bluuebunny/crossref_metadata_2025_split huggingface dataset:
In silico recognition of a prognostic signature in basal-like breast cancer patients
Authors: Conte Federica , Sibilio Pasquale , Grimaldi Anna Maria , Salvatore Marco , Paci Paola , Incoronato Mariarosaria 
Published: February 2022

Background
Triple-negative breast cancers (TNBCs) display poor prognosis, have a high risk of tumour recurrence, and exhibit high resistance to drug treatments. Based on their gene expression profiles, the majority of TNBCs are classified as basal-like breast cancers. Currently, there are not available widely-accepted prognostic markers to predict outcomes in basal-like subtype, so the selection of new prognostic indicators for this BC phenotype represents an unmet clinical challenge.

Results
Here, we attempted to address this challenging issue by exploiting a bioinformatics pipeline able to integrate transcriptomic, genomic, epigenomic, and clinical data freely accessible from public repositories. This pipeline starts from the application of the well-established network-based SWIM methodology on the transcriptomic data to unveil important (switch) genes in relation with a complex disease of interest. Then, survival and linear regression analyses are performed to associate the gene expression profiles of the switch genes with both the patients’ clinical outcome and the disease aggressiveness. This allows us to identify a prognostic gene signature that in turn is fed to the last step of the pipeline consisting of an analysis at DNA level, to investigate whether variations in the expression of identified prognostic switch genes could be related to genetic (copy number variations) or epigenetic (DNA methylation differences) alterations in their gene loci, or to the activities of transcription factors binding to their promoter regions. Finally, changes in the protein expression levels corresponding to the so far identified prognostic switch genes are evaluated by immunohistochemical staining results taking advantage of the Human Protein Atlas.

Conclusion
The application of the proposed pipeline on the dataset of The Cancer Genome Atlas (TCGA)-Breast Invasive Carcinoma (BRCA) patients affected by basal-like subtype led to an in silico recognition of a basal-like specific gene signature composed of 11 potential prognostic biomarkers to be further investigated.
Potentialities of the relationship between tourism and education: Report of experience of the tourism awareness project in the city of São Bernardo, Maranhão
Authors: Amador Alanny Davila Silva , Carvalho Karoliny Diniz 
Published: February 2022

The text presents a report of experience of a socio-educational action entitled Tourism Incentive Project (PROINTUR) developed by a group of students in the 6th period of the Bachelor in Tourism Course of the Federal University of Maranhão (UFMA), São Bernardo campus. The action was developed at the Deborah Correia Lima Teaching Center, and its main goal was to raise awareness among the school community regarding the importance of tourism as a socio-historical, spatial and cultural phenomenon, a factor for promoting economic growth, and an agent for social inclusion. The importance of tourism for community development is discussed, as well as tourism education actions, especially in the school context. This is followed by a presentation of the results achieved by the project. The work was based on bibliographic research, addressing the relationship between tourism and tourism education (Rabelo, 1998; Ribas, 2008; Fonseca Filho, 2007) and by pedagogical activities such as lectures, group dynamics and conversation circles with tourism and its production chain, tourist potential, and local development as the generating themes. The results of the intervention carried out show that the school community has knowledge about the importance of tourism; however, it has a restricted view of the tourist potential of the municipality of São Bernardo and the functions exercised by the bachelors degree in tourism as a transforming agent of the local reality.
Relationship between hepatic gene expression, intestinal microbiota and inferred functional metagenomic analysis in NAFLD
Authors: Pettinelli Paulina , Arendt Bianca M. , Schwenger Katherine J.P. , Sivaraj Saranya , Bhat Mamatha , Comelli Elena M. , Lou Wendy , Allard Johane P. 
Published: February 2022

ABSTRACT

INTRODUCTION:
We previously reported a lower fecal abundance of Ruminococcus spp., Faecalibacterium prausnitzii, and Coprococcus spp. in non-alcoholic fatty liver disease (NAFLD). Here we assess the associations between hepatic gene expression, the specific taxa, and bacterial pathways.

METHODS:
The relationships between hepatic genes that were differentially expressed in NAFLD patients vs healthy controls (HC), and the abundance of these specific taxa were studied. Inferred functional metagenomic analysis using Piphillin was also performed to investigate associations with bacterial pathways.

