bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic prediction for growth using a low-density SNP panel in dromedary camels
Authors: Bitaraf Sani Morteza , Zare Harofte Javad , Banabazi Mohammad Hossein , Esmaeilkhanian Saeid , Shafei Naderi Ali , Salim Nader , Teimoori Abbas , Bitaraf Ahmad , Zadehrahmani Mohammad , Burger Pamela Anna , Landi Vincenzo , Silawi Mohammad , Taghipour Sheshdeh Afsaneh , Faghihi Mohammad Ali 
Published: April 2021

AbstractFor thousands of years, camels have produced meat, milk, and fiber in harsh desert conditions. For a sustainable development to provide protein resources from desert areas, it is necessary to pay attention to genetic improvement in camel breeding. By using genotyping-by-sequencing (GBS) method we produced over 14,500 genome wide markers to conduct a genome- wide association study (GWAS) for investigating the birth weight, daily gain, and body weight of 96 dromedaries in the Iranian central desert. A total of 99 SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.002). Genomic breeding values (GEBVs) were estimated with the BGLR package using (i) all 14,522 SNPs and (ii) the 99 SNPs by GWAS. Twenty-eight SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.001). Annotation of the genomic region (s) within ± 100 kb of the associated SNPs facilitated prediction of 36 candidate genes. The accuracy of GEBVs was more than 0.65 based on all 14,522 SNPs, but the regression coefficients for birth weight, daily gain, and body weight were 0.39, 0.20, and 0.23, respectively. Because of low sample size, the GEBVs were predicted using the associated SNPs from GWAS. The accuracy of GEBVs based on the 99 associated SNPs was 0.62, 0.82, and 0.57 for birth weight, daily gain, and body weight. This report is the first GWAS using GBS on dromedary camels and identifies markers associated with growth traits that could help to plan breeding program to genetic improvement. Further researches using larger sample size and collaboration of the camel farmers and more profound understanding will permit verification of the associated SNPs identified in this project. The preliminary results of study show that genomic selection could be the appropriate way to genetic improvement of body weight in dromedary camels, which is challenging due to a long generation interval, seasonal reproduction, and lack of records and pedigrees.
MicroRNA treatment modulates osteogenic differentiation potential of mesenchymal stem cells derived from human chorion and placenta
Authors: Marupanthorn Kulisara , Tantrawatpan Chairat , Kheolamai Pakpoom , Tantikanlayaporn Duangrat , Manochantr Sirikul 
Published: April 2021

AbstractMesenchymal stem cells (MSCs) are important in regenerative medicine because of their potential for multi-differentiation. Bone marrow, chorion and placenta have all been suggested as potential sources for clinical application. However, the osteogenic differentiation potential of MSCs derived from chorion or placenta is not very efficient. Bone morphogenetic protein-2 (BMP-2) plays an important role in bone development. Its effect on osteogenic augmentation has been addressed in several studies. Recent studies have also shown a relationship between miRNAs and osteogenesis. We hypothesized that miRNAs targeted to Runt-related transcription factor 2 (Runx-2), a major transcription factor of osteogenesis, are responsible for regulating the differentiation of MSCs into osteoblasts. This study examines the effect of BMP-2 on the osteogenic differentiation of MSCs isolated from chorion and placenta in comparison to bone marrow-derived MSCs and investigates the role of miRNAs in the osteogenic differentiation of MSCs from these sources. MSCs were isolated from human bone marrow, chorion and placenta. The osteogenic differentiation potential after BMP-2 treatment was examined using ALP staining, ALP activity assay, and osteogenic gene expression. Candidate miRNAs were selected and their expression levels during osteoblastic differentiation were examined using real-time RT-PCR. The role of these miRNAs in osteogenesis was investigated by transfection with specific miRNA inhibitors. The level of osteogenic differentiation was monitored after anti-miRNA treatment. MSCs isolated from chorion and placenta exhibited self-renewal capacity and multi-lineage differentiation potential similar to MSCs isolated from bone marrow. BMP-2 treated MSCs showed higher ALP levels and osteogenic gene expression compared to untreated MSCs. All investigated miRNAs (miR-31, miR-106a and miR148) were consistently downregulated during the process of osteogenic differentiation. After treatment with miRNA inhibitors, ALP activity and osteogenic gene expression increased over the time of osteogenic differentiation. BMP-2 has a positive effect on osteogenic differentiation of chorion- and placenta-derived MSCs. The inhibition of specific miRNAs enhanced the osteogenic differentiation capacity of various MSCs in culture and this strategy might be used to promote bone regeneration. However, further in vivo experiments are required to assess the validity of this approach.
Assessing probabilistic modelling for wind speed from numerical weather prediction model and observation in the Arctic
Authors: Chen Hao , Birkelund Yngve , Anfinsen Stian Normann , Staupe-Delgado Reidar , Yuan Fuqing 
Published: April 2021

