bluuebunny/crossref_metadata_2025_split huggingface dataset:
Challenges in the Management of Wilms Tumor in a Developing Country: A Twenty Years’ Experience From a Single Center in Pakistan
Authors: Khan Muhammad Rahil , Maaz Ata Ur Rehman , Ashraf Muhammad Shamvil 
Published: August 2022

Background:
Wilms Tumor (WT) is one of the most curable childhood cancers. High cure rates seen in the developed countries are not reproduced in developing countries. Lack of access to cancer treatment facilities, financial constraints, late presentation, and abandonment have previously been described. We reviewed our data over the last 20 years to highlight some of these challenges.

Methods:
This is a retrospective chart review of children with WT at our center up to the age of 18 years between 1 November 1997 and 30 November 2017. Demographic details, presentation characteristics and treatment details were recorded. Factors associated with poor outcome were analyzed.

Results:
Two hundred eleven children were registered; 117(55.5%) were males. Median age at presentation was 3 (range 0 to 18) years. Presentation data were available for 184/211 patients, staging details for 159/211 and metastatic status for 178/211. Of the available dataset, 60% presented without prior treatment, whereas 40% presented atleast after primary surgical excision. High-stage (stage III or above) disease was present in 79 (49.7%) patients; 61 (34.3%) was presented with metastases or recurrence; 63 (29.8%) abandoned or refused treatment; 99/172 (57.6%) patients finished treatment, 23 (13.4%) died during treatment, and 6 died before treatment. Of the 99 patients who finished treatment 83 (83.8%) are well off therapy; 15(15.2%) relapsed; 6 (40%) are alive after salvage therapy, while 9 (60%) died.

Conclusions:
Our data highlights the challenges of managing WT in resource poor environments. Prior surgery, incomplete staging work-up and abandonment are some of the most frequently encountered barriers. A multipronged approach is required to overcome these challenges.
Re-evaluate the Prognostic Value of Absolute Lymphocyte Count in Pediatric Immune Thrombocytopenia
Authors: Yang Ximei , Wan Xianghui , Huang Chao , Fu Jingjing , Hu Xiaolu , Le Ping , Ke Jiangwei 
Published: August 2022

To re-evaluate the prognostic value of absolute lymphocyte count (ALC) in pediatric immune thrombocytopenia (ITP) from the perspective of age. A total of 242 ITP pediatric patients, including 141 newly diagnosed ITP (nITP), 89 chronic ITP (cITP), and 12 persistent ITP, were retrospectively reviewed for this study. These patients were divided into 3 groups according to age (group 1, ≤24 m; group 2, 24−72 m; and group 3, >72 m). The ALC detected at admission was significantly different between nITP and cITP patients without considering their age difference (5.22 vs. 3.55×109/L, P<0.001). However, no significant difference was discovered after age stratification (≤24 m: 6.52 vs. 5.34×109/L, P=0.161; 24−72 m: 3.78 vs. 3.63×109/L, P=0.748; >72 m: 2.53 vs. 2.40×109/L, P=0.748). ROC analysis showed that the prognostic value of ALC in ITP children was limited (area under curve (AUC): ≤24 m, 24−72 m, and >72 m were 0.591, 0.570, and 0.542, respectively). Analysis of covariance showed there was no significant difference in ALC between nITP and cITP when considering age as a covariate (P=0.131). Instead, the ROC showing that platelet to lymphocyte ratio (PLR) has prognostic value in pediatric ITP independent of age stratification (≤24 m: AUC, 0.688; 24−72 m: AUC, 0.741; >72 m: AUC, 0.680). In conclusion, there was no significant difference of ALC between nITP and cITP patients when stratified by different age groups, and PLR may be an optional prognostic indicator for ITP.
Seeking Standardized Definitions for HLA-incompatible Kidney Transplants: A Systematic Review
Authors: Jatana Sukhdeep S. , Zhao Hedi , Bow Laurine M. , Cozzi Emanuele , Batal Ibrahim , Horak Tillie , Amar-Zifkin Alexandre , Schinstock Carrie , Askar Medhat , Dadhania Darshana M. , Cooper Matthew , Naesens Maarten , Kraus Edward S. , Sapir-Pichhadze Ruth ,   on behalf of the Banff Antibody-Mediated Injury Working Group
Published: August 2022

Background.
There is no standard definition for “HLA incompatible” transplants. For the first time, we systematically assessed how HLA incompatibility was defined in contemporary peer-reviewed publications and its prognostic implication to transplant outcomes.

