bluuebunny/crossref_metadata_2025_split huggingface dataset:
SMILE: mutual information learning for integration of single-cell omics data
Authors: Xu Yang , Das Priyojit , McCord Rachel Patton 
Published: October 2021

AbstractMotivationDeep learning approaches have empowered single-cell omics data analysis in many ways and generated new insights from complex cellular systems. As there is an increasing need for single-cell omics data to be integrated across sources, types and features of data, the challenges of integrating single-cell omics data are rising. Here, we present an unsupervised deep learning algorithm that learns discriminative representations for single-cell data via maximizing mutual information, SMILE (Single-cell Mutual Information Learning).ResultsUsing a unique cell-pairing design, SMILE successfully integrates multisource single-cell transcriptome data, removing batch effects and projecting similar cell types, even from different tissues, into the shared space. SMILE can also integrate data from two or more modalities, such as joint-profiling technologies using single-cell ATAC-seq, RNA-seq, DNA methylation, Hi-C and ChIP data. When paired cells are known, SMILE can integrate data with unmatched feature, such as genes for RNA-seq and genome-wide peaks for ATAC-seq. Integrated representations learned from joint-profiling technologies can then be used as a framework for comparing independent single source data.Availability and implementationThe source code of SMILE including analyses of key results in the study can be found at: https://github.com/rpmccordlab/SMILE, implemented in Python.Supplementary informationSupplementary data are available at Bioinformatics online.
‘Someone to Talk to’: A Short-Term Tele-Therapy Intervention with Older People during the Coronavirus Pandemic
Authors: Eliezer Kopel , Knei-Paz Cigal , Zvi Lilach , Schnall Itiya , Gitlitz Tamar , Gavriel-Fried Belle 
Published: October 2021

Abstract
The Coronavirus pandemic (COVID-19) and its concomitant social isolation have affected older citizens more than any other sector of the population. This article describes the theoretical and practical principles of a short-term tele-therapy intervention model developed and implemented as a pilot project during the Coronavirus pandemic to support older residents of the community, who faced a variety of needs stemming from the lockdowns and social isolation. The intervention was developed and directed in collaboration with faculty members from a university school of social work and social workers from the municipal social services in Israel, and was conducted by first year social work students as part of their first field experience. This intervention combined Perlman’s model of problem solving, a telephone crisis intervention model and a strengths-based approach. Participants and students indicated that they benefitted from the programme and felt that the therapeutic relationships were meaningful. These outcomes and reports suggest that this type of intervention is successful and can be applied to older people during other crises or in other populations, communities and countries as part of the field experience of social work students.
Normative brain mapping of interictal intracranial EEG to localize epileptogenic tissue
Authors: Taylor Peter N , Papasavvas Christoforos A , Owen Thomas W , Schroeder Gabrielle M , Hutchings Frances E , Chowdhury Fahmida A , Diehl Beate , Duncan John S , McEvoy Andrew W , Miserocchi Anna , de Tisi Jane , Vos Sjoerd B , Walker Matthew C , Wang Yujiang 
Published: October 2021

AbstractThe identification of abnormal electrographic activity is important in a wide range of neurological disorders, including epilepsy for localizing epileptogenic tissue. However, this identification may be challenging during non-seizure (interictal) periods, especially if abnormalities are subtle compared to the repertoire of possible healthy brain dynamics. Here, we investigate if such interictal abnormalities become more salient by quantitatively accounting for the range of healthy brain dynamics in a location-specific manner.To this end, we constructed a normative map of brain dynamics, in terms of relative band power, from interictal intracranial recordings from 234 participants (21 598 electrode contacts). We then compared interictal recordings from 62 patients with epilepsy to the normative map to identify abnormal regions. We proposed that if the most abnormal regions were spared by surgery, then patients would be more likely to experience continued seizures postoperatively.We first confirmed that the spatial variations of band power in the normative map across brain regions were consistent with healthy variations reported in the literature. Second, when accounting for the normative variations, regions that were spared by surgery were more abnormal than those resected only in patients with persistent postoperative seizures (t = −3.6, P = 0.0003), confirming our hypothesis. Third, we found that this effect discriminated patient outcomes (area under curve 0.75 P = 0.0003).Normative mapping is a well-established practice in neuroscientific research. Our study suggests that this approach is feasible to detect interictal abnormalities in intracranial EEG, and of potential clinical value to identify pathological tissue in epilepsy. Finally, we make our normative intracranial map publicly available to facilitate future investigations in epilepsy and beyond.
Guidance for Systematic Integration of Undernutrition in Attributing Cause of Death in Children
Authors: Paganelli Christina R , Kassebaum Nicholas , Strong Kathleen , Suchdev Parminder S , Voskuijl Wieger , Bassat Quique , Blau Dianna M , Denno Donna M 
Published: October 2021

