at the individual level.ConclusionsConsistent with theoretical considerations, simulations, and other experimental domains, GLM and averaging analyses generate the same group-level experimental conclusions. We release this dataset publicly for use in future development and optimization of algorithms.
Spatial community variability: Interactive effects of predators and isolation on stochastic community assembly
Authors: Pelinson Rodolfo Mei , Leibold Mathew A. , Schiesari Luis 
Published: December 2020

ABSTRACTIn the absence of environmental heterogeneity, spatial variation among local communities can be mostly attributed to demographic stochasticity (i.e., ecological drift) and historical contingency in colonization (i.e. random dispersal and priority effects). The consequences of demographic stochasticity are highly dependent on community size, gamma, and alpha diversity, which, along with historical contingency, can be strongly affected by dispersal limitation and the presence of predators. We used freshwater insect communities to experimentally test whether and how the presence of a generalist predatory fish and dispersal limitation (i.e., isolation by distance from a source habitat) can change the relative importance of stochastic and non-stochastic processes on community variability. We found that dispersal limitation can have both negative and positive effects on community variability, and their importance may depend on the presence of predatory fish. Negative effects happened because predatory insects cannot always successfully colonize highly isolated ponds, causing herbivores and detritivores to increase in abundance. As a consequence, community size increases, decreasing the importance of demographic stochasticity on community structure. However, when fish is absent, these effects are counterbalanced by an increase in the importance of priority effects generating more distinct communities in more isolated ponds. Such effects can be caused by either pre or post-colonization mechanisms and were absent in the presence of fish predators, likely because fish prevented both predatory and non-predatory insects from becoming more abundant, irrespective of their order of colonization.
LISA: A Case For Learned Index based Acceleration of Biological Sequence Analysis
Authors: Ho Darryl , Kalikar Saurabh , Misra Sanchit , Ding Jialin , Md Vasimuddin , Tatbul Nesime , Li Heng , Kraska Tim 
Published: December 2020

ABSTRACTNext Generation Sequencing (NGS) is transforming fields like genomics, transcriptomics, and epigenetics with rapidly increasing throughput at reduced cost. This also demands overcoming performance bottlenecks in the downstream analysis of the sequencing data. A key performance bottleneck is searching for exact matches of entire or substrings of short DNA/RNA sequence queries in a long reference sequence database. This task is typically performed by using an index of the reference - such as FM-index, suffix arrays, suffix trees, hash tables, or lookup tables.In this paper, we propose accelerating this sequence search by substituting or enhancing the indexes with machine learning based indexes - called learned indexes - and present LISA (Learned Indexes for Sequence Analysis). We evaluate LISA through a number of case studies – that cover widely used software tools; short and long reads; human, animal, and plant genome datasets; DNA and RNA sequences; various traditional indexing techniques (FM-indexes, hash tables and suffix arrays) – and demonstrate significant performance benefits in a majority of them. For example, our experiments on real datasets show that LISA achieves speedups of up to 2.2 fold and 4.7 fold over the state-of-the-art FM-index based implementations for exact sequence search modules in popular tools bowtie2 and BWA-MEM2, respectively.Code availabilityLISA-based FM-index:https://github.com/IntelLabs/Trans-Omics-Acceleration-Library/tree/master/src/LISA-FMILISA-based hash-table:https://github.com/IntelLabs/Trans-Omics-Acceleration-Library/tree/master/src/LISA-hashLISA applied to BWA-MEM2:https://github.com/bwa-mem2/bwa-mem2/tree/bwa-mem2-lisa.
The experience of patients in an outpatient infusion facility: a qualitative study
Authors: Zijlstra Emma , Hagedoorn Mariët , Lechner Stefan C.M. , van der Schans Cees P. , Mobach Mark P. 
Published: December 2020

Purpose
As hospitals are now being designed with an increasing number of single rooms or cubicles, the individual preference of patients with respect to social contact is of great interest. The purpose of this study is to gain a better understanding of the experience of patients in an outpatient infusion center.

Design/methodology/approach
A total of 29 semi-structured interviews were conducted, transcribed and analyzed by using direct content analysis.

Findings
Findings showed that patients perceived a lack of acoustic privacy and therefore tried to emotionally isolate themselves or withheld information from staff. In addition, patients complained about the sounds of infusion pumps, but they were neutral about the interior features. Patients who preferred non-talking desired enclosed private rooms and perceived negative distraction because of spatial crowding. In contrast, patients who preferred talking, or had no preference, desired shared rooms and perceived positive distraction because of spatial crowding.

Research limitations/implications
In conclusion, results showed a relation between physical aspects (i.e. physical enclosure) and the social environment.

