bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autologous T cell responses to primary human colorectal cancer spheroids are enhanced by ectonucleotidase inhibition
Authors: Bonnereau Julie , Courau Tristan , Asesio Nicolas , Salfati Delphine , Bouhidel Fatiha , Corte Hélène , Hamoudi Sarah , Hammoudi Nassim , Lavolé Julie , Vivier-Chicoteau Justine , Chardiny Victor , Maggiori Leon , Blery Mathieu , Remark Romain , Bonnafous Cécile , Cattan Pierre , Toubert Antoine , Bhat Purnima , Allez Matthieu , Aparicio Thomas , Le Bourhis Lionel 
Published: July 2022

ObjectiveT cells are major effectors of the antitumoural immune response. Their activation by tumour-associated antigens can unleash their proliferation and cytotoxic functions, leading to tumour cell elimination. However, tumour-related immunosuppressive mechanisms including the overexpression of immune checkpoints like programmed cell death protein-1 (PD-1), are also engaged, promoting immune escape. Current immunotherapies targeting these pathways have demonstrated weak efficacy in colorectal cancer (CRC). It is thus crucial to find new targets for immunotherapy in this cancer type.DesignIn a prospective cohort of patients with CRC, we investigated the phenotype of tumour-related and non-tumour related intestinal T cells (n=44), particularly the adenosinergic pathway, correlating with clinical phenotype. An autologous coculture model was developed between patient-derived primary tumour spheroids and their autologous tumour-associated lymphocytes. We used this relevant model to assess the effects of CD39 blockade on the antitumour T cell response.ResultsWe show the increased expression of CD39, and its co-expression with PD-1, on tumour infiltrating T cells compared with mucosal lymphocytes. CD39 expression was higher in the right colon and early-stage tumours, thus defining a subset of patients potentially responsive to CD39 blockade. Finally, we demonstrate in autologous conditions that CD39 blockade triggers T cell infiltration and tumour spheroid destruction in cocultures.ConclusionIn CRC, CD39 is strongly expressed on tumour infiltrating lymphocytes and its inhibition represents a promising therapeutic strategy for treating patients.
Pattern of congenital anomalies among pediatric surgical patients in a tertiary care hospital in northern Tanzania
Authors: Magwesela Faraja Mussa , Rabiel Happiness , Mung'ong'o Catherine Mlelwa 
Published: July 2022

BackgroundCongenital anomalies are major causes of morbidity and mortality in children under 5 years of age and make a significant contribution to the surgical burden of diseases. Most anomalies have multifactorial causes and commonly affect the central nervous, cardiovascular, gastrointestinal and musculoskeletal systems. Countries with improved pediatric surgical care have shown dramatic reductions in morbidity and mortality rates. The aim of this study was to analyze the pattern of congenital anomalies presenting in our surgical departments in patients under 5 years of age.MethodsA retrospective descriptive study was done. Data were obtained from clinical records of patients under 5 years of age, who underwent surgical correction of their congenital anomalies between 2017 and 2021. Analysis was done to identify the proportion of congenital anomalies managed in our setting.ResultsCongenital anomalies contributed 4.6% of overall surgical burden. Totally, 822 patients with congenital anomalies were included for analysis. The most commonly diagnosed congenital anomaly was inguinal hernia, followed by hydrocephalus, neural tube defects and cleft lips. The most commonly affected system was the central nervous system, anterior abdominal wall, orofacial and digestive system in decreasing order of frequency. Most of our patients presented outside the neonatal period (84.4%), and few (16.1%) had more than one system affected. Male children comprised 64%.ConclusionsDelayed presentation of children with congenital anomalies is still a significant problem in our area. Prevention through nutritional supplementation and antenatal screening is crucial. The true epidemiology of congenital anomalies in northern Tanzania is still obscure.
Extreme dilaton black holes in 2 + 1 dimensions: quasinormal modes
Authors: Fernando Sharmanthie , González P. A. , Vásquez Yerko 
Published: July 2022