RESULTS:
Fifteen NAFLD and 6 HC participated. Of 728 hepatic genes examined, 176 correlated with the abundance of Ruminococcus spp., 138 with F. prausnitzii, and 92 with Coprococcus spp. For Ruminococcus spp., genes were enriched in Gene Ontology (GO) terms related to apoptotic process, response to external and cytokine stimuli, and regulation of signaling. Several genes related to the KEGG pathway insulin resistance were correlated with F. prausnitzii. The hepatic genes associated with F. prausnitzii were enriched in GO terms related to cellular response to different stimuli, apoptotic process, and regulation of metabolic pathways. For Coprococcus spp., only the GO term response to external stimulus was enriched. There was a distinct pattern of associations between hepatic genes and bacterial taxa in NAFLD versus HC. For bacterial pathways, 65 and 18 hepatic genes correlated with bacterial metabolic functions in NAFLD and HC, respectively.

DISCUSSION:
Hepatic gene expression related to insulin resistance, inflammation, external stimuli, and apoptosis correlated with bacterial taxa. NAFLD patients showed a higher presence of bacterial pathways associated with lipid metabolism.
ATAS NAMA ISLAM: KAJIAN PENOLAKAN HIZBUT TAHRIR INDONESIA (HTI) TERHADAP PLURALISME
Authors: Setia Paelani 
Published: February 2022

This study discuss the views of Hizbut Tahrir Indonesia (HTI) regarding religious pluralism. HTI as an organization that is sincere in interpreting the Qur'an literally and firmly rejects religious pluralism, which many people agree on as a concept that must be applied in Indonesia. This is a logical consequence where Indonesia is inhabited by various religions bound by a sense of unity in Pancasila and Bhinneka Tunggal Ika. For HTI, this is a failure of the state to build and maintain the unity that Islam should bind through a single power (Khilafah Islamiyah). This concept has been widely criticized by scholars based on two approaches, namely the Qur'an and sociological. Clearly, the Qur'an has acknowledged the existence of pluralism through the existence and truth of the books before the Qur'an, the acknowledgment of prophets and apostles other than the 25 people, as well as the acknowledgment of the Qur'an for the existence of other religions. HTI's rejection of pluralism was also refuted by HTI's own inconsistencies as the attitude of rejecting globalization but acting as a player of globalization, the attitude of rejecting democracy but taking advantage of the openness of freedom of opinion as a result of democracy, and the attitude of blaming the system of liberalism and secularism as the factors that give rise to deviant religious sects are purely psychological and sociological factors.
Staying or leaving? Teacher professional characteristics and attrition in Arizona traditional public and charter schools
Authors: Pivovarova Margarita , Powers Jeanne M. 
Published: February 2022

In this study, we analyzed public school teacher employment data from 2009 to 2015 to understand why teacher attrition is 54% higher in charter schools compared to traditional public schools. We investigated the factors associated with the differences in exit rates of teachers from traditional public and charter schools in Arizona which has a large charter school sector. Our findings suggest that the major factors behind the gap in retention rates between school sectors in Arizona are teachers’ professional characteristics: less experienced teachers and teachers with alternative certification are more likely to exit schools and, in particular, charter schools which also employ a significantly larger share of these teachers. We argue that charter school and school district leadership might consider interventions, mentoring, and support for teachers in the early stages of their career targeted at novice teachers.
Experimental Study on Progressive Damage Evolution in Rocks Subjected to Post-peak Cyclic Loading History
Authors: Taheri Abbas , Shirani Faradonbeh Roohollah , Munoz Henry 
Published: February 2022