Practical implications
The findings allow facility managers to better understand the patients’ experiences in an outpatient infusion facility and to make better-informed decisions. Patients with different preferences desired different physical aspects. Therefore, nursing staff of outpatient infusion centers should assess the preferences of patients. Moreover, architects should integrate different types of treatment places (i.e. enclosed private rooms and shared rooms) in new outpatient infusion centers to fulfill different preferences and patients should have the opportunity to discuss issues in private with nursing staff.

Originality/value
This study emphasizes the importance of a mix of treatment rooms, while new hospital designs mainly include single rooms or cubicles.
Guest editorial: age is a construct, not a characteristic
Authors: Kuppelwieser Volker , Klaus Philipp 
Published: December 2020

Purpose
In aging societies all over the world, an increased understanding of age and age-related insights is critical to theory development, generalizations, model adaptations and managerial insights. Researchers and managers mostly rely on chronological age for adapting their approaches; they assume chronological age as a customers’ characteristic and neglect differing behaviors between individuals of the same age. When motivations enter the fray, chronological age as an individual’s attribute becomes indiscriminate. Consequently, findings adopting this age concept differ widely.

Design/methodology/approach
This special issue of the Journal of Services Marketing consists of ten articles that focus on different aspects of aging.

Findings
The articles change perspectives on age when describing ageing from an individual’s perspective. The articles also comment on social needs and discuss well-being in later life stages.

Originality/value
The authors offer a broad view on age and ageing to promote age-related research.
Mortality and morbidity after emergency peripartum hysterectomy in a provincial referral hospital in Papua New Guinea: A seven‐year audit
Authors: Bolnga John W. , Mola Glen D. L. , Ao Paula , Sapau Wendy , Verave Ovoi , Lufele Elvin , Laman Moses 
Published: December 2020

BackgroundEmergency peripartum hysterectomy (EPH) is a life‐saving surgical procedure performed at the time of caesarean section or within 24 h of vaginal delivery and is usually a procedure of last resort in obstetric haemorrhage when other interventions fail.AimTo investigate the incidence, indications, risk factors and complications of EPH in a provincial referral hospital in Papua New Guinea (PNG).Materials and methodsThis was a seven‐year retrospective observational study investigating the rate of EPH at a provincial hospital between January 2012 and December 2018. Patient medical records that included socio‐demographics, obstetric risk factors, indications for EPH and maternal and perinatal outcomes were reviewed.ResultsOf the 19 215 deliveries during the study period, 26 women had EPH, giving an incidence of 1.35 per 1000 deliveries. The majority of women (18/26) were referred from peripheral health facilities. Overall, 21 women survived and five died (mortality index, 19%). Uterine rupture was the most common indication for EPH (13/26), and it was associated with a high maternal death rate of 15.4% (2/13) and significantly higher perinatal deaths when compared to babies born to mothers with other indications (13/13 (100%) versus 5/13 (38.5%); P = 0.002). Neonates born to mothers with uterine atony were more likely to survive (8/11 (72.7%) versus 0/15 (0%); P < 0.001), although maternal mortality was higher at 27.3% (3/11).ConclusionUterine rupture and uterine atony after prolonged labour are common indications of EPH and associated with significant maternal and perinatal mortality. Improving pre‐hospital management of prolonged labour remains critical in PNG.
Utilizing an Artificial Neural Network to Predict Self‐Management in Patients With Chronic Obstructive Pulmonary Disease: An Exploratory Analysis
Authors: Bugajski Andrew , Lengerich Alexander , Koerner Rebecca , Szalacha Laura 
Published: December 2020