Methods.
We combined 2 independent searches of MEDLINE, EMBASE, and the Cochrane Library from 2015 to 2019. Content-expert reviewers screened for original research on outcomes of HLA-incompatible transplants (defined as allele or molecular mismatch and solid-phase or cell-based assays). We ascertained the completeness of reporting on a predefined set of variables assessing HLA incompatibility, therapies, and outcomes. Given significant heterogeneity, we conducted narrative synthesis and assessed risk of bias in studies examining the association between death-censored graft failure and HLA incompatibility.

Results.
Of 6656 screened articles, 163 evaluated transplant outcomes by HLA incompatibility. Most articles reported on cytotoxic/flow T-cell crossmatches (n = 98). Molecular genotypes were reported for selected loci at the allele-group level. Sixteen articles reported on epitope compatibility. Pretransplant donor-specific HLA antibodies were often considered (n = 143); yet there was heterogeneity in sample handling, assay procedure, and incomplete reporting on donor-specific HLA antibodies assignment. Induction (n = 129) and maintenance immunosuppression (n = 140) were frequently mentioned but less so rejection treatment (n = 72) and desensitization (n = 70). Studies assessing death-censored graft failure risk by HLA incompatibility were vulnerable to bias in the participant, predictor, and analysis domains.

Conclusions.
Optimization of transplant outcomes and personalized care depends on accurate HLA compatibility assessment. Reporting on a standard set of variables will help assess generalizability of research, allow knowledge synthesis, and facilitate international collaboration in clinical trials.
Temporal Characteristics of Neonatal Chick Retinal Ganglion Cell Responses: Effects of Luminance, Contrast, and Color
Authors: CS Deepak , Krishnan Abhijith , Narayan K S 
Published: August 2022

AbstractWe perform microelectrode array recordings of neonatal chick retina explants and report stimulus-dependent response properties of different retinal ganglion cell (RGC) types to various luminance and contrast adaptation conditions. The isolated single units indicate wavelength-sensitive response properties for all the retinal ganglion cell types recorded from. Responses to different luminance and contrast conditions investigated as a function of wavelength indicates a combination of adaptation and sensitization features in the recorded population of RGCs. We further demonstrate the presence of complementary response properties in most of the RGCs to blue (450 nm) and green (530 nm) light input and infer that luminance, contrast and color information are encoded in a wide variety of metrics such as latency, response event duration and pairwise correlations.
Pair housing does not alter incubation of craving, extinction, and reinstatement after heroin self-administration in female and male rats
Authors: Nett Kelle E. , LaLumiere Ryan T. 
Published: August 2022

AbstractRationaleEvidence suggests that single housing in rats acts as a chronic stressor, raising the possibilities that it contributes to measures of heroin craving and that pair housing ameliorates such measures.ObjectivesThis study aimed to determine whether pair housing after heroin self-administration reduces the incubation of craving, extinction, and reinstatement of heroin seeking.MethodsSingle-housed female and male Sprague-Dawley rats underwent daily 6-h heroin self-administration, wherein active lever presses produced a heroin infusion paired with light/tone cues. One d after self-administration, rats underwent a baseline cued-seeking test wherein active lever presses only produced light/tone cues. Immediately following this cued-seeking test, rats were either pair-housed with a weight- and sex-matched naïve rat or remained single-housed for the rest of the study. For 14 d, rats remained in their homecages, after which they underwent a cued-seeking test to assess the incubation of craving compared to their baseline test. Rats then underwent extinction sessions followed by cue-induced and heroin-primed reinstatements.ResultsThe findings reveal that pair-housed rats did not differ from single-housed rats in terms of the incubation of craving, extinction, or reinstatement of heroin seeking. Additionally, the results did not reveal any evidence of sex-based differences in the study.ConclusionsThe present work indicates that pair housing during the forced abstinence period does not alter measures of heroin craving/seeking. These findings suggest that the chronic stress of single housing specifically during forced abstinence does not contribute to the degree of such measures.
Electrophysiological signature of the interplay between habits and inhibition in response to smoking-related cues in individuals with a smoking habit: an ERP study
Authors: Dampuré Julien , Agudelo-Orjuela Paola , Van Der Meij Maartje , Belin David , Barber Horacio A. 
Published: August 2022