AbstractMapping Arctic renewable energy resources, particularly wind, is important to ensure the transition into renewable energy in this environmentally vulnerable region. The statistical characterisation of wind is critical for effectively assessing energy potential and planning wind park sites and is, therefore, an important input for wind power policymaking. In this article, different probability density functions are used to model wind speed for five wind parks in the Norwegian Arctic region. A comparison between wind speed data from numerical weather prediction models and measurements is made, and a probability analysis for the wind speed interval corresponding to the rated power, which is largely absent in the existing literature, is presented. The results of the present study suggest that no single probability function outperforms across all scenarios. However, some differences emerged from the models when applied to different wind parks. The Nakagami and Generalised extreme value distributions were chosen for the numerical weather predicted prediction and the observed wind speed modelling, respectively, due to their superiority and stability compared with other methods. This paper, therefore, provides a novel direction for understanding the numerical weather prediction wind model and shows that its speed statistical features are better captured than those of real wind.
Assessment of the conjunctival microcirculation for patients presenting with acute myocardial infarction compared to healthy controls
Authors: Brennan Paul F. , McNeil Andrew J. , Jing Min , Awuah Agnes , Moore Julie S. , Mailey Jonathan , Finlay Dewar D. , Blighe Kevin , McLaughlin James A. D. , Nesbit M. Andrew , Trucco Emanuele , Moore Tara C. B. , Spence Mark S. 
Published: April 2021

AbstractMicrocirculatory dysfunction occurs early in cardiovascular disease (CVD) development. Acute myocardial infarction (MI) is a late consequence of CVD. The conjunctival microcirculation is readily-accessible for quantitative assessment and has not previously been studied in MI patients. We compared the conjunctival microcirculation of acute MI patients and age/sex-matched healthy controls to determine if there were differences in microcirculatory parameters. We acquired images using an iPhone 6s and slit-lamp biomicroscope. Parameters measured included diameter, axial velocity, wall shear rate and blood volume flow. Results are for all vessels as they were not sub-classified into arterioles or venules. The conjunctival microcirculation was assessed in 56 controls and 59 inpatients with a presenting diagnosis of MI. Mean vessel diameter for the controls was 21.41 ± 7.57 μm compared to 22.32 ± 7.66 μm for the MI patients (p < 0.001). Axial velocity for the controls was 0.53 ± 0.15 mm/s compared to 0.49 ± 0.17 mm/s for the MI patients (p < 0.001). Wall shear rate was higher for controls than MI patients (162 ± 93 s−1 vs 145 ± 88 s−1, p < 0.001). Blood volume flow did not differ significantly for the controls and MI patients (153 ± 124 pl/s vs 154 ± 125 pl/s, p = 0.84). This pilot iPhone and slit-lamp assessment of the conjunctival microcirculation found lower axial velocity and wall shear rate in patients with acute MI. Further study is required to correlate these findings further and assess long-term outcomes in this patient group with a severe CVD phenotype.
Discovery of a low-latitude ionospheric trough associated with the inner radiation belt
Authors: Karpachev A. T. 
Published: April 2021

AbstractThe dynamics of ionospheric troughs that developed during a great geomagnetic storm on 11–13 April 2001 are studied using measurements of electron density obtained by the CHAMP satellite at an altitude of 410–465 km. Subauroral, mid-latitude and low-latitude troughs were observed at nighttime, sometimes simultaneously. The subauroral trough is usually defined as the main ionospheric trough, whereas the mid-latitude trough is associated with the magnetospheric ring current. It appeared at the beginning of the storm recovery phase around latitudes of 40°–45° GMLat (L = 1.7–2.0) and existed for a long period of time throughout the late recovery phase of the residual ring current at latitudes of 50°–55° GMLat (L ~ 2.4–3.0). For the first time, a low-latitude trough was revealed. It developed at latitudes of 34°–45° GMLat (L = 1.45–2.00) in association with the precipitation of energetic particles from the inner radiation belt.
Alteration of the gut fecal microbiome in children living with HIV on antiretroviral therapy in Yaounde, Cameroon
Authors: Abange William Baiye , Martin Casey , Nanfack Aubin Joseph , Yatchou Laeticia Grace , Nusbacher Nichole , Nguedia Clement Assob , Kamga Hortense Gonsu , Fokam Joseph , Kennedy Sean P. , Ndjolo Alexis , Lozupone Catherine , Nkenfou Celine Nguefeu 
Published: April 2021

