bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maize Golden2-like transcription factors boost rice chloroplast
development, photosynthesis, and grain yield
Authors: Yeh Su-Ying , Lin Hsin-Hung , Chang Yao-Ming , Chang Yu-Lun , Chang Chao-Kang , Huang Yi-Cin , Ho