AbstractThe rigid, stimulus-bound nature of drug seeking that characterizes Substance-use disorder (SUD) has been related to a dysregulation of motivational and early attentional reflexive and inhibitory reflective systems. However, the mechanisms by which these systems are engaged by drug-paired conditioned stimuli CSs) when they promote the enactment of seeking habits in individuals with a SUD have not been elucidated. The present study aimed behaviorally and electrophysiologically to characterize the nature of the interaction between the reflexive and reflective systems recruited by CSs in individuals with a smoking habit. For this, we measured the behavioral performance and associated ERPs of 20 individuals with a smoking habit and 20 controls, who never smoked regularly, in a modified Go/NoGo task during which smoking-related CSs, appetitive, and neutral pictures, presented either in first-person or as a third-person visual perspective were displayed 250 ms before the Go/NoGo cue. We show that smoking-related cues selectively influence early incentive motivation-related attentional bias (N2 after picture onset), motor readiness and behavioral inhibition (Go-P3, NoGo-P3 and Pc) of individuals with a smoking habit only when presented from a first-person perspective. These data together identify the neural signature of the aberrant engagement of the reflexive and reflective systems during the recruitment of an incentive habit by CSs presented as if they had been response-produced, i.e., as conditioned reinforcers.
A Tale of Two Trees: Modeling Apical and Basal Tree Contribution to L2/3 V1 Pyramidal Cell Orientation Selectivity
Authors: Petousakis Konstantinos-Evangelos , Park Jiyoung , Papoutsi Athanasia , Smirnakis Stelios , Poirazi Panayiota 
Published: August 2022

Pyramidal neurons, a mainstay of cortical regions, receive a plethora of inputs from various areas onto their morphologically distinct apical and basal trees. Both trees differentially contribute to the somatic response, defining distinct anatomical and possibly functional sub-units. To elucidate the contribution of each tree to the encoding of visual stimuli at the somatic level, we modeled the response pattern of a L2/3 V1 pyramidal neuron to orientation tuned synaptic input. Towards this goal, we used a morphologically detailed computational model of a single cell that replicates electrophysiological and two-photon imaging data. Our simulations predict a synergistic effect of apical and basal trees on somatic action potential generation: basal tree activity, in the form of either depolarization or dendritic spiking, is necessary for producing somatic activity, despite the fact that most somatic spikes are heavily driven by apical dendritic spikes. This model provides evidence for synergistic computations taking place in the basal and apical trees of the L2/3 V1 neuron along with mechanistic explanations for tree-specific contributions and emphasizes the potential role of predictive and attentional feedback input in these cells.Abstract FigureAbstract FigureGraphical Representation of AP Generation in a L2/3 V1 Pyramidal Neuron ModelAction potential generation requires the spatiotemporal coincidence of apical sodium spikes with either basal sodium spikes or significant basal depolarizations, allowing the neuron to respond to salient stimuli that may or may not be affected by attentional and/or predictive signals from higher-order areas.
Gender imbalances in citation rates are mediated by field specific author gender distributions
Authors: Riemann Steffen , Roheger Mandy , Kohlschmidt Jan , Kirschke Jennifer , Lillo Margherita , Flöel Agnes , Meinzer Marcus 
Published: August 2022

AbstractGender biases are well documented in science and typically favor male scientists. In this context, a particularly pervasive gender bias is undercitation of publications authored by women, resulting in profound negative effects on academic visibility and career advancement. This bias has been well documented in fields where author gender distributions are strongly skewed towards men (e.g., astronomy, physics, neuroscience). By investigating citation practices in a field that has traditionally been more accessible to female scientists (Speech and Language Pathology, SLP), we demonstrate that gendered citation practices are mediated by author gender distribution, rather than being a universal pattern. Specifically, our results revealed a citation pattern in SLP that (a) overall tends to favor female authors, (b) persists after controlling for potential confounding factors and, (c) is particularly strong when female authors are citing publications involving female first and senior author teams. This research also implies that the implementation of effective measures to increase the number and influence of underrepresented individuals in specific fields of science may be suitable to mitigate downstream disadvantages for career advancement of either sex.
Temporal Mapper: transition networks in simulated and real neural dynamics
Authors: Zhang Mengsen , Chowdhury Samir , Saggar Manish 
Published: August 2022