AbstractMultiple factors, such as immune disruption, prophylactic co-trimoxazole, and antiretroviral therapy, may influence the structure and function of the gut microbiome of children infected with HIV from birth. In order to understand whether HIV infection altered gut microbiome and to relate changes in microbiome structure and function to immune status, virological response and pediatric ART regimens, we characterized the gut microbiome of 87 HIV-infected and 82 non-exposed HIV-negative children from Yaounde, a cosmopolitan city in Cameroon. We found that children living with HIV had significantly lower alpha diversity in their gut microbiome and altered beta diversity that may not be related to CD4+ T cell count or viral load. There was an increased level ofAkkermansiaandFaecalibacteriumgenera and decreased level ofEscherichiaand otherGamma proteobacteriain children infected with HIV, among other differences. We noted an effect of ethnicity/geography on observed gut microbiome composition and that children on ritonavir-boosted protease inhibitor (PI/r)-based ART had gut microbiome composition that diverged more from HIV-negative controls compared to those on non-nucleoside reverse-transcriptase inhibitors-based ART. Further studies investigating the role of this altered gut microbiome in increased disease susceptibility are warranted for individuals who acquired HIV via mother-to-child transmission.
Time-of-flight secondary ion mass spectrometry fragment regularity in gallium-doped zinc oxide thin films
Authors: Saw K. G. , Esa S. R. 
Published: April 2021

AbstractTime-of-flight secondary ion mass spectrometry fragment analysis remains a challenging task. The fragment appearance regularity (FAR) rule is particularly useful for two-element compounds such as ZnO. Ion fragments appearing in the form of ZnxOy obey the rule $$2x \ge 2y + 1$$

2
x
≥
2
y
+
1

in the positive secondary ion spectrum and $$2x \le 2y + 1$$

2
x
≤
2
y
+
1

in the negative spectrum where the valence of Zn is + 2 and that of O is − 2. Fragment analysis in gallium-doped ZnO (GZO) films can give insights into the bonding of the elements in this important semiconductor. Fragment analysis of 1 and 7 wt% GZO films shows that only the negative ion fragments obey the FAR rule where ZnO‒, 66ZnO‒, 68ZnO‒ and ZnO2‒ ion fragments appear. In the positive polarity, subdued peaks from out-of-the-rule ZnO+, 66ZnO+ and 68ZnO+ ion fragments are observed. The Ga ion peaks are present in both the positive and negative spectra. The secondary ion spectra of undoped ZnO also shows consistency with the FAR rule. This implies that Ga doping even in amounts that exceed the ZnO lattice limit of solubility does not affect the compliance with the FAR rule.
En face image-based classification of diabetic macular edema using swept source optical coherence tomography
Authors: Fujiwara Atsushi , Kanzaki Yuki , Kimura Shuhei , Hosokawa Mio , Shiode Yusuke , Doi Shinichiro , Takahashi Kosuke , Matoba Ryo , Morizane Yuki 
Published: April 2021

