bluuebunny/crossref_metadata_2025_split huggingface dataset:
An in-planta comparative study of Plasmopara viticola proteome reveals different infection strategies towards susceptible and Rpv3-mediated resistance hosts
Authors: Figueiredo Joana , Santos Rita B. , Guerra-Guimarães Leonor , Leclercq Céline C. , Renaut Jenny , Malhó Rui , Figueiredo Andreia 
Published: December 2022

AbstractPlasmopara viticola, an obligate biotrophic oomycete, is the causal agent of one of the most harmful grapevine diseases, downy mildew. Within this pathosystem, much information is gathered on the host, as characterization of pathogenicity and infection strategy of a biotrophic pathogen is quite challenging. Molecular insights into P. viticola development and pathogenicity are just beginning to be uncovered, mainly by transcriptomic studies. Plasmopara viticola proteome and secretome were only predicted based on transcriptome data. In this study, we have identified the in-planta proteome of P. viticola during infection of a susceptible (‘Trincadeira’) and a Rpv3-mediated resistance (‘Regent’) grapevine cultivar. Four hundred and twenty P. viticola proteins were identified on a label-free mass spectrometry-based approach of the apoplastic fluid of grapevine leaves. Overall, our study suggests that, in the compatible interaction, P. viticola manipulates salicylic-acid pathway and isoprenoid biosynthesis to enhance plant colonization. Furthermore, during the incompatible interaction, development-associated proteins increased while oxidoreductases protect P. viticola from ROS-associated plant defence mechanism. Up to our knowledge this is the first in-planta proteome characterization of this biotrophic pathogen, thus this study will open new insights into our understanding of this pathogen colonization strategy of both susceptible and Rpv3-mediated resistance grapevine genotypes.
A new copper-supported zinc ferrite as a heterogeneous magnetic nanocatalyst for the synthesis of bis(pyrazolyl)methanes and oxidation of sulfides
Authors: Ghorbani-Choghamarani Arash , Aghavandi Hamid , Talebi Seyed Mahdi 
Published: December 2022

AbstractIn this paper, we report the synthesis of ZnFe2O4@SiO2@APTES@DHBS-Cu as a novel magnetic nanocatalyst, in a mild and green environment. The structure of the described magnetic compound was characterized by different physicochemical techniques including XRD, EDS, AAS, SEM, FT-IR, X-ray elemental mapping, TGA, and VSM analyses. The prepared magnetic nanoparticles exhibit excellent catalytic activity in synthesizing bis (pyrazolyl)methanes and oxidation of sulfide derivatives under green conditions. The heterogeneous nature of the catalyst was confirmed via the hot filtration experiment. Further, ZnFe2O4@SiO2@APTES@DHBS-Cu showed high efficiency and reusability that could be reused for at least five consecutive runs.
COVID-19 contagion across remote communities in tropical forests
Authors: Takasaki Yoshito , Abizaid Christian , Coomes Oliver T. 
Published: December 2022

AbstractUnderstanding COVID-19 contagion among poor populations is hampered by a paucity of data, and especially so in remote rural communities with limited access to transportation, communication, and health services. We report on the first study on COVID-19 contagion across rural communities without road access. We conducted telephone surveys with over 400 riverine communities in the Peruvian Amazon in the early phase of the pandemic. During the first wave (April–June, 2020), COVID-19 spread from cities to most communities through public and private river transportation according to their remoteness. The initial spread was delayed by transportation restrictions but at the same time was driven in unintended ways by government social assistance. During the second wave (August, 2020), although people’s self-protective behaviors (promoted through communication access) helped to suppress the contagion, people responded to transportation restrictions and social assistance in distinct ways, leading to greater contagion among Indigenous communities than mestizo communities. As such, the spatial contagion during the early phase of the pandemic in tropical forests was shaped by river transportation and social behaviors. These novel findings have important implications for research and policies on pandemics in rural areas.
Identification of a novel peptide ligand for the cancer-specific receptor mutation EGFRvIII using high-throughput sequencing of phage-selected peptides
Authors: Mansour Sourour , Adhya Indranil , Lebleu Coralie , Dumpati Rama , Rehan Ahmed , Chall Santu , Dai Jingqi , Errasti Gauthier , Delacroix Thomas , Chakrabarti Raj 
Published: December 2022