AbstractWe study neutral massless scalar field perturbations around an extreme dilaton black hole in 2 + 1 dimensions: the wave equations of the massless scalar field is shown to be exactly solvable in terms of Whittaker functions. Thus, the quasinormal modes are computed exactly and shown to be purely imaginary: we show the existence of stable and unstable modes. Interestingly, the quasinormal modes do not depend on the black holes parameters and the fundamental mode is always unstable and depends only on the parameters of the test field. Also, we determine the quasinormal frequencies via the improved asymptotic iteration method which shows a good agreement with the analytical results.
Sequential Fair Allocation
Authors: Sinclair Sean R. , Banerjee Siddhartha , Yu Christina Lee 
Published: July 2022

We consider the problem of dividing limited resources to individuals arriving over T rounds. Each round has a random number of individuals arrive, and individuals can be characterized by their type (i.e. preferences over the different resources). A standard notion of 'fairness' in this setting is that an allocation simultaneously satisfy envy-freeness and efficiency. For divisible resources, when the number of individuals of each type are known upfront, the above desiderata are simultaneously achievable for a large class of utility functions. However, in an online setting when the number of individuals of each type are only revealed round by round, no policy can guarantee these desiderata simultaneously.
We show that in the online setting, the two desired properties (envy-freeness and efficiency) are in direct contention, in that any algorithm achieving additive counterfactual envy-freeness up to a factor of LT necessarily suffers a efficiency loss of at least 1 / LT. We complement this uncertainty principle with a simple algorithm, Guarded-Hope, which allocates resources based on an adaptive threshold policy and is able to achieve any fairness-efficiency point on this frontier.
Dietary Supplementation of Crystalline Amino Acid Improves Growth Performance and Health of Yellow Catfish That Reduced by Plant Proteins Replacement of Fishmeal
Authors: Wang Shidong , Li Xue , Zhang Muzi , Jiang Haibo , Li Ming 
Published: July 2022

To evaluate the growth and health of yellow catfish (

5.50
±
0.61

g) under the conditions of unbalanced and balanced amino acid composition, an 8-week growth experiment was conducted. Three isoenergetic and isonitrogenous diets were formulated with a graded level of fishmeal: control group was formulated with 560.00 g/kg fishmeal, and 25%PP group and 25%PP + AA group were formulated with 420.00 g/kg fishmeal (replace 25% of fishmeal with plant protein), and then 25%PP + AA group was supplemented with threonine, glycine, alanine, methionine, isoleucine, histidine, and lysine. Compared with control group, weight gain (WG), specific growth rate (SGR), and survival (SUR) in 25%PP group were significantly the lowest (

p
<
0.05

), but feed conversion ratio (FCR) was higher than those in control group (

p
<
0.05

). After supplementation of crystalline amino acid, the WG, SGR, SUR, and FCR in 25%PP + AA group were recovered to the level of control group (

p
>
0.05

). Compared with control group, the activities of trypsin and lipase were significantly increased in 25%PP group and 25%PP + AA group (

p
<
0.05

). Liver impairment was exhibited in 25%PP group, mainly manifested as significantly increased contents of aspartate aminotransferase (AST) and alanine transaminase (ALT) (

p
<
0.05

). Supplementation of crystalline amino acids based on a 25%PP diet significantly reduced activities of AST and ALT (

p
<
0.05

). In addition, total antioxidant capacity (T-AOC), superoxide dismutase (SOD), acid phosphatase (ACP), and alkaline phosphatase (AKP) activities in 25%PP group increased significantly (

p
<
0.05

). Data from 25%PP + AA group showed that crystalline amino acid supplementation ameliorated antioxidant (T-AOC and SOD) and immune (ACP and AKP) (

p
<
0.05

). One of the characteristics of intestinal damage is shortening of villi height, which was significantly reduced in 25%PP group (

