bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pleomorphic Adenoma Gene 1 Is Needed For Timely Zygotic Genome Activation and Early Embryo Development
Authors: Madissoon Elo , Damdimopoulos Anastasios , Katayama Shintaro , Krjutškov Kaarel , Einarsdottir Elisabet , Mamia Katariina , De Groef Bert , Hovatta Outi , Kere Juha , Damdimopoulou Pauliina 
Published: June 2019

AbstractPleomorphic adenoma gene 1 (PLAG1) is a transcription factor involved in cancer and growth. We discovered a de novo DNA motif containing a PLAG1 binding site in the promoters of genes activated during zygotic genome activation (ZGA) in human embryos. This motif was located within an Alu element in a region that was conserved in the murine B1 element. We show that maternally provided Plag1 is needed for timely mouse preimplantation embryo development. Heterozygous mouse embryos lacking maternal Plag1 showed disrupted regulation of 1,089 genes, spent significantly longer time in the 2-cell stage, and started expressing Plag1 ectopically from the paternal allele. The de novo PLAG1 motif was enriched in the promoters of the genes whose activation was delayed in the absence of Plag1. Further, these mouse genes showed a significant overlap with genes upregulated during human ZGA that also contain the motif. By gene ontology, the mouse and human ZGA genes with de novo PLAG1 motifs were involved in ribosome biogenesis and protein synthesis. Collectively, our data suggest that PLAG1 affects embryo development in mice and humans through a conserved DNA motif within Alu/B1 elements located in the promoters of a subset of ZGA genes.
Sequence and expression analysis of HSP70 family genes in Artemia franciscana
Authors: Junprung Wisarut , Norouzitallab Parisa , De Vos Stephanie , Tassanakajon Anchalee , Nguyen Viet Dung , Van Stappen Gilbert , Bossier Peter 
Published: June 2019

AbstractThus far, only one gene from the heat shock protein 70 (HSP70) family has been identified in Artemia franciscana. Here, we used the draft Artemia transcriptome database to search for other genes in the HSP70 family. Four novel HSP70 genes were identified and designated heat shock cognate 70 (HSC70), heat shock 70 kDa cognate 5 (HSC70-5), Immunoglobulin heavy-chain binding protein (BIP), and hypoxia up-regulated protein 1 (HYOU1). For each of these genes, we obtained nucleotide and deduced amino acid sequences, and reconstructed a phylogenetic tree. Expression analysis revealed that in the juvenile state, the transcription of HSP70 and HSC70 was significantly (P < 0.05) higher in a population of A. franciscana selectively bred for increased induced thermotolerance (TF12) relative to a control population (CF12). Following non-lethal heat shock treatment at the nauplius stage, transcription of HSP70, HSC70, and HSC70-5 were significantly (P < 0.05) up-regulated in TF12. In contrast, transcription of the other HSP70 family members in A. franciscana (BIP, HYOU1, and HSPA4) showed no significant (P > 0.05) induction. Gene expression analysis demonstrated that not all members of the HSP70 family are involved in the response to heat stress and selection and that especially altered expression of HSC70 plays a role in a population selected for increased thermotolerance.
Morph-specific protein patterns in the femoral gland secretions of a colour polymorphic lizard
Authors: Mangiacotti Marco , Fumagalli Marco , Cagnone Maddalena , Viglio Simona , Bardoni Anna Maria , Scali Stefano , Sacchi Roberto 
Published: June 2019