AbstractWe report here the selection and characterization of a novel peptide ligand using phage display targeted against the cancer-specific epidermal growth factor tyrosine kinase receptor mutation variant III (EGFRvIII). This receptor is expressed in several kinds of cancer: ovarian cancer, breast cancer and glioblastoma, but not in normal tissues. A 12-mer random peptide library was screened against EGFRvIII. Phage-selected peptides were sequenced in high-throughput by next generation sequencing (NGS), and their diversity was studied to identify highly abundant clones expected to bind with the highest affinities to EGFRvIII. The enriched peptides were characterized and their binding capacity towards stable cell lines expressing EGFRvIII, EGFR wild type (EGFR WT), or a low endogenous level of EGFR WT was confirmed by flow cytometry analysis. The best peptide candidate, VLGREEWSTSYW, was synthesized, and its binding specificity towards EGFRvIII was validated in vitro. Additionally, computational docking analysis suggested that the identified peptide binds selectively to EGFRvIII. The novel VLGREEWSTSYW peptide is thus a promising EGFRvIII-targeting agent for future applications in cancer diagnosis and therapy.
Enhancement of DNA hypomethylation alterations by gastric and bile acids promotes chromosomal instability in Barrett’s epithelial cell line
Authors: Abe Iku , Suzuki Koichi , Kimura Yasuaki , Tamaki Sawako , Endo Yuhei , Ichida Kosuke , Muto Yuta , Watanabe Fumiaki , Saito Masaaki , Konishi Fumio , Rikiyama Toshiki 
Published: December 2022

AbstractGastric and bile acid reflux leads to chronic inflammation, resulting in methylation alterations in Barrett’s esophagus (BE) together with chromosomal instability (CIN). We investigated DNA hypomethylation following acid exposure and confirmed its significance in BE-related carcinogenesis by inducing CIN in vitro. OACP4C, an esophageal cancer cell line, and CP-A, a non-dysplastic cell line originating from BE, were exposed to acidic conditions using deoxycholic acid. CP-A exhibited substantially increased DNA hypomethylation of alpha satellite sequences in the centromere region, as well as increased levels of alpha satellite transcripts, but no changes were observed in the long interspersed nucleotide element-1 sequences distributed throughout the entire genome. These changes were not clearly found in OACP4C. Copy number changes at specific chromosomes were identified in CP-A, along with an increased number of cells exhibiting abnormal segregations, whereas these changes were rarely observed in OACP4C. The changes were maintained after several cell divisions. These findings suggest that alpha satellites are likely targets of DNA hypomethylation induced by acid exposure. CP-A was more sensitive to acid exposure than OACP4C, indicating that acid-induced DNA hypomethylation is involved in cancer development rather than progression, which could be involved in the underlying mechanism of esophagogastric junction carcinoma development.
Value of p53 sequencing in the prognostication of head and neck cancer: a systematic review and meta-analysis
Authors: Basyuni Shadi , Nugent Gareth , Ferro Ashley , Barker Eleanor , Reddin Ian , Jones Oliver , Lechner Matt , O’Leary Ben , Jones Terry , Masterson Liam , Fenton Tim , Schache Andrew 
Published: December 2022

AbstractThis review aimed to examine the relationship between TP53 mutational status, as determined by genomic sequencing, and survival in squamous cell carcinoma of the head and neck. The databases Medline, Embase, Web of Science (core collection), Scopus and Cochrane Library were searched from inception to April 2021 for studies assessing P53 status and survival. Qualitative analysis was carried out using the REMARK criteria. A meta-analyses was performed and statistical analysis was carried out to test the stability and reliability of results. Twenty-five studies met the inclusion criteria, of which fifteen provided enough data for quantitative evaluation. TP53 mutation was associated with worse overall survival (HR 1.75 [95% CI 1.45–2.10], p < 0.001), disease-specific survival (HR 4.23 [95% CI 1.19–15.06], p = 0.03), and disease-free survival (HR 1.80 [95% CI 1.28–2.53], p < 0.001). Qualitative assessment identified room for improvement and the pooled analysis of all anatomical subsites leads to heterogeneity that may erode the validity of the observed overall effect and its subsequent extrapolation and application to individual patients. Our systematic review and meta-analysis supports the utility of TP53 mutational as a prognostic factor for survival in head and neck squamous cell carcinoma. A well designed prospective, multi-centre trial is needed to definitively answer this question.
A non-avian dinosaur with a streamlined body exhibits potential adaptations for swimming
Authors: Lee Sungjin , Lee Yuong-Nam , Currie Philip J. , Sissons Robin , Park Jin-Young , Kim Su-Hwan , Barsbold Rinchen , Tsogtbaatar Khishigjav 
Published: December 2022