AbstractCharacterizing large-scale dynamic organization of the brain relies on both data-driven and mechanistic modeling, which demands a low vs. high level of prior knowledge and assumptions about how constituents of the brain interact. However, the conceptual translation between the two is not straightforward. The present work aims to provide a bridge between data-driven and mechanistic modeling. We conceptualize brain dynamics as a complex landscape that is continuously modulated by internal and external changes. The modulation can induce transitions between one stable brain state (attractor) to another. Here, we provide a novel method – Temporal Mapper – built upon established tools from the field of Topological Data Analysis to retrieve the network of attractor transitions from time-series data alone. For theoretical validation, we use a biophysical network model to induce transitions in a controlled manner, which provides simulated time series equipped with a ground-truth attractor transition network. Our approach reconstructs the ground-truth transition network from simulated time-series data better than existing time-varying approaches. For empirical relevance, we apply our approach to fMRI data gathered during a continuous multitask experiment. We found that occupancy of the high-degree nodes and cycles of the transition network was significantly associated with subjects’ behavioral performance. Taken together, we provide an important first step towards integrating data-driven and mechanistic modeling of brain dynamics.
Exact polynomial-time isomorphism testing in directed graphs through comparison of vertex signatures in Krylov subspaces
Authors: O’Shea Robert John 
Published: August 2022

AbstractMotivationThe complexity of the isomorphism problem in directed graphs has remained unsolved to date. This study examines the properties of Krylov matrices, demonstrating that they may be used to generate vertex “signatures” to allow exact analogy testing in directed graphs.ResultsA “vertex signature” is defined by initialising a Krylov matrix with a binary vector indicating the vertex position. This study demonstrates that signatures of analogous vertices are related by a linear-ordering transformation. It is demonstrated that equality of ordered vertex signatures is necessary and sufficient to demonstrate analogy. Thus, analogous vertices may be identified by checking each of the n candidates sequentially. This result is extended to analogous vertex sets. Thus, the isomorphic mapping may be constructed iteratively ℴ(n5) time by building a set of vertex analogies sequentially. The algorithm is applied to a dataset of enzyme structures, with comparison to a common heuristic algorithm.Availability and ImplementationSource code is provided at github.com/robertoshea/graph_isomorphism_directed.Contactrobert.1.oshea@kcl.ac.ukSupplementary DataSupplementary results are attached.
Basolateral amygdala and orbitofrontal cortex, but not dorsal hippocampus, are necessary for the control of reward-seeking by occasion setters
Authors: Fraser Kurt M. , Janak Patricia H. 
Published: August 2022

ABSTRACTReward-seeking in the world is driven by cues that can have ambiguous predictive and motivational value. To produce adaptive, flexible reward-seeking it is necessary to exploit occasion setters, other distinct features in the environment, to resolve the ambiguity of Pavlovian reward-paired cues. Despite this, very little research has investigated the neurobiological underpinnings of occasion setting and as a result little is known about which brain regions are critical for occasion setting. To address this, we exploited a recently developed task that was amenable to neurobiological inquiry where a conditioned stimulus is only predictive of reward delivery if preceded in time by the non-overlapping presentation of a separate cue - an occasion setter. This task required male rats to maintain and link cue-triggered expectations across time to produce adaptive reward-seeking. We interrogated the contributions of the basolateral amygdala and orbitofrontal cortex to occasion setting as these regions are thought to be critical for the computation and exploitation of state value, respectively. Reversible inactivation of either structure prior to the occasion-setting task resulted in a profound inability of rats to use the occasion setter to guide reward seeking. In contrast, inactivation of the dorsal hippocampus, a region fundamental for context-specific responding was without effect nor did inactivation of the basolateral amygdala or orbitofrontal cortex in a standard Pavlovian conditioning preparation affect conditioned responding. We conclude that neural activity within the orbitofrontal cortex and basolateral amygdala circuit is necessary to update and resolve ambiguity in the environment to promote cue-driven reward-seeking.
Using agent-based models to predict pollen deposition in a dioecious crop
Authors: Broussard Melissa A. , Jochym Mateusz , Tomer Nathan , Jesson Linley , Shaw Allison K. , Crowder David W. , Bosque-Pérez Nilsa A. , Li Jing , Peace Angela , Fonseka Dilini , Howlett Brad , Pattemore David 
Published: August 2022