Abstract
Because of the release of in situ rock stress, rocks surrounding deep underground excavations are mostly driven into a post-peak damage state. Thus, investigations on cyclic loading-induced damage of rocks are of paramount significance in terms of the long-term stability of rock structures. In this study, using a damage-controlled testing method, the effect of post-peak cyclic loading on the failure behavior of different rock types was comprehensively evaluated. This investigation revealed that post-peak cyclic loading imposes no significant influence on the overall failure behavior of rocks. The evolution of damage variables also indicated that the large portion of axial strain damage (Da) occurs during the first cycle at the peak strength, whereas lateral strain damage (Dl) evolved more rapidly than Da did in the post-peak regime under further loading and unloading cycles. The cumulative permanent axial strain (∑εap) evolved nonlinearly with the axial stress ratio (σi/σa−peak) in the post-peak regime, which was manifested as sparse-dense-sparse hysteretic loops. A rapid reduction in the crack damage stress ratio was observed for rocks in the initial sparse hysteretic loops, which was followed by a lower decrease rate in the subsequent dense hysteretic loops, and an almost constant value was finally reached in the last sparse hysteretic loops. Furthermore, tangent Young’s modulus (Etan) and Poisson’s ratio (υ) evolved in three main stages: One, Etan first increased and then decreased in the initial sparse hysteretic loops, while υ continuously increased, representing significant deformation in the lateral direction. Two, Etan decreased in the dense hysteretic loops, while υ increased at a higher rate for stronger rocks because of the decrease in Da accumulation. Three, the increase rate of υ declined in the second set of sparse hysteretic loops, and Etan decreased until complete failure occurred.
Configuration and Assessment of a Submersible Fluorometer for Evaluating Fluorescent Dye Deposition
Authors: Larbi Peter A. 
Published: February 2022

Abstract
Fluorescent tracer dyes are popularly used in agricultural spray application studies to evaluate on-target canopy deposition and off-target drift, and the methods/instruments used for evaluating dye deposit must assure reliability of the data generated. A laboratory setup was configured to adapt a submersible fluorometer for controlled and reliable measurement of pyranine dye fluorescence in liquid samples. The system setup was blanked using a clean sample of de-ionized water and calibrated using standard dye solutions of known concentration (100 to 1,000,000 parts per trillion [ppt]) made from two dyes of different levels of purity (pyranine 98 % and pyranine 85 %). Pyranine 85 % fluorescence readings were consistently lower with reduction factor averaging ∼0.62 times that of pyranine 98 % within a range from 500 to 1,000,000 ppt. The results were verified using a standard laboratory fluorometer. Spray deposition assessment of string, plastic card, cotton ribbon, and artificial foliage samplers was accomplished using the configured fluorometer system setup. The results showed no significant difference among dye purity levels (P = 0.430), no statistically significant interaction between dye purity and concentration (P = 0.484), and no statistically significant interaction between dye purity and sampler type (P = 0.173). Consequently, the configured setup can produce measurements with similar quality as the standard laboratory fluorometer and both dyes tested may be equally used for spray deposition and drift assessments, or for similar applications.
The ZIP3 Zinc Transporter Is Localized to Mossy Fiber Terminals and Is Required for Kainate-Induced Degeneration of CA3 Neurons
Authors: Bogdanovic Milos , Asraf Hila , Gottesman Noa , Sekler Israel , Aizenman Elias , Hershfinkel Michal 
Published: February 2022

Tight regulation of neuronal Zn2+is critical for physiological function. Multiple Zn2+transporters are expressed in the brain, yet their spatial distribution and distinct roles are largely unknown. Here, we show developmental regulation of the expression of Zn2+transporters ZIP1 and ZIP3 in mouse hippocampal neurons, corresponding to previously described increase in neuronal vesicular Zn2+during the first postnatal month. Rates of Zn2+uptake in cultured mouse hippocampal neurons, monitored using FluoZin-3 fluorescence, were higher in mature neurons, which express higher levels of ZIP1 and ZIP3. Zn2+uptake was attenuated by ∼50% following silencing of either ZIP1 or ZIP3. Expression of both ZIP1 and ZIP3 was ubiquitous on somas and most neuronal processes in the cultured neurons. In contrast, we observed distinct localization of the transporters in adult mouse hippocampal brain, with ZIP1 predominantly expressed in the CA3 stratum pyramidale, and ZIP3 primarily localized to the stratum lucidum. Consistent with their localization, silencing of ZIP1 expressionin vivoreduced Zn2+uptake in CA3 neurons while ZIP3 silencing reduced Zn2+influx into dentate gyrus (DG) granule cells in acute hippocampal slices. Strikingly,in vivosilencing of ZIP3, but not ZIP1, protected CA3 neurons from neurodegeneration following kainate-induced seizures. Our results indicate that distinct Zn2+transporters control Zn2+accumulation and toxicity in different neuronal populations in the hippocampus and suggest that selective regulation of Zn2+transporters can prevent seizure induced brain damage.SIGNIFICANCE STATEMENTZinc plays a major role in neuronal function and its dysregulation is associated with neurodegeneration. Multiple zinc transporters are expressed in neurons, yet little is known on their distinct roles. Here, we show that the plasma membrane ZIP1 and ZIP3 zinc transporters are expressed on distinct neuronal populations in the CA3 region of the hippocampus. We show that ZIP1 mediates zinc influx into postsynaptic cells, while ZIP3 is responsible for zinc re-uptake from this synapse into dentate granule cells. We further show that silencing of ZIP3, but not ZIP1, can rescue the postsynaptic cells from kainate-induced neurodegeneration. This suggests that neuronal zinc toxicity and degeneration can be modulated by regulation of specific zinc transporters function.
Prior Expectations in Visual Speed Perception Predict Encoding Characteristics of Neurons in Area MT
Authors: Zhang Ling-Qi , Stocker Alan A. 
Published: February 2022