p
<
0.05

). In short, unbalanced amino acid intake can impact growth, survival, and physiological status of yellow catfish. Diet supplemented with unbalanced amino acid can cause abnormal accumulation of amino acid content in muscle, resulting in unnecessary consumption of nutrients. Dietary supplementation of crystalline amino acid improves growth performance and health of yellow catfish that reduced by plant proteins replacement of fishmeal.
Assessment of Androgen Receptor Splice Variant-7 as a Biomarker of Clinical Response in Castration-Sensitive Prostate Cancer
Authors: Sowalsky Adam G. , Figueiredo Ines , Lis Rosina T. , Coleman Ilsa , Gurel Bora , Bogdan Denisa , Yuan Wei , Russo Joshua W. , Bright John R. , Whitlock Nichelle C. , Trostel Shana Y. , Ku Anson T. , Patel Radhika A. , True Lawrence D. , Welti Jonathan , Jimenez-Vacas Juan M. , Rodrigues Daniel Nava , Riisnaes Ruth , Neeb Antje , Sprenger Cynthia T. , Swain Amanda , Wilkinson Scott , Karzai Fatima , Dahut William L. , Balk Steven P. , Corey Eva , Nelson Peter S. , Haffner Michael C. , Plymate Stephen R. , de Bono Johann S. , Sharp Adam 
Published: July 2022

Abstract

Purpose:
Therapies targeting the androgen receptor (AR) have improved the outcome for patients with castration-sensitive prostate cancer (CSPC). Expression of the constitutively active AR splice variant-7 (AR-V7) has shown clinical utility as a predictive biomarker of AR-targeted therapy resistance in castration-resistant prostate cancer (CRPC), but its importance in CSPC remains understudied.

Experimental Design:
We assessed different approaches to quantify AR-V7 mRNA and protein in prostate cancer cell lines, patient-derived xenograft (PDX) models, publicly available cohorts, and independent institutional clinical cohorts, to identify reliable approaches for detecting AR-V7 mRNA and protein and its association with clinical outcome.

Results:
In CSPC and CRPC cohorts, AR-V7 mRNA was much less abundant when detected using reads across splice boundaries than when considering isoform-specific exonic reads. The RM7 AR-V7 antibody had increased sensitivity and specificity for AR-V7 protein detection by immunohistochemistry (IHC) in CRPC cohorts but rarely identified AR-V7 protein reactivity in CSPC cohorts, when compared with the EPR15656 AR-V7 antibody. Using multiple CRPC PDX models, we demonstrated that AR-V7 expression was exquisitely sensitive to hormonal manipulation. In CSPC institutional cohorts, AR-V7 protein quantification by either assay was associated neither with time to development of castration resistance nor with overall survival, and intense neoadjuvant androgen-deprivation therapy did not lead to significant AR-V7 mRNA or staining following treatment. Neither pre- nor posttreatment AR-V7 levels were associated with volumes of residual disease after therapy.

Conclusions:
This study demonstrates that further analytical validation and clinical qualification are required before AR-V7 can be considered for clinical use in CSPC as a predictive biomarker.
Characterizing Dynamic Neural Representations of Scene Attractiveness
Authors: Kaiser Daniel 
Published: July 2022

Abstract
Aesthetic experiences during natural vision are varied: They can arise from viewing scenic landscapes, interesting architecture, or attractive people. Recent research in the field of neuroaesthetics has taught us a lot about where in the brain such aesthetic experiences are represented. Much less is known about when such experiences arise during the cortical processing cascade. Particularly, the dynamic neural representation of perceived attractiveness for rich natural scenes is not well understood. Here, I present data from an EEG experiment, in which participants provided attractiveness judgments for a set of diverse natural scenes. Using multivariate pattern analysis, I demonstrate that scene attractiveness is mirrored in early brain signals that arise within 200 msec of vision, suggesting that the aesthetic appeal of scenes is first resolved during perceptual processing. In more detailed analyses, I show that even such early neural correlates of scene attractiveness are partly related to interindividual variation in aesthetic preferences and that they generalize across scene contents. Together, these results characterize the time-resolved neural dynamics that give rise to aesthetic experiences in complex natural environments.
Treatment of preschool children with obsessive compulsive disorder
Authors: Inci Izmir Sevim Berrin , Ercan Eyüp Sabri 
Published: July 2022