AbstractPurposeThe main objective of this study was to utilize an artificial neural network in an exploratory fashion to predict self‐management behaviors based on reported symptoms in a sample of stable patients with chronic obstructive pulmonary disease (COPD).Design and MethodsPatient symptom data were collected over 21 consecutive days. Symptoms included distress due to cough, chest tightness, distress due to mucus, dyspnea with activity, dyspnea at rest, and fatigue. Self‐management abilities were measured and recorded periodically throughout the study period and were the dependent variable for these analyses. Self‐management ability scores were broken into three equal tertiles to signify low, medium, and high self‐management abilities. Data were entered into a simple artificial neural network using a three‐layer model. Accuracy of the neural network model was calculated in a series of three models that respectively used 7, 14, and 21 days of symptom data as input (independent variables). Symptom data were used to determine if the model could accurately classify participants into their respective self‐management ability tertiles (low, medium, or high scores). Through analysis of synaptic weights, or the strength or amplitude of a connection between variables and parts of the neural network, the most important variables in classifying self‐management abilities could be illuminated and served as another outcome in this study.FindingsThe artificial neural network was able to predict self‐management ability with 93.8% accuracy if 21 days of symptom data were included. The neural network performed best when predicting the low and high self‐management abilities but struggled in predicting those with medium scores. By analyzing the synaptic weights, the most important variables determining self‐management abilities were gender, followed by chest tightness, age, cough, breathlessness during activity, fatigue, breathlessness at rest, and phlegm.ConclusionsThe results of this study suggest that self‐management abilities could potentially be predicted through understanding and reporting of patient’s symptoms and use of an artificial neural network. Future research is clearly needed to expand on these findings.Clinical RelevanceSymptom presentation in chronically ill patients directly impacts self‐management behaviors. Patients with COPD experience a number of symptoms that have the potential to impact their ability to manage their chronic disease, and artificial neural networks may help clinicians identify patients at risk for poor self‐management abilities.
Cash transfers and child nutritional outcomes: a systematic review and meta-analysis
Authors: Manley James , Balarajan Yarlini , Malm Shahira , Harman Luke , Owens Jessica , Murthy Sheila , Stewart David , Winder-Rossi Natalia Elena , Khurshid Atif 
Published: December 2020

BackgroundCash transfer (CT) programmes are implemented widely to alleviate poverty and provide safety nets to vulnerable households with children. However, evidence on the effects of CTs on child health and nutrition outcomes has been mixed. We systematically reviewed evidence of the impact of CTs on child nutritional status and selected proximate determinants.MethodsWe searched articles published between January 1997 and September 2018 using Agris, Econlit, Eldis, IBSS, IDEAS, IFPRI, Google Scholar, PubMed and World Bank databases. We included studies using quantitative impact evaluation methods of CTs with sample sizes over 300, targeted to households with children under 5 years old conducted in countries with gross domestic product per capita below US$10 000 at baseline. We conducted meta-analysis using random-effects models to assess the impact of CT programmes on selected child nutrition outcomes and meta-regression analysis to examine the association of programme characteristics with effect sizes.ResultsOut of 2862 articles identified, 74 articles were eligible for inclusion. We find that CTs have significant effects of 0.03±0.03 on height-for-age z-scores (p<0.03) and a decrease of 2.1% in stunting (95% CI −3.5% to −0.7%); consumption of animal-source foods (4.5%, 95% CI 2.9% to 6.0%); dietary diversity (0.73, 95% CI 0.28 to 1.19) and diarrhoea incidence (−2.7%, 95% CI −5.4% to −0.0%; p<0.05). The effects of CTs on weight-for-age z-scores and wasting were not significant (0.02, 95% CI −0.03 to 0.08; p<0.42) and (1.2%, 95% CI: −0.1% to 2.5%; p<0.07), respectively. We found that specific programme characteristics differentially modified the effect on the nutrition outcomes studied.ConclusionWe found that CT programmes targeted to households with young children improved linear growth and contributed to reduced stunting. We found that the likely pathways were through increased dietary diversity, including through the increased consumption of animal-source foods and reduced incidence of diarrhoea. With heightened interest in nutrition-responsive social protection programmes to improve child nutrition, we make recommendations to inform the design and implementation of future programmes.
Ag2S/ZnS nanocomposites: Synthesis, structure and optical properties
Authors: Ramazanov M. A. , Nuriyeva S. G. , Shirinova H. A. , Karimova A. H. , Nuriyev M. A. 
Published: December 2020

Ag2S/ZnS nanocomposites were synthesized using a novel method, and their structural features and optical properties were also investigated. For the structural investigation of the core/shell-like nanocomposites, X-ray powder diffraction technique (XRD) and scanning electron microscopy (SEM) were used. Optical features of Ag2S/ZnS nanocomposites were studied by UV-Vis absorption and photoluminescence spectroscopy (PL). According to the SEM images, the sizes of the Ag2S, ZnS nanoparticles and Ag2S/ZnS core/shell-like nanocomposites are in the region of the 10–15; 25–50 and 15–80 nm, respectively. Furthermore, the absorption spectroscopy indicates that the bandgap of Ag2S/ZnS nanocomposites is approximately 2.4 eV. By comparison of the intensities of the emission spectra, it was clear that the intensity of Ag2S/ZnS is much lower than that of ZnS.
Simplicity from Complexity – MicroRNAs and the Maintenance of Skin Homeostasis
Authors: Quah Shan , Sampath Prabha 
Published: December 2020