Bayesian inference provides an elegant theoretical framework for understanding the characteristic biases and discrimination thresholds in visual speed perception. However, the framework is difficult to validate because of its flexibility and the fact that suitable constraints on the structure of the sensory uncertainty have been missing. Here, we demonstrate that a Bayesian observer model constrained by efficient coding not only well explains human visual speed perception but also provides an accurate quantitative account of the tuning characteristics of neurons known for representing visual speed. Specifically, we found that the population coding accuracy for visual speed in area MT (“neural prior”) is precisely predicted by the power-law, slow-speed prior extracted from fitting the Bayesian observer model to psychophysical data (“behavioral prior”) to the point that the two priors are indistinguishable in a cross-validation model comparison. Our results demonstrate a quantitative validation of the Bayesian observer model constrained by efficient coding at both the behavioral and neural levels.SIGNIFICANCE STATEMENTStatistical regularities of the environment play an important role in shaping both neural representations and perceptual behavior. Most previous work addressed these two aspects independently. Here we present a quantitative validation of a theoretical framework that makes joint predictions for neural coding and behavior, based on the assumption that neural representations of sensory information are efficient but also optimally used in generating a percept. Specifically, we demonstrate that the neural tuning characteristics for visual speed in brain area MT are precisely predicted by the statistical prior expectations extracted from psychophysical data. As such, our results provide a normative link between perceptual behavior and the neural representation of sensory information in the brain.
Development and internal validation of a predictive model for the estimation of pheochromocytoma recurrence risk after radical surgery
Authors: Parasiliti-Caprino Mirko , Bioletto Fabio , Lopez Chiara , Maletta Francesca , Caputo Marina , Gasco Valentina , La Grotta Antonio , Limone Paolo , Borretta Giorgio , Volante Marco , Papotti Mauro , Terzolo Massimo , Morino Mario , Pasini Barbara , Veglio Franco , Ghigo Ezio , Arvat Emanuela , Maccario Mauro 
Published: February 2022

Objective
Various features have been identified as predictors of relapse after complete resection of pheochromocytoma, but a comprehensive multivariable model for recurrence risk prediction is lacking. The aim of this study was to develop and internally validate an integrated predictive model for post-surgical recurrence of pheochromocytoma.

Methods
The present research retrospectively enrolled 177 patients affected by pheochromocytoma and submitted to radical surgery from 1990 to 2016, in nine referral centers for adrenal diseases. Cox regression analysis was adopted for model development, and a bootstrapping procedure was used for internal validation.

Results
Variables independently associated with recurrence were tumor size (hazard ratio (HR): 1.01, 95% CI: 1.00–1.02), positive genetic testing (HR: 5.14, 95% CI: 2.10–12.55), age (HR: 0.97, 95% CI: 0.94–0.99), and Pheochromocytoma of the Adrenal Gland Scaled Score (PASS) (HR: 1.16, 95% CI: 1.04–1.29). The predictive performance of the overall model, evaluated by Somers’ D, was equal to 0.594, and was significantly higher than the ones of any single predictor alone (P  = 0.002 compared to tumor size; P  = 0.004 compared to genetic testing; P  = 0.048 compared to age; P  = 0.006 compared to PASS). Internal validation by bootstrapping techniques estimated an optimistic bias of 6.3%, which reassured about a small tendency towards overfit.