AbstractThis retrospective study was performed to classify diabetic macular edema (DME) based on the localization and area of the fluid and to investigate the relationship of the classification with visual acuity (VA). The fluid was visualized using en face optical coherence tomography (OCT) images constructed using swept-source OCT. A total of 128 eyes with DME were included. The retina was segmented into: Segment 1, mainly comprising the inner nuclear layer and outer plexiform layer, including Henle’s fiber layer; and Segment 2, mainly comprising the outer nuclear layer. DME was classified as: foveal cystoid space at Segment 1 and no fluid at Segment 2 (n = 24), parafoveal cystoid space at Segment 1 and no fluid at Segment 2 (n = 25), parafoveal cystoid space at Segment 1 and diffuse fluid at Segment 2 (n = 16), diffuse fluid at both segments (n = 37), and diffuse fluid at both segments with subretinal fluid (n = 26). Eyes with diffuse fluid at Segment 2 showed significantly poorer VA, higher ellipsoid zone disruption rates, and greater central subfield thickness than did those without fluid at Segment 2 (P < 0.001 for all). These results indicate the importance of the localization and area of the fluid for VA in DME.
Simple method for detecting idiopathic interstitial pneumonias by measuring vertical lung length on chest X-ray
Authors: Karayama Masato , Aoshima Yoichiro , Yasui Hideki , Hozumi Hironao , Suzuki Yuzo , Furuhashi Kazuki , Fujisawa Tomoyuki , Enomoto Noriyuki , Nakamura Yutaro , Inui Naoki , Suda Takafumi 
Published: April 2021

AbstractDetection of idiopathic interstitial pneumonias (IIPs) on chest X-ray is difficult for non-specialist physicians, especially in patients with mild IIPs. The current study aimed to evaluate the usefulness of a simple method for detecting IIPs by measuring vertical lung length (VLL) in chest X-rays to quantify decreased lung volume. A total of 280 consecutive patients with IIPs were randomly allocated to exploratory and validation cohorts, and 140 controls were selected for each cohort by propensity score-matching. Upper (uVLL; from apex to tracheal carina), lower (lVLL; from carina to costophrenic angle), and total VLL (tVLL; from apex to costophrenic angle), and the l/uVLL ratio were measured on chest X-rays. Patients in the exploratory cohort had significantly decreased uVLL, lVLL, tVLL, and l/uVLL ratio compared with controls (all p < 0.001). Receiver operating characteristic curve analyses demonstrated that lVLL (area under the curve [AUC] 0.86, sensitivity 0.65, specificity 0.92), tVLL (AUC 0.83, sensitivity 0.75, specificity 0.80), and l/uVLL ratio (AUC 0.80, sensitivity 0.72, specificity 0.79) had high diagnostic accuracies for IIPs. These results were reproduced in the validation cohort. IIP patients thus have decreased VLLs, and measurements of VLL may thus aid the accurate detection of IIPs.
Predicting regional coastal sea level changes with machine learning
Authors: Nieves Veronica , Radin Cristina , Camps-Valls Gustau 
Published: April 2021

AbstractAll ocean basins have been experiencing significant warming and rising sea levels in recent decades. There are, however, important regional differences, resulting from distinct processes at different timescales (temperature-driven changes being a major contributor on multi-year timescales). In view of this complexity, it deems essential to move towards more sophisticated data-driven techniques as well as diagnostic and prognostic prediction models to interpret observations of ocean warming and sea level variations at local or regional sea basins. In this context, we present a machine learning approach that exploits key ocean temperature estimates (as proxies for the regional thermosteric sea level component) to model coastal sea level variability and associated uncertainty across a range of timescales (from months to several years). Our findings also demonstrate the utility of machine learning to estimate the possible tendency of near-future regional sea levels. When compared to actual sea-level records, our models perform particularly well in the coastal areas most influenced by internal climate variability. Yet, the models are widely applicable to evaluate the patterns of rising and falling sea levels across many places around the globe. Thus, our approach is a promising tool to model and anticipate sea level changes in the coming (1–3) years, which is crucial for near-term decision making and strategic planning about coastal protection measures.
Association analysis of miRNA-related genetic polymorphisms in miR-143/145 and KRAS with colorectal cancer susceptibility and survival
Authors: Wang Danyang , Liu Qingmin , Ren Yanjun , Zhang Yan , Wang Xin , Liu Bing 
Published: April 2021