AbstractColour polymorphism occurs when two or more genetically-based colour morphs permanently coexist within an interbreeding population. Colouration is usually associated to other life-history traits (ecological, physiological, behavioural, reproductive …) of the bearer, thus being the phenotypic marker of such set of genetic features. This visual badge may be used to inform conspecifics and to drive those decision making processes which may contribute maintaining colour polymorphism under sexual selection context. The importance of such information suggests that other communication modalities should be recruited to ensure its transfer in case visual cues were insufficient. Here, for the first time, we investigated the potential role of proteins from femoral gland secretions in signalling colour morph in a polymorphic lizard. As proteins are thought to convey identity-related information, they represent the ideal cues to build up the chemical modality used to badge colour morphs. We found strong evidence for the occurrence of morph-specific protein profiles in the three main colour-morphs of the common wall lizard, which showed both qualitative and quantitative differences in protein expression. As lizards are able to detect proteins by tongue-flicking and vomeronasal organ, this result support the hypothesis that colour polymorphic lizards may use a multimodal signal to inform about colour-morph.
Sequence and structural patterns detected in entangled proteins reveal the importance of co-translational folding
Authors: Baiesi Marco , Orlandini Enzo , Seno Flavio , Trovato Antonio 
Published: June 2019

AbstractProteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence of specific patterns adopted by protein sequences and structures to deal with backbone self-entanglement. A large scale analysis of the Protein Data Bank shows that loops significantly intertwined with another chain portion are typically closed by weakly bound amino acids. Why is this energetic frustration maintained? A possible picture is that entangled loops are formed only toward the end of the folding process to avoid kinetic traps. Consistently, these loops are more frequently found to be wrapped around a portion of the chain on their N-terminal side, the one translated earlier at the ribosome. Finally, these motifs are less abundant in natural native states than in simulated protein-like structures, yet they appear in 32% of proteins, which in some cases display an amazingly complex intertwining.
Nanofiber-expanded human CD34+ cells heal cutaneous wounds in streptozotocin-induced diabetic mice
Authors: Kanji Suman , Das Manjusri , Joseph Matthew , Aggarwal Reeva , Sharma Sudarshana M. , Ostrowski Michael , Pompili Vincent J. , Mao Hai-Quan , Das Hiranmoy 
Published: June 2019

AbstractDespite advances in diabetic wound care, the significant number of amputations that occur every year demands more effective therapeutics. Herein, we offer an aminated polyethersulfone nanofiber-expanded human umbilical cord blood-derived CD34+ cells (henceforth CD34+ cells) effective therapy, tested in cutaneous wounds developed in streptozotocin-induced diabetic NOD/SCID mice. We show that systemic administration of CD34+ cells homed to the wound site and significantly accelerated wound closure. Wound closure was associated with improved re-epithelialization and increased neovascularization; and with decreased sustained pro-inflammatory activity of NF-κB and its downstream effector molecules TNF-α, IL-1β, and IL-6 at the wound bed. This finding was further supported by the observation of a decreased number of myeloperoxidase positive neutrophils, and concomitantly increased levels of IL-10. In addition, improved granulation tissue formation was observed along with higher collagen deposition and myofibroblasts and decreased expressions of MMP-1. Mechanistically, CD34+ cells reduced the level of MMP-1 expression by inhibiting recruitment of NF-κB to the MMP-1 promoter site in dermal fibroblasts. In summary, we provide evidence of a novel nanofiber-expanded CD34+ stem cell therapeutic development for treating diabetic wounds by defining their cellular and molecular mechanisms.
Detection of novel biomarkers for early detection of Non-Muscle-Invasive Bladder Cancer using Competing Endogenous RNA network analysis
Authors: Kouhsar Morteza , Azimzadeh Jamalkandi Sadegh , Moeini Ali , Masoudi-Nejad Ali 
Published: June 2019