AbstractStreamlining a body is a major adaptation for aquatic animals to move efficiently in the water. Whereas diving birds are well known to have streamlined bodies, such body shapes have not been documented in non-avian dinosaurs. It is primarily because most known non-avian theropods are terrestrial, barring a few exceptions. However, clear evidence of streamlined bodies is absent even in the purported semiaquatic groups. Here we report a new theropod, Natovenator polydontus gen. et sp. nov., from the Upper Cretaceous of Mongolia. The new specimen includes a well-preserved skeleton with several articulated dorsal ribs that are posterolaterally oriented to streamline the body as in diving birds. Additionally, the widely arched proximal rib shafts reflect a dorsoventrally compressed ribcage like aquatic reptiles. Its body shape suggests that Natovenator was a potentially capable swimming predator, and the streamlined body evolved independently in separate lineages of theropod dinosaurs.
Macrophages regulate vascular smooth muscle cell function during atherosclerosis progression through IL-1β/STAT3 signaling
Authors: Xue Yuzhou , Luo Minghao , Hu Xiankang , Li Xiang , Shen Jian , Zhu Wenyan , Huang Longxiang , Hu Yu , Guo Yongzheng , Liu Lin , Wang Lingbang , Luo Suxin 
Published: December 2022

AbstractVascular smooth muscle cells (VSMCs) play a central role in atherosclerosis progression, but the functional changes in VSMCs and the associated cellular crosstalk during atherosclerosis progression remain unknown. Here we show that scRNA-seq analysis of proximal adjacent (PA) and atherosclerotic core (AC) regions of human carotid artery plaques identifies functional alterations in macrophage-like VSMCs, elucidating the main state differences between PA and AC VSMCs. And, IL-1β mediates macrophage-macrophage-like VSMC crosstalk through regulating key transcription factors involved in macrophage-like VSMCs functional alterations during atherosclerosis progression. In vitro assays reveal VSMCs trans-differentiated into a macrophage-like phenotype and then functional alterations in response to macrophage-derived stimuli. IL-1β promots the adhesion, inflammation, and apoptosis of macrophage-like VSMCs in a STAT3 dependent manner. The current findings provide interesting insight into the macrophages-macrophage-like VSMC crosstalk, which would drive functional alterations in the latter cell type through IL-1β/STAT3 axis during atherosclerosis progression.
A high-throughput multispectral imaging system for museum specimens
Authors: Chan Wei-Ping , Rabideau Childers Richard , Ashe Sorcha , Tsai Cheng-Chia , Elson Caroline , Keleher Kirsten J. , Sipe Rachel L. Hawkins , Maier Crystal A. , Sourakov Andrei , Gall Lawrence F. , Bernard Gary D. , Soucy Edward R. , Yu Nanfang , Pierce Naomi E. 
Published: December 2022

AbstractWe present an economical imaging system with integrated hardware and software to capture multispectral images of Lepidoptera with high efficiency. This method facilitates the comparison of colors and shapes among species at fine and broad taxonomic scales and may be adapted for other insect orders with greater three-dimensionality. Our system can image both the dorsal and ventral sides of pinned specimens. Together with our processing pipeline, the descriptive data can be used to systematically investigate multispectral colors and shapes based on full-wing reconstruction and a universally applicable ground plan that objectively quantifies wing patterns for species with different wing shapes (including tails) and venation systems. Basic morphological measurements, such as body length, thorax width, and antenna size are automatically generated. This system can increase exponentially the amount and quality of trait data extracted from museum specimens.
Temperature is a better predictor of stable carbon isotopic compositions in marine particulates than dissolved CO2 concentration
Authors: Liu Qianqian , Kandasamy Selvaraj , Zhai Weidong , Wang Huawei , Veeran Yoganandan , Gao Aiguo , Chen Chen-Tung Arthur 
Published: December 2022