AbstractMinimally invasive tissue sampling (MITS) is increasingly being used to better understand causes of death in low-resource settings. Undernutrition (eg, wasting, stunting) is prevalent among children globally and yet not consistently coded or uniformly included on death certificates in MITS studies when present. Consistent and accurate attribution of undernutrition is fundamental to understanding its contribution to child deaths. In May 2020, members of the MITS Alliance Cause of Death Technical Working Group convened a panel of experts in public health, child health, nutrition, infectious diseases, and MITS to develop guidance for systematic integration of undernutrition, as assessed by anthropometry, in cause of death coding, including as part of the causal chain or as a contributing condition, in children &lt;5 years of age. The guidance presented here will support MITS and other researchers, public health practitioners, and clinicians with a systematic approach to assigning and interpreting undernutrition in death certification.
https://botryosphaeriales.org/, an online platform for up-to-date classification and account of taxa of Botryosphaeriales
Authors: Wu N a , Dissanayake Asha J , Manawasinghe Ishara S , Rathnayaka Achala R , Liu Jian-Kui , Phillips Alan j.l , Promputtha Itthayakorn , Hyde Kevin D 
Published: October 2021

Abstract
Fungi are eukaryotes that inhabit various ecosystems worldwide and have a decomposing effect that other organisms cannot replace. Fungi are divided into two main groups depending on how their sexual spores are formed, viz. Ascomycota and Basidiomycota. The members of Botryosphaeriales (Dothideomycetes, Ascomycota) are ubiquitous. They are pathogenic on a wide range of hosts, causing diverse diseases including dieback, canker, leaf spots and root rots and are also reported as saprobes and endophytes worldwide. As an important fungal group, of which most are plant pathogens, it is necessary to organize data and information on Botryosphaeriales so that scientific literature can be used effectively. For this purpose, a new website, https://botryosphaeriales.org is established to gather all published data together with updates on the present taxonomy of Botryosphaeriales. The website consists of an easy-to-operate searching system and provides an up-to-date classification together with accounts of Botryosphaeriales taxa, including colour illustrations, descriptions, notes and numbers of species in each genus, as well as their classification. Thus, readers will be able to obtain information on botryosphaerialean taxa through this platform.
Database URL: https://botryosphaeriales.org/
Effects of Provision Type and Pesticide Exposure on the Larval Development ofOsmia lignaria(Hymenoptera: Megachilidae)
Authors: Kopit Andi M , Klinger Ellen , Cox-Foster Diana L , Ramirez Ricardo A , Pitts-Singer Theresa L 
Published: October 2021

AbstractWild and managed bee populations are in decline, and one of many environmental causes is the impact of pesticides on developing bees. For solitary bees, delayed larval development could lead to asynchronous adult emergence, unhealthy and inefficient adult pollinators, and decreased brood production and survival. We examined a methodology for testing Osmia lignaria Say (Hymenoptera: Megachilidae) larval responses to pesticide exposure using a laboratory bioassay. We created two provision types: a homogenized blend of O. lignaria provisions from an apple orchard and homogenized almond pollen pellets collected by honey bees plus sugar water. Pesticides were administered to the provisions to compare toxic effects. We recorded larval developmental durations for second–fifth instar and for fifth instar to cocoon initiation for larvae fed provisions treated with water (control) or doses of three pesticides and a representative spray-tank mixture (acetamiprid, boscalid/pyraclostrobin, dimethoate, and acetamiprid plus boscalid/pyraclostrobin). All larvae survived to cocoon initiation when only water was added to provisions. Impacts of pesticide treatments significantly differed between the apple and almond homogenates. The greatest treatment effects occurred when the homogenized almond provision was mixed with acetamiprid alone and when combined with boscalid/pyraclostrobin. Optimizing bioassays through the use of appropriate larval food for exposing solitary bee larvae to agrochemicals is crucial for assessing risks for pollinators.
Welfare Effects of Housing Transaction Taxes: A Quantitative Analysis with an Assignment Model
Authors: Määttänen Niku , Terviö Marko 
Published: October 2021

Abstract
We evaluate the welfare cost of housing transaction taxes with a new assignment model-based framework, where welfare effects are driven by distortions in the matching of houses and households. We calibrate the model with data from the Helsinki metropolitan region to assess the impact of a reform where an ad valorem transaction tax is replaced with a revenue-equivalent property tax. The aggregate welfare gain from this reform increases rapidly with the initial transaction tax rate, with the Laffer curve peaking at about 10%. The proportion of households that lose out from the reform is nevertheless increasing in the tax rate. We compare our model-based counterfactual aggregate welfare results with welfare calculations based on reduced-form estimates from previous policy evaluation studies; they are broadly in line, despite the latter using data from different housing markets at various levels and changes of the tax rate.
Profiling the Quito basin (Ecuador) using seismic ambient noise
Authors: Pacheco D , Mercerat E D , Courboulex F , Bonilla L F , Laurendeau A , Alvarado A 
Published: October 2021

SUMMARY
Quito, the capital of Ecuador, with more than 2.5 M inhabitants, is exposed to a high seismic hazard due to its proximity to the Pacific subduction zone and active crustal faults, both capable of generating significant earthquakes. Furthermore, the city is located in an intermontane piggy-back basin prone to seismic wave amplification. To understand the basin’s seismic response and characterize its geological structure, 20 broad and medium frequency band seismic stations were deployed in Quito’s urban area between May 2016 and July 2018 that continuously recorded ambient seismic noise. We first compute horizontal-to-vertical spectral ratios to determine the resonant frequency distribution in the entire basin. Secondly, we cross-correlate seismic stations operating simultaneously to retrieve interstations surface-wave Green’s functions in the frequency range of 0.1–2 Hz. We find that Love waves travelling in the basin’s longitudinal direction (NNE–SSW) show much clearer correlograms than those from Rayleigh waves. We then compute Love wave phase-velocity dispersion curves and invert them in conjunction with the HVSR curves to obtain shear-wave velocity profiles throughout the city. The inversions highlight a clear difference in the basin’s structure between its northern and southern parts. In the centre and northern areas, the estimated basin depth and mean shear-wave velocity are about 200 m and 1800 ms−1, respectively, showing resonance frequency values between 0.6 and 0.7 Hz. On the contrary, the basement’s depth and shear-wave velocity in the southern part are about 900 m and 2500 ms−1, having a low resonance frequency value of around 0.3 Hz. This difference in structure between the centre-north and the south of the basin explains the spatial distribution of low-frequency seismic amplifications observed during the Mw 7.8 Pedernales earthquake in April 2016 in Quito.
Joint inversion of gravity and magnetic data using correspondence maps with application to geothermal fields
Authors: Carrillo Jonathan , Perez-Flores Marco A , Gallardo Luis A , Schill Eva 
Published: October 2021

SUMMARY
Current geophysical joint inversion methods can be roughly divided into structurally or property driven. While structural coupling plays a key role in fully heterogeneous environments, it is blind to the actual physical properties, which limit its application. On the other hand, approaches based on direct property-correlations promise strong coupled models using petrophysical linkages derived from rock physics or through the search for cross-property relationships in the objective function directly, for example, fuzzy-clusters or correspondence maps. We apply a correspondence maps (CM) methodology to the joint estimation of density and magnetization in 3-D environments using gravity and magnetic data. CM joint inversion has yet to be applied to the specific combination of gravity and magnetic data, nor compared to other approaches like cross-gradient coupling or fuzzy-clustering. The CM searches for cross-property functional relationships; it has the potential to allow a gradual property variation that is not restricted to a predetermined number of homogeneous zones. We tested the algorithm using two illustrative synthetic examples to analyse the compositional and geometrical improvements and thoroughly investigate its capacity to recover a study model based on potential features in a geothermal scenario using polynomials. We investigated the case of using lower and higher polynomials than required for recovering the second synthetic model. The nature of the inversion suggested instability when high-grade polynomials were used, which was successfully overcome by gradually increasing the number of coefficients. The strategy was satisfactorily implemented to the field data.
We applied the algorithm over the Los Humeros geothermal field in Mexico and fit a quadratic relationship between density and magnetization that exhibits two main zones consistent with previous works. The first one contains relatively low density and high magnetization. The second zone contains low density and low magnetization values. In this last zone, we emphasize that an observed link between low density, low magnetization, and major fault zones with high relevance to geothermal exploration is resulting from joint inversion, only. We achieved an enhanced petrophysical and structural integrated subsurface imaging in synthetic and field cases at the expense of slightly increased RMS misfit value.
Crystal structure and conformational stability of a galectin-1 tandem-repeat mutant with a short linker
Authors: Nonaka Yasuhiro , Ogawa Takashi , Shoji Hiroki , Nishi Nozomu , Kamitori Shigehiro , Nakamura Takanori 
Published: October 2021

Abstract
Modification of the domain architecture of galectins has been attempted to analyze their biological functions and to develop medical applications. Several types of galectin-1 repeat mutants were previously reported but, however, it was not clear whether the native structure of the wild type was retained. In this study, we determined the crystal structure of a galectin-1 tandem-repeat mutant with a short linker peptide, and compared the unfolding profiles of the wild type and mutant by chemical denaturation. The structure of the mutant was consistent with that of the dimer of the wild type, and both carbohydrate-binding sites were retained. The unfolding curve of the wild type with lactose suggested that the dimer dissociation and the tertiary structure unfolding was concomitant at micromolar protein concentrations. The midpoint denaturant concentration of the wild type was dependent on the protein concentration and lower than that of the mutant. Linking the two subunits significantly stabilized the tertiary structure. The mutant exhibited higher T-cell growth-inhibition activity and comparable hemagglutinating activity. Structural stabilization may prevent the oxidation of the internal cysteine residue.
Comparative law at the heart of immigration law: Criminal inadmissibility and conjugal immigration in Canada and the United States
Authors: Szigeti Péter D 
Published: October 2021

Abstract
Immigration law is necessarily a comparative legal practice in at least three aspects: (i) comparing a would-be immigrant’s criminal history to the destination state’s criminal laws; (ii) comparing an immigrant’s diplomas and education to the destination state’s educational system; and (iii) comparing immigrants’ marriages and intimate relationships to domestic family law regimes. For all of these questions, the methodological dilemmas of comparative law are repeated within immigration law. This article is an overview of all the comparative methods used in North American immigration laws since the 1880s, for evaluating criminal records and intimate partnerships. The methods range from plain translations to complex systemic comparisons. Over the last 130 years, almost all methods had some, either good faith or strategic use; with the biggest transformations happening in the comparison of marriages. Effectively, private international law has been replaced by a separate “immigration marriage law,” which has globalized at astonishing speed.
Distinct Role of Dopamine in the PFC and NAc During Exposure to Cocaine-Associated Cues
Authors: Kawahara Yukie , Ohnishi Yoshinori N , Ohnishi Yoko H , Kawahara Hiroshi , Nishi Akinori 
Published: October 2021

Abstract

Background
Dopamine neurotransmission plays a critical role in reward in drug abuse and drug addiction. However, the role of dopamine in the recognition of drug-associated environmental stimuli, retrieval of drug-associated memory, and drug-seeking behaviors is not fully understood.

Methods
Roles of dopamine neurotransmission in the prefrontal cortex (PFC) and nucleus accumbens (NAc) in the cocaine-conditioned place preference (CPP) paradigm were evaluated using in vivo microdialysis.

Results
In mice that had acquired cocaine CPP, dopamine levels in the PFC, but not in the NAc, increased in response to cocaine-associated cues when mice were placed in the cocaine chamber of an apparatus with 2 separated chambers. The induction of the dopamine response and the development of cocaine CPP were mediated through activation of glutamate NMDA (N-methyl-D-aspartate)/AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor signaling in the PFC during conditioning. Activation of dopamine D1 or D2 receptor signaling in the PFC was required for cocaine-induced locomotion, but not for the induction of the dopamine response or the development of cocaine CPP. Interestingly, dopamine levels in the NAc increased in response to cocaine-associated cues when mice were placed at the center of an apparatus with 2 connected chambers, which requires motivated exploration associated with cocaine reward.

Conclusions
Dopamine neurotransmission in the PFC is activated by the exposure to the cocaine-associated cues, whereas dopamine neurotransmission in the NAc is activated in a process of motivated exploration of cues associated with cocaine reward. Furthermore, the glutamate signaling cascade in the PFC is suggested to be a potential therapeutic target to prevent the progression of drug addiction.
Comparison Theorems for 3D Manifolds With Scalar Curvature Bound
Authors: Munteanu Ovidiu , Wang Jiaping 
Published: October 2021

Abstract
Two sharp comparison results are derived for 3D complete noncompact manifolds with scalar curvature bounded from below. The 1st one concerns the Green’s function. When the scalar curvature is nonnegative, it states that the rate of decay of an energy quantity over the level set is strictly less than that of the Euclidean space unless the manifold itself is isometric to the Euclidean space. The result is in turn converted into a sharp area comparison for the level set of the Green’s function when in addition the Ricci curvature of the manifold is assumed to be asymptotically nonnegative at infinity. The 2nd result provides a sharp upper bound of the bottom spectrum in terms of the scalar curvature lower bound, in contrast to the classical result of Cheng, which involves a Ricci curvature lower bound.
Are clinicians using routinely collected data to drive practice improvement? A cross-sectional survey
Authors: Gawthorne Julie , Fasugba Oyebola , Levi Chris , Mcinnes Elizabeth , Ferguson Caleb , Mcneil John j , Cadilhac Dominique a , Everett Bronwyn , Fernandez Ritin , Fry Margaret , Goldsmith Helen , Hickman Louise , Jackson Deborah , Maguire Jane , Murray Edel , Perry Lin , Middleton Sandy 
Published: October 2021

Abstract

Background
Clinical registry participation is a measure of healthcare quality. Limited knowledge exists on Australian hospitals’ participation in clinical registries and whether this registry data informs quality improvement initiatives.

Objective
To identify participation in clinical registries, determine if registry data inform quality improvement initiatives, and identify registry participation enablers and clinicians’ educational needs to improve use of registry data to drive practice change.

Methods
A self-administered survey was distributed to staff coordinating registries in seven hospitals in New South Wales, Australia. Eligible registries were international-, national- and state-based clinical, condition-/disease-specific and device/product registries.

Results
Response rate was 70% (97/139). Sixty-two (64%) respondents contributed data to 46 eligible registries. Registry reports were most often received by nurses (61%) and infrequently by hospital executives (8.4%). Less than half used registry data ‘always’ or ‘often’ to influence practice improvement (48%) and care pathways (49%). Protected time for data collection (87%) and benchmarking (79%) were ‘very likely’ or ‘likely’ to promote continued participation. Over half ‘strongly agreed’ or ‘agreed’ that clinical practice improvement training (79%) and evidence–practice gap identification (77%) would optimize use of registry data.

Conclusions
Registry data are generally only visible to local speciality units and not routinely used to inform quality improvement. Centralized on-going registry funding, accessible and transparent integrated information systems combined with data informed improvement science education could be first steps to promote quality data-driven clinical improvement initiatives.