AbstractBladder Cancer (BC) is one of the most common cancers in the world. Recent studies show that non-coding RNAs such as lncRNAs and circRNAs play critical roles in the progression of this cancer, but their regulatory relationships and functions are still largely unknown. As a new regulatory process within the cell, the coding and non-coding RNAs compete with each other to sponge their target miRNAs. This mechanism is described as “the competing endogenous RNA (ceRNA) hypothesis” which provides a new perspective to understand the regulation of gene expression in health and diseases such as cancer. In this study, to investigate the role of non-coding RNAs in BC, a new approach was used to reconstruct the ceRNA network for Non-Muscle Invasive Bladder Cancer (NMIBC) based on the expression data of coding and non-coding genes. Analysis of ceRNA networks in the early stage of BC led to the detection of an important module containing the lncRNA MEG3 as the central gene. The results show that the lncRNAs CARMN, FENDRR and ADAMTS9-AS2 may regulate MEG3 in NMIBC through sponging some important miRNAs such as miR-143-3p, miR-106a-5p and miR-34a-3p. Also, the lncRNA AC007608.2 is shown to be a potential BC related lncRNA for the first time based on ceRNA stage-specific network analysis. Furthermore, hub and altered genes in stage-specific and between stage networks led to the detection of hsa_circ_0017586 and hsa_circ_0001741 as novel potential circRNAs related to NMIBC. Finally, the hub genes in the networks were shown to be valuable candidates as biomarkers for the early stage diagnosis of BC.
A Comparison of Three Discourse Elicitation Methods in Aphasia and Age-Matched Adults: Implications for Language Assessment and Outcome
Authors: Stark Brielle C. 
Published: June 2019

Purpose
Discourse analysis is commonly used to assess language ability and to evaluate language change following intervention in aphasia. The purpose of this study was to identify differences in language produced during different discourse tasks in a large aphasia group and an age- and education-matched control group.

Method

Four structured discourse tasks across 3 discourse types (expositional, narrative, and procedural) were evaluated in a group of adults with aphasia (
n
= 90) and an age-matched control group (
n
= 84) drawn from AphasiaBank. CLAN software was used to extract primary linguistic variables (mean length of utterance, propositional density, type–token ratio, words per minute, open–closed class word ratio, noun–verb ratio, and tokens), which served as proxies for various language abilities. Using a series of repeated-measures analyses of covariance, with significantly correlated demographic and descriptive variables as covariates, main effects of discourse type were evaluated.

Results
Despite an impoverished output from the aphasia group (i.e., the control group produced significantly more overall output), there was a main effect of discourse type on most primary linguistic variables in both groups, suggesting that, in adults with and without language impairments, each discourse type taxed components of the spoken language system to varying extents. Post hoc tests fleshed out these results, demonstrating that, for example, narrative discourse produced speech highest in propositional density.

Conclusion
Each discourse type taxes the language system in different ways, verifying the importance of using several discourse tasks and selecting the most sensitive discourse tasks when evaluating specific language abilities and outcomes.
Volubility, Consonant Emergence, and Syllabic Structure in Infants and Toddlers Later Diagnosed With Childhood Apraxia of Speech, Speech Sound Disorder, and Typical Development: A Retrospective Video Analysis
Authors: Overby Megan S. , Caspari Susan S. , Schreiber James 
Published: June 2019

Purpose

Studies of infants' early vocalizations have proven helpful in describing the developmental characteristics of various communication disorders. However, few studies have addressed the early vocalizations of infants and toddlers who were later diagnosed, as older children, with childhood apraxia of speech (CAS). We refer to these infants and toddlers as
LCAS
. Extant studies also often lack a comparison group of infants and toddlers who were later diagnosed, as older children, with a speech sound disorder (SSD). We refer to these infants and toddlers as
LSSD
. We aimed to compare the volubility, consonant emergence, and syllabic structure from birth to age of 2 years, as observed in home videos, among 3 groups of infants and toddlers: LCAS, LSSD, and typically developing (TD).

Method
We assessed the speech-language skills of 17 children (3.5–8.8 years old; 7 with CAS, 5 with SSD, and 5 TD) and transcribed home videos (obtained from parents) of these same children from birth to age of 2 years. Early vocalizations were coded as nonresonant or resonant. Nonresonant vocalizations could not be transcribed with the International Phonetic Alphabet. Resonant (speechlike) vocalizations were broadly transcribed, and resonant consonants were categorized by place, manner, and voicing.

Results
Effect size comparisons revealed LCAS infants and toddlers were less voluble, used fewer resonant consonants, had a less diverse phonetic repertoire, and acquired resonant consonants later than either the LSSD or TD participants. For LSSD infants and toddlers, means for these dependent variables were lower than the means demonstrated by the TD group, but effect size were not strong due to LSSD variability.