AbstractThe stable carbon isotopic composition of marine particulate organic matter (δ13CPOM) varies with source and environmental conditions. Dissolved carbon dioxide (CO2) concentration is thought to influence δ13CPOM more than temperature, but this relationship is poorly constrained in marginal seas. Here we present δ13CPOM, hydrographic and carbonate system variables at the deep chlorophyll maxima of the southern Yellow Sea in late summer 2017. We find δ13CPOM values varied between stable and cyclonic gyre regions, but indicated autochthonous organic matter production and were more strongly correlated with temperature than dissolved CO2 concentration throughout. We find that the relationship between temperature and δ13CPOM was independent of CO2 concentration, whereas the relationship between δ13CPOM and CO2 concentration was dependent on temperature also being correlated with CO2 concentration. We suggest that temperature is the primary determinant of marine δ13CPOM due to temperature-dependent metabolism in phytoplankton, irrespective of inorganic carbon acquisition mode.
Whole-muscle fat analysis identifies distal muscle end as disease initiation site in facioscapulohumeral muscular dystrophy
Authors: Heskamp Linda , Ogier Augustin , Bendahan David , Heerschap Arend 
Published: December 2022

Abstract
Background
Facioscapulohumeral dystrophy (FSHD) is a major muscular dystrophy characterized by asymmetric fatty replacement of muscles. We aimed to determine the initiation site and progression profile of the disease in lower extremity muscles of FSHD patients by assessing fat infiltration along their full proximo-distal axis using quantitative MRI.

Methods
Nine patients underwent MRI of lower extremities to assess end-to-end muscle fat fractions (FFs) and inflammatory lesions. Seven patients underwent the same MRI ~3.5 years later. Individual muscles (n = 396) were semi-automatically segmented to calculate average FFs over all slices covering whole muscles. To assess disease progression we determined FF changes in 5 adjacent muscle segments.

Results
We provide evidence that fat replacement commonly starts at the distal end of affected muscles where the highest FFs occur (p < 0.001). It progresses in a wave-like manner in the proximal direction at an increasing rate with the highest value (4.9 ± 2.7%/year) for muscles with baseline FFs of 30–40%. Thereafter it proceeds at a slower pace towards the proximal muscle end. In early phases of disease, inflammatory lesions preferentially occur at the distal muscle end. Compared with whole-muscle analysis, the common FF assessments using only few MR slices centrally placed in muscles are significantly biased (~50% in progression rate).

Conclusions
These findings identify the distal end of leg muscles as a prime location for disease initiation in FSHD and demonstrate a wave-like progression towards the proximal end, consistent with proposed disease mechanisms. End-to-end whole-muscle fat assessment is essential to properly diagnose FSHD and its progression.
Printable and flexible photodetectors via scalable fabrication for reading applications
Authors: Bairaktaris Georgios , Khan Fasihullah , Jayawardena K. D. J. Imalka , Frohlich David M. , Sporea Radu A. 
Published: December 2022

AbstractPrinting techniques have been widely adopted in the fabrication of flexible electronic components. However, its application is still limited in complex control and communication circuitry due to the low performance and low fabrication uniformity amongst printed devices, compared to conventional electronics. Thus, the electronic systems in real-world applications are hybrid integrations of printed and conventional electronics. Here we demonstrate a low-cost, low-complexity, fully-printable flexible photodetector that can withstand over 100 1 mm-radius bending cycles using a simple and scalable two-step fabrication process. The prototypes are implemented in an augmented book system to automatically detect the ambient light through optical apertures on paper of a printed book, and then transmit the information to an adjunct device. This technique demonstrates the utility of low-cost materials and processes for robust large area sensing applications and could act as a gateway to pertinent multimedia information.
Short-Term Acoustic Effects of Speech Therapy in Transgender Women: A Randomized Controlled Trial
Authors: Leyns Clara , Daelman Julie , Adriaansen Anke , Tomassen Peter , Morsomme Dominique , T'Sjoen Guy , D'haeseleer Evelien 
Published: December 2022

Purpose:
This study measured and compared the acoustic short-term effects of pitch elevation training (PET) and articulation-resonance training (ART) and the combination of both programs, in transgender women.