The aim was to examine the clinical features of Obsessive-Compulsive Disorder (OCD) in preschool and the effectiveness of aripiprazole with a standardized Cognitive-Behavioral Family Therapy (CBFT) in the treatment of preschoolers with OCD. Twelve preschool children, 36–72 months of age were diagnosed with OCD according to the Diagnostic and Statistical Manual of Mental Disorders, the Fifth Edition criteria by a fellowship-trained child and adolescent psychiatrist. They were evaluated with Kiddie Schedule for Affective Disorders and Schizophrenia for School-Age Children Present and Lifetime version and Childhood Yale-Brown Obsessive Compulsive Scale (CY-BOCS) at baseline, at the end of the 12th and 24th weeks of treatment. The baseline mean of total CY-BOCS score decreased from 33.67 to 13.83 at the 12th week and 5.58 at the end of the 24th week of treatment. Also, 66.7% of them had at least one psychiatric comorbidity. Overall, this study revealed the effect of aripiprazole with CBFT in preschool-aged children with OCD. Also, the presence of comorbidity that is seen frequently in preschoolers with OCD may complicate the treatment. Therefore, there is a need to increase awareness of OCD and its comorbidities in preschoolers to supply treatment at an early age.
Changing characteristics over time of individuals receiving COVID-19 vaccines in Denmark: A population-based descriptive study of vaccine uptake
Authors: Reilev Mette , Olesen Morten , Kildegaard Helene , Støvring Henrik , Andersen Jacob H. , Hallas Jesper , Lund Lars Christian , Ladebo Louise , Ernst Martin T. , Damkier Per , Jensen Peter B. , Pottegård Anton , Rasmussen Lotte 
Published: July 2022

Aims: The Danish authorities implemented a differential rollout of the COVID-19 vaccines where individuals at high risk of COVID-19 were prioritized. We describe the temporal uptake and characteristics of COVID-19 vaccine recipients in Denmark. Methods: Using nationwide healthcare registries, we identified all Danish residents ⩾5 years of age who received at least one dose of a COVID-19 vaccine from 27 December 2020–29 January 2022. We charted the daily number of newly vaccinated individuals and the cumulative vaccine coverage over time, stratified by vaccine type, age groups and vaccination priority groups, and described characteristics of vaccine recipients during two-month-intervals and in vaccination priority groups. Results: By 29 January 2022, 88%, 86% and 64% of Danish residents ⩾5 years ( n=5,562,008) had received a first, second and third dose, respectively, of a COVID-19 vaccine, most commonly the BNT162b2 vaccine (84%). Uptake ranged from 48% in 5–11-year-olds to 98% in 65–74-year-olds. Individuals vaccinated before June 2021 were older (median age 61–70 years vs 10–35 years in later periods) and had more comorbidities such as hypertension (22–28% vs 0.77–2.8% in later periods), chronic lung disease (9.4–15% vs 3.7–4.6% in later periods) and diabetes (9.3–12% vs 0.91–2.4% in later periods). Conclusions: We document substantial changes over time in, for example, age, sex and medical history of COVID-19 vaccine recipients. Though these results are related to the differential vaccine rollout in Denmark, similar findings are probable in other countries and should be considered when designing and interpreting studies on the effectiveness and safety of COVID-19 vaccines.
The returns to school-quality-adjusted education of immigrants in Germany
Authors: Le-Quang Huy , Vallizadeh Ehsan 
Published: July 2022

AbstractThis paper explores the role of school quality in immigrants’ home countries on their earnings in Germany, using native Germans as a benchmark. We propose an empirical analysis that highlights two important insights. First, there is a substantial gap in the returns to education between natives and immigrants in Germany, especially when we consider the quality of schooling in the source country where education was obtained. In particular, lower school quality reduces the endowment advantage that immigrants possess from their education. Second, quality-adjusted education helps us to better understand the potential driving force behind the native–immigrant wage gap. We show that this measure accounts for a substantial fraction of the unexplained part in the Oaxaca–Blinder decomposition. These findings emphasize the role of the school quality in explaining the imperfect transferability of human capital of immigrants in Germany.
J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments
Authors: Angaroni Fabrizio , Guidi Alessandro , Ascolani Gianluca , d’Onofrio Alberto , Antoniotti Marco , Graudenzi Alex 
Published: July 2022