Conclusions
Findings imply there might be clinical “red flags” that could assist the identification of infants and toddlers at risk for later diagnosis of CAS. Data did not support red flags for identifying infants and toddlers at risk for later diagnosis of SSD. Because of significant study limitations, results obtained should be considered preliminary.

Supplemental Material

https://doi.org/10.23641/asha.8233334
Optically variable AGN in the three-year VST survey of the COSMOS field
Authors: De Cicco D. , Paolillo M. , Falocco S. , Poulain M. , Brandt W. N. , Bauer F. E. , Vagnetti F. , Longo G. , Grado A. , Ragosta F. , Botticella M. T. , Pignata G. , Vaccari M. , Radovich M. , Salvato M. , Covone G. , Napolitano N. R. , Marchetti L. , Schipani P. 
Published: June 2019

Context. The analysis of the variability of active galactic nuclei (AGN) at different wavelengths and the study of possible correlations of different spectral windows are a current main field of inquiry. Optical variability has been largely used to identify AGN in multivisit surveys. The strength of a selection based on optical variability lies in the opportunity of analyzing data from surveys of large sky areas by ground-based telescopes. However, the effectiveness of optical variability selection with respect to other multiwavelength techniques has been poorly studied down to the depth that is expected from next-generation surveys.
Aims. Here we present the results of our r-band analysis of a sample of 299 optically variable AGN candidates in the VST survey of the COSMOS field, counting 54 visits spread over three observing seasons spanning more than three years. This dataset is more than three times larger than the dataset presented in our previous analysis, and the observing baseline is about eight times longer.
Methods. We push toward deeper magnitudes (r(AB) ∼ 23.5 mag) than were reached in past studies. We made wide use of ancillary multiwavelength catalogs in order to confirm the nature of our AGN candidates, and constrained the accuracy of the method based on spectroscopic and photometric diagnostics. We also performed tests aimed at assessing the relevance of dense sampling in view of future wide-field surveys.
Results. We demonstrate that the method allows the selection of high-purity (> 86%) samples. We take advantage of the longer observing baseline to achieve great improvement in the completeness of our sample with respect to X-ray and spectroscopically confirmed samples of AGN (59% vs. ∼15% in our previous work), as well as in the completeness of unobscured and obscured AGN. The effectiveness of the method confirms the importance of developing future more refined techniques for the automated analysis of larger datasets.
The introduction of English grammar studies into China in the 19thcentury
Authors: Pellin Tommaso 
Published: June 2019

During the first half of the 19th century, Protestant missionaries based in China started teaching some English to the students attending their schools; in the second half of the century Chinese scholars opened their own language schools and wrote their grammarbooks of English.This contribution describes four of the grammarbooks for English that marked milestones in that period: Morrison’sA Grammar of the English Language(1823), Lobscheid’sChinese-English grammar(1864), Cáo Xiāng’sYīngzìrùmén(1874), and Wāng Fèngzǎo’sYīngwén jǔyú(1878). Its aim is to sketch the lines of the introduction of some of the key terms for grammar, within the theoretical framework of the phenomenon of grammatization of Chinese: the mutual influence from contemporary grammatical studies of Chinese and other languages will be highlighted.
A proposed radiological classification system of Hoffa’s fracture based on fracture configuration and consequent optimal treatment strategy along with the review of literature
Authors: Bagaria Vaibhav , Sharma Gaurav , Waghchoure Chaitanya , Chandak Rajendra M , Nemade Amit , Tadepelli Kalyan , Pawar Prashant 
Published: June 2019