Abstract
Background: There is accumulating evidence of aberrant expression of miR-143 and miR-145 and their target gene KRAS in colorectal cancer (CRC). We hypothesize that single nucleotide polymorphisms (SNPs) within or near mRNA–microRNA (miRNA) binding sites may affect miRNA/target gene interaction, resulting in differential mRNA/protein expression and promoting the development and progression of CRC. Methods: We conducted a case–control study of 507 patients with CRC recruited from a tertiary hospital and 497 population-based controls to assess the association of genetic polymorphisms in miR-143/145 and the KRAS 3′ untranslated region (3′UTR) with susceptibility to CRC and patients’ survival. In addition, genetic variations of genomic regions located from 500 bp upstream to 500 bp downstream of the miR-143/miR-145 gene and the 3′UTR of KRAS were selected for analysis using the Haploview and HaploReg software. Results: Using publicly available expression profiling data, we found that miR-143/145 and KRAS expression were all reduced in rectal cancer tissue compared with adjacent non-neoplastic large intestinal mucosa. The rs74693964 C/T variant located 65 bp downstream of miR-145 genomic regions was observed to be associated with susceptibility to CRC (adjusted odds ratio (OR): 2.414, 95% CI: 1.385–4.206). Cumulative effects of miR-143 and miR-145 on CRC risk were observed (Ptrend=0.03). Patients having CRC carrying variant genotype TT of KRAS rs712 had poorer survival (log-rank P=0.044, adjusted hazard ratio (HR): 4.328, 95% CI: 1.236–15.147). Conclusions: Our results indicate that miRNA-related polymorphisms in miR-143/145 and KRAS are likely to be deleterious and represent potential biomarkers for susceptibility to CRC and patients’ survival.
The Effect of Practice on Variability in Childhood Apraxia of Speech: A Multidimensional Analysis
Authors: Case Julie , Grigos Maria I. 
Published: April 2021

Purpose
Variability has been interpreted in differing ways according to context (e.g., development, speech impairment, and learning). A challenge arises when interpreting variability in the context of learning for children with speech impairment characterized by high movement variability, as in childhood apraxia of speech (CAS). The objective of this study is to investigate changes in variability in CAS with practice in comparison to patterns seen in children with non-CAS speech sound disorders (SSD) and typical development.

Method
Speech production variability was examined in 24 children (5–6 years of age) with CAS, non—CAS SSD, and typical development in production of nonwords of varied motoric complexity. Multidimensional analyses were performed using measures of token-to-token speech consistency (percent word consistency), acoustic variability (acoustic spatiotemporal index), and movement variability (lip aperture spatiotemporal index). Changes in variability were examined in each group of children by comparing the first half to the last half of nonword tokens in the same data collection session. The impact of token complexity on practice effects was also explored across groups of children.

Results

All children displayed increased speech consistency within this practice period (
p =
.01). Only children with CAS displayed increased movement variability following practice (
p =
.01). Differences in acoustic and kinematic variability were observed across complexity levels in all groups, though these did not interact with practice effects.

Discussion
These findings suggest that increased movement variability in children with CAS might be facilitating perceptual consistency. It is believed that this finding reflects an inefficient strategy adapted by children with CAS in the absence of motor-based cueing and feedback to guide speech performance with practice.
Curriculum Vocabulary Learning of Fourth Graders Using the Vocabulary Scenario Technique
Authors: Spielvogel Joanna H. , Ehren Barbara J. 
Published: April 2021

Purpose
The purpose of this study was to determine if a direct, explicit method of teaching vocabulary with the Vocabulary Scenario Technique – General Education 16 Encounter (VSTGE16) protocol would yield gains in the vocabulary knowledge of fourth grade students in a general education classroom. Two research questions examined whether fourth grade students receiving VST-GE16 instruction with 16 instructor-led encounters per word, eight words taught per week for 90 min a week over 4 weeks demonstrated greater gains on a multiple-choice synonym test and a fill-in-the-blank words-in-context test than fourth grade students taught the same number of words, in the same time frame, using a vocabulary teaching method typically employed by a fourth grade teacher.

Method

The study was a quasi-experimental design, with a pretest and posttest multiple-choice synonym and fill-in-the-blank words-in-context measures administered. Students with complete data sets were included in the analyses (synonym,
N
= 38; words-in-context,
N
= 37). Participants in both groups were taught eight curriculum vocabulary words per week for 90 min a week across four consecutive weeks (32 words).

Results

An analysis of covariance on posttreatment outcomes yielded the following: The treatment group scored significantly higher on the synonym measure,
F
(1, 35) = 14.76,
p
< .001;
g =
1.04, and the words-in-context measure,
F
(1, 34) = 43.66,
p
< .001;
g
= 1.59, than did the comparison group.

Conclusions

The results indicated that the VST-GE16 protocol has potential as an effective, efficient method to use when directly teaching curriculum vocabulary words to fourth grade students in general education classrooms
.