Abstract
Background
The combined effects of biological variability and measurement-related errors on cancer sequencing data remain largely unexplored. However, the spatio-temporal simulation of multi-cellular systems provides a powerful instrument to address this issue. In particular, efficient algorithmic frameworks are needed to overcome the harsh trade-off between scalability and expressivity, so to allow one to simulate both realistic cancer evolution scenarios and the related sequencing experiments, which can then be used to benchmark downstream bioinformatics methods.

Result
We introduce a Julia package for SPAtial Cancer Evolution (J-SPACE), which allows one to model and simulate a broad set of experimental scenarios, phenomenological rules and sequencing settings.Specifically, J-SPACE simulates the spatial dynamics of cells as a continuous-time multi-type birth-death stochastic process on a arbitrary graph, employing different rules of interaction and an optimised Gillespie algorithm. The evolutionary dynamics of genomic alterations (single-nucleotide variants and indels) is simulated either under the Infinite Sites Assumption or several different substitution models, including one based on mutational signatures. After mimicking the spatial sampling of tumour cells, J-SPACE returns the related phylogenetic model, and allows one to generate synthetic reads from several Next-Generation Sequencing (NGS) platforms, via the ART read simulator. The results are finally returned in standard FASTA, FASTQ, SAM, ALN and Newick file formats.

Conclusion
J-SPACE is designed to efficiently simulate the heterogeneous behaviour of a large number of cancer cells and produces a rich set of outputs. Our framework is useful to investigate the emergent spatial dynamics of cancer subpopulations, as well as to assess the impact of incomplete sampling and of experiment-specific errors. Importantly, the output of J-SPACE is designed to allow the performance assessment of downstream bioinformatics pipelines processing NGS data. J-SPACE is freely available at: https://github.com/BIMIB-DISCo/J-Space.jl.
A detailed workflow to develop QIIME2-formatted reference databases for taxonomic analysis of DNA metabarcoding data
Authors: Dubois Benjamin , Debode Frédéric , Hautier Louis , Hulin Julie , Martin Gilles San , Delvaux Alain , Janssen Eric , Mingeot Dominique 
Published: July 2022

Abstract
Background
The DNA metabarcoding approach has become one of the most used techniques to study the taxa composition of various sample types. To deal with the high amount of data generated by the high-throughput sequencing process, a bioinformatics workflow is required and the QIIME2 platform has emerged as one of the most reliable and commonly used. However, only some pre-formatted reference databases dedicated to a few barcode sequences are available to assign taxonomy. If users want to develop a new custom reference database, several bottlenecks still need to be addressed and a detailed procedure explaining how to develop and format such a database is currently missing. In consequence, this work is aimed at presenting a detailed workflow explaining from start to finish how to develop such a curated reference database for any barcode sequence.

Results
We developed DB4Q2, a detailed workflow that allowed development of plant reference databases dedicated to ITS2 and rbcL, two commonly used barcode sequences in plant metabarcoding studies. This workflow addresses several of the main bottlenecks connected with the development of a curated reference database. The detailed and commented structure of DB4Q2 offers the possibility of developing reference databases even without extensive bioinformatics skills, and avoids ‘black box’ systems that are sometimes encountered. Some filtering steps have been included to discard presumably fungal and misidentified sequences. The flexible character of DB4Q2 allows several key sequence processing steps to be included or not, and downloading issues can be avoided. Benchmarking the databases developed using DB4Q2 revealed that they performed well compared to previously published reference datasets.

Conclusion
This study presents DB4Q2, a detailed procedure to develop custom reference databases in order to carry out taxonomic analyses with QIIME2, but also with other bioinformatics platforms if desired. This work also provides ready-to-use plant ITS2 and rbcL databases for which the prediction accuracy has been assessed and compared to that of other published databases.