Background: Coronal fractures of distal end femur, referred as Hoffa’s fracture are not uncommon, yet easily missed injuries lacking proper classification system and consensus for ideal treatment. While most trauma surgeons adopt different strategies based on the fracture configuration and their own experience, there are no set ways to classify these based on the most appropriate treatment strategy. Methods: Thirty cases of Hoffa fracture from tertiary care centres were studied for the fracture pattern, fragment size, comminution and possible variations to formulate a radiological classification and treatment guidelines. Additionally, a literature search was used to analyze 77 case studies based on Hoffa fracture to find out the common fracture patterns and treatment modalities adopted for varying fracture patterns in these studies. Six independent observers participated in testing the inter-observer reliability of the proposed classification. Results: A new proposed radiological classification for Hoffa fracture consists of four main types. Type 1 is with fracture fragment >2.5 cm, Type 2 with fragment <2.5 cm, Type 3 is comminuted fracture, Type 4 are subdivided as Type 4a – Anterior, Type 4b – Bicondylar, Type 4c – Osteochondral type and Type 4d – With supracondylar extension. Optimum treatment modality depends on the type of Hoffa’s fracture and has been suggested in the study. Interobserver reliability demonstrated that overall agreement was 0.907692 with a fixed marginal Kappa of 0.881067 and free Marginal Kappa at 0.892308. Intra-observer reliability test for the classification system showed a strong Kappa value of +1.0. Conclusion: The new suggested classification helps identify different types of Hoffa’s fracture. This is likely to help decide optimal surgical treatment depending on the nature of the injury. The classification system has high inter and intra-observer reliability that enables its universal applicability.
Kp forecasting with a recurrent neural network
Authors: Sexton Ernest Scott , Nykyri Katariina , Ma Xuanye 
Published: June 2019

In an effort to forecast the planetary Kp-index beyond the current 1-hour and 4-hour predictions, a recurrent neural network is trained on three decades of historical data from NASA’s Omni virtual observatory and forecasts Kp with a prediction horizon of up to 24 h. Using Matlab’s neural network toolbox, the multilayer perceptron model is trained on inputs comprised of Kp for a given time step as well as from different sets of the following six solar wind parameters, Bz, n, V, |B|, σB and $ {\sigma }_{{B}_z}$. The purpose of this study was to test which combination of the solar wind and Interplanetary Magnetic Field (IMF) parameters used for training gives the best performance as defined by correlation coefficient, C, between the predicted and actually measured Kp values and Root Mean Square Error (RMSE). The model consists of an input layer, a single nonlinear hidden layer with 28 neurons, and a linear output layer that predicts Kp up to 24 h in advance. For 24 h prediction, the network trained on Bz, n, V, |B|, σB performs the best giving C in the range from 0.8189 (for 31 predictions) to 0.8211 (for 9 months of predictions), with the smallest RMSE.
Laparoscopic Approach in Surgical Staging of Endometrial Cancer
Authors: Mouraz Mariana , Ferreira Cátia Sofia , Gonçalves Sónia , Martins Nuno Nogueira , Martins Francisco Nogueira 
Published: June 2019

Objective To compare laparoscopy with laparotomy for surgical staging of endometrial cancer.
Methods A cohort of women with preoperative diagnosis of endometrial cancer who underwent surgical staging was retrospectively evaluated. The main study end points were: morbidity and mortality, hospital length of stay, perioperative adverse events and recurrence rate. Data analysis was performed with the software SPSS v25 (IBM Corp., Armonk, NY, USA), categorical variables using a Chi-square and Fisher test, and continuous variables using the Student t-test.
Results A total of 162 patients were analyzed. One-hundred and thirty eight patients met the inclusion criteria, 41 of whom underwent staging by laparoscopy and 97 by laparotomy. Conversions from laparoscopy to laparotomy happened in 2 patients (4.9%) and were secondary to technical difficulties and poor exposure. Laparoscopy had fewer postoperative adverse events when compared with laparotomy (7.3% vs 23.7%, respectively; p = 0.005), but similar rates of intraoperative complications, despite having a significantly longer operative time (median, 175 vs 130 minutes, respectively; p < 0.001). Hospital stay was significantly lower in laparoscopy versus laparotomy patients (median, 3 vs 7 days, respectively; p < 0.001). No difference in recurrence or mortality rates were observed.
Conclusion Laparoscopic surgical staging for endometrial cancer is feasible and safe. Patients have lower postoperative complication rates and shorter hospital stays when compared with the approach by laparotomy.