Conclusions
We proposed a multivariable model for the prediction of post-surgical recurrence of pheochromocytoma, derived by the integration of genetic, histopathological, and clinical data. This predictive tool may be of value for a comprehensive tailoring of post-surgical follow-up in radically operated pheochromocytoma patients.
Implementation of an Inpatient Reproductive Health Screening Consult Service
Authors: Goldstein Rachel L. , Keppler Hannah , Pineda Noelle , Weng Yingjie , Carlson Jennifer L. 
Published: February 2022

OBJECTIVES
Reproductive health is an important issue in the care of adolescents and young adults (AYA). Unfortunately, many AYAs, particularly those with chronic medical conditions, may not regularly access primary care to address these issues. This study evaluates the impact of an inpatient reproductive health consult service on reproductive health care.

METHODS
A reproductive health-focused screening consult service was initiated in June 2017 at an academic teaching hospital. Patients aged 15 to 26 admitted to pediatric ward teams were eligible for screening. A retrospective chart review was conducted from December 2016 to June 2019 to determine the effect of the consult service on the primary outcome, documentation of a psychosocial assessment, and reproductive health concerns.

RESULTS
Nine hundred twenty-nine encounters were analyzed (345 preintervention and 584 during intervention), representing 675 patients. The proportion of encounters with a documented psychosocial assessment increased from 14.8% to 41.3% during the intervention (P &lt; .001); a reproductive health screening consult was responsible for 37.3% (109 of 292) of the documented assessments. There were high self-reported rates of sexual activity (38%), substance use (47%), and mood concerns (48%) among hospitalized AYA; all behaviors were documented at statistically significant increased frequencies (P &lt; .001) during the intervention compared with preintervention.

CONCLUSIONS
Initiation of an inpatient reproductive health screening consult service led to increased documentation of psychosocial assessments, including increased documentation of sexual health history and other risk factors. With improved screening of reproductive and psychosocial needs, targeted interventions can meet underrecognized needs among hospitalized AYA.
Fabrication of magnetic ordered mesoporous carbon for quantitative analysis of acidic phytohormones in mushroom samples prior to their determination by ultra-high-performance liquid chromatography–tandem mass spectrometry
Authors: Zhang Qianchun , Chen Yan , Yang Yanqun , Liu Yulan , Wen Ming , Wang Xingyi 
Published: February 2022

AbstractA novel method was established for analysing trace four acidic phytohormones, namely, indole-3-acetic acid, 3-indolebutyric acid, abscisic acid, and 1-naphthylacetic acid, using magnetic ordered mesoporous carbon (MOMC). MOMC was facilely synthesised via self-assembly strategy with a direct carbonisation process. The properties of MOMC were characterised using various instruments. MOMC exhibited excellent adsorption capacity towards the analytes. Various critical parameters which may influence the enrichment efﬁciency were evaluated, including amount of MOMC, extraction conditions, and desorption conditions. An efficient method based on MOMC magnetic solid-phase extraction coupled with ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC–MS/MS) was developed to analyse the trace four acidic phytohormones, with good correlation coefﬁcients (R2 = 0.9965–0.9998) and low limits of detection (0.13–9.7 ng L−1, S/N = 3). Trace acidic phytohormones in Agaricus bisporus and Hypsizygus marmoreus samples were determined with satisfactory recoveries (91.8–108%) and reproducibility (2.6–6.3%). The features indicated that MOMC provides an efficient platform for mushroom sampling; the developed method is convenient, promising, and sensitive for the detection of trace phytohormones in complicated mushroom samples.
Management of diabetic foot ulcers: dermatology perspective
Authors: Daryago Adi Agung Anantawijaya , Fitriani Fitriani , Kartowigno Soenarto , Aryani Inda Astri , Yahya Yulia Farida , Diba Sarah , Stephanie Aurelia 
Published: February 2022

Diabetes mellitus (DM) is a chronic and complex disease that affects various parts of the body. It can lead to multiple systemic complications and also cutaneous manifestation. Diabetic foot ulcer (DFU) is one of the most devastating complications of DM in dermatology. The main etiology is an increase in plasma glucose, risk factors, or comorbidities due to DM itself. Neglected DFU can lead to further complications, including high amputation and mortality rates; thus, the healing of ulcers is the main objective of the treatment. Management is divided into the standard of care and adjuvant therapies. This study aims to optimize DFU management, so it can provide proper treatment and prevent complications.