Skin homeostasis is indispensable for terrestrial life. The skin, sitting at the interface between the dry external environment and the aqueous interior, acts as a barrier to delimit each from the other. Maintaining this barrier function is critical – if it is compromised, pathogen ingress and water loss may have potentially severe consequences. Skin function is supported by an intricate regulatory network incorporating both protein-coding genes as well as non-coding RNA transcripts. This review will focus on microRNAs, a subset of non-coding RNAs which target specific messenger RNAs for post-transcriptional repression. MicroRNAs regulate every aspect of skin biology, from initial cell fate determination during embryogenesis, to steady state keratinocyte maturation and barrier renewal, as well as coordination of the healing process in response to skin damage. An increased appreciation for the role of microRNAs in skin pathologies not only sheds light on the importance of these small RNAs in healthy skin function, but also provides an expanding repertoire of potential therapeutic targets through which these conditions may be addressed. Mammalian skin appears simple. Its core function is to shield the body from the external environment. Water must be retained to sustain life, whilst harmful pathogens and other environmental insults must be kept out. This simplicity in function belies the array of intricate processes necessary to maintain the skin’s barrier function – multiple series of highly-ordered molecular and cellular events control constant epidermal rejuvenation, as well as rapid repair of any epithelial damage sustained. For internal homeostasis to be maintained, epithelial integrity is essential, and contingent upon precise spatiotemporal control of protein expression in the skin.
Antitumor Effects of CAR T Cells Redirected to the EDB Splice Variant of Fibronectin
Authors: Wagner Jessica , Wickman Elizabeth , Shaw Timothy I. , Anido Alejandro Allo , Langfitt Deanna , Zhang Jinghui , Porter Shaina N. , Pruett-Miller Shondra M. , Tillman Heather , Krenciute Giedre , Gottschalk Stephen 
Published: December 2020

Abstract
Chimeric antigen receptor (CAR) T-cell therapy has had limited success in early-phase clinical studies for solid tumors. Lack of efficacy is most likely multifactorial, including a limited array of targetable antigens. We reasoned that targeting the cancer-specific extra domain B (EDB) splice variant of fibronectin might overcome this limitation because it is abundantly secreted by cancer cells and adheres to their cell surface. In vitro, EDB-CAR T cells recognized and killed EDB-positive tumor cells. In vivo, 1 × 106 EDB-CAR T cells had potent antitumor activity in both subcutaneous and systemic tumor xenograft models, resulting in a significant survival advantage in comparison with control mice. EDB-CAR T cells also targeted the tumor vasculature, as judged by IHC and imaging, and their antivascular activity was dependent on the secretion of EDB by tumor cells. Thus, targeting tumor-specific splice variants such as EDB with CAR T cells is feasible and has the potential to improve the efficacy of CAR T-cell therapy.
Kindlin3-Dependent CD11b/CD18-Integrin Activation Is Required for Potentiation of Neutrophil Cytotoxicity by CD47–SIRPα Checkpoint Disruption
Authors: Bouti Panagiota , Zhao Xi Wen , Verkuijlen Paul J.J.H. , Tool Anton T.J. , van Houdt Michel , Köker Nezihe , Köker Mustafa Yavuz , Keskin Ozlem , Akbayram Sinan , van Bruggen Robin , Kuijpers Taco W. , Matlung Hanke L. , van den Berg Timo K. 
Published: December 2020

Abstract
The CD47–signal regulatory protein-alpha (SIRPα) immune checkpoint constitutes a therapeutic target in cancer, and initial clinical studies using inhibitors of CD47–SIRPα interactions in combination with tumor-targeting antibodies show promising results. Blockade of CD47–SIRPα interaction can promote neutrophil antibody-dependent cellular cytotoxicity (ADCC) toward antibody-opsonized targets. Neutrophils induce killing of antibody-opsonized tumor cells by a process identified as trogoptosis, a necrotic/lytic type of cancer cell death that involves trogocytosis, the antibody-mediated endocytic acquisition of cancer membrane fragments by neutrophils. Both trogocytosis and killing strictly depend on CD11b/CD18-(Mac-1)–mediated neutrophil–cancer cell conjugate formation, but the mechanism by which CD47–SIRPα checkpoint disruption promotes cytotoxicity has remained elusive. Here, by using neutrophils from patients with leukocyte adhesion deficiency type III carrying FERMT3 gene mutations, hence lacking the integrin-associated protein kindlin3, we demonstrated that CD47–SIRPα signaling controlled the inside-out activation of the neutrophil CD11b/CD18-integrin and cytotoxic synapse formation in a kindlin3-dependent fashion. Our findings also revealed a role for kindlin3 in trogocytosis and an absolute requirement in the killing process, which involved direct interactions between kindlin3 and CD18 integrin. Collectively, these results identified a dual role for kindlin3 in neutrophil ADCC and provide mechanistic insights into the way neutrophil cytotoxicity is governed by CD47–SIRPα interactions.