Method:

A randomized controlled study with cross-over design was used. Thirty transgender women were included and received 14 weeks of speech training. All participants started with 4 weeks of sham training; after which they were randomly assigned to one of two groups: One group continued with PET (5 weeks), followed by ART (5 weeks); the second group received both trainings in opposite order. Participants were recorded 4 times, in between the training blocks: pre, post 1 (after sham), post 2 (after training 1), and post 3 (after training 2). Speech samples included a sustained vowel, continuous speech during reading, and spontaneous speech and were analyzed using Praat software. Fundamental frequency (
f
o
), intensity, voice range profile, vowel formant frequencies (
F
1–2–3–4–5
of /a/−/i/−/u/), formant contrasts, vowel space, and vocal quality (Acoustic Voice Quality Index) were determined.

Results and Conclusions:

Fundamental frequencies increased after both the PET and ART program, with a higher increase after PET. The combination of both interventions showed a mean increase of the
f
o
of 49 Hz during a sustained vowel, 49 Hz during reading, and 29 Hz during spontaneous speech. However, the lower limit (percentile 5) of the
f
o
during spontaneous speech did not change. Higher values were detected for
F
1–2
of /a/,
F
3
of /u/, and vowel space after PET and ART separately.
F
1–2–3
of /a/,
F
1–3–4
of /u/, vowel space, and formant contrasts increased after the combination of PET and ART; hence, the combination induced more increases in formant frequencies. Intensity and voice quality measurements did not change. No order effect was detected; that is, starting with PET or ART did not change the outcome.
The Impact of Learning Modality on Team-Based Learning Outcomes in Undergraduate Anatomy and Physiology
Authors: Kirjava Shade Avery , Krause Bentley Andrew 
Published: December 2022

Purpose:
Team-based learning (TBL) is an instructional design that has been increasingly used in anatomy and physiology education. The appropriateness of TBL methods for students with diverse preferred sensory learning modalities has not been adequately examined. This study aimed to show the influence of students' preferred sensory modality for learning on TBL outcomes.

Method:
Communication sciences and disorders majors enrolled in anatomy and physiology courses completed VARK (Visual, Aural, Read/write, and Kinesthetic), a questionnaire quantifying their preferred learning modality. Students' traditional and TBL measures of academic success were compared by preferred learning modality.

Results:

A multivariate analysis of variance failed to find any difference in TBL or other outcomes by preferred learning modality (
p
= .252).

Conclusions:
The results of this study show no evidence of differences in academic outcomes in TBL projects between learners with different preferred learning modalities as measured by VARK. The role of TBL and of instructional sensory modality on learning outcomes should continue to be examined.
Brazil Reflects a Global Gender Disparity in Speech-Language Pathology: A Comparison of Leadership and Representation Within the Profession
Authors: Sarmet Max , Zeredo Jorge L. , Serra Lucieny Silva Martins , da Silva Eduardo Magalhães 
Published: December 2022

Purpose:
Speech-language pathologists (SLPs) are professionals marked by occupational gender segregation, with speech-language pathology jobs being dominated by women worldwide. In the United States, male participation in leadership and prominent positions within the profession has been gradually increasing, but the proportion of men compared to women is still very low. This study aimed to verify the prevalence of Brazilian men who are SLPs, assess the participation of male SLPs in leadership positions within the profession, and compare this gender distribution with that of other countries.

Method:
In this retrospective, descriptive cross-sectional study, we considered information contained in public databases and information obtained through utilizing the Brazilian Access to Information Law. Male representation in Brazil was assessed considering the distribution of active male speech-language pathology professionals, participation in collegiates of the Brazilian federal and regional speech-language pathology councils, participation in the board of the Brazilian Society of Speech-Language Pathology, participation in editorial boards, authorship in Brazilian journals, and prevalence in public health care. Besides the data gathered in Brazil, for comparison purposes, data on scientific representation in the United States and that of speech-language pathology societies in 40 countries were collected.

Results:
Males represent 4.8% of the Brazilian active speech-language pathology professionals. Representation in public health care was low (3.0%), which reveals a significant gender disparity. Male participation in leadership positions averaged at around 14%–25%, which can illustrate a potential growth in the field of male professionals.

Conclusions:
The gender disparity seen globally remains present in Brazilian SLPs. The findings of this study can benefit the profession by recognizing this inequality and stimulating the search for solutions that favor gender equality considering Brazilian sociocultural features.