AbstractPollination involves complex interactions between plants and pollinators, and variation in plant or pollinator biology can lead to variability in pollination services that are difficult to predict. Models that effectively predict pollination services could enhance the ability to conserve plant-pollinator mutualisms in natural systems and increase crop yields in managed systems. However, while most pollination models have focused either on effects of plant or pollination biology, few models have integrated plant-pollinator interactions. Moreover, crop management causes variation in plant-pollinator interactions and pollination services, but management is rarely considered in pollination models. Here we used extensive datasets for kiwifruit (Actinidia chinensis var. deliciosa) to develop an agent-based model to track insect-provided pollination services with variation in crop cultivars, pollinator traits, and orchard layouts. This allowed us to predict pollination outcomes in a dioecious crop under a range of management scenarios. Our sensitivity analysis indicated that flower density and the proportion of female flowers are the most important factors in successful pollination, both of which growers control via cultivar selection and cultural management practices. Our analysis also indicated that economically viable pollination services and crop yields are attained with ∼60% female flowers and a peak foraging activity of 6 to 8 bees per 1,000 open flowers with diminishing returns for additional pollinators. The quality of pollination service varied across simulated orchard layouts, highlighting the potential use of this model as a framework to screen novel orchard configurations. More broadly, linking complex plant and pollinator interactions in pollination models can help identify factors that may improve crop yields and provide a framework for identifying factors important to pollination in natural ecosystems.HIGHLIGHTS- We develop a model using extensive empirical datasets to predict pollen deposition based on the interactions between flowers and pollinators in a dioecious crop system- We conducted a thorough sensitivity analysis, and analysis of the effect of stochastic variance between model runs, which can be used to inform future design of stochastic agent-based models- Our model effectively predicted the outcomes of varying management regimes of orchard layouts and pollinator introductions on pollination in a dioecious crop- Our model can be extended for other functionally dioecious crops or plant communities where managers want to understand how their decisions impact pollination
Acrylamide Induces Protein Aggregation in CNS through Suppression of FoxO1-mediated Autophagy
Authors: He Xi-Biao , Huang Haozhi , Wu Yi , Guo Fang 
Published: August 2022

ABSTRACTProteotoxic stress is a major stimulus and risk factor for the neuropathogenesis in central nervous system (CNS), which is tightly associated with neurodegenerative diseases. Here, we identify acrylamide (ACR), a type-2 alkene that is commonly detected in deep-fried starch food and used in water industry and biomedical laboratories, as a potent and universal inducer of proteotoxic stress in mouse brain, as well as in cultured mouse neural stem cells, neurons and astrocytes, three major cell types in CNS. Aggregations of ubiquitin-labeled misfolded proteins and neurodegeneration-related proteins including amyloid precursor protein and presenilin 1 were drastically induced by ACR, leading to cell-defensive aggresome formation that was able to temporarily counteract with ACR toxicity. However, a defected clearance of aggresomes eventually led to apoptotic cell death, which was largely attributed to the breakdown of cytoskeleton and impairment of macroautophagy/autophagy, as evidenced by an aggregation of filament actin and an almost complete loss of LC3-positive autophagosomes. A series of core autophagy-related genes responsible for autophagosome formation were down-regulated, indicating an ACR-induced transcriptional suppression of autophagy. In addition, FoxO1, the master transactivator of these genes, were both transcriptionally repressed and nuclear excluded by ACR. Overexpression of FoxO1 rescued ACR-induced autophagy defects and attenuated the proteotoxicity. In summary, we spotlight proteotoxic stress as a novel feature of ACR neurotoxicity in CNS, and implicate FoxO1 as a critical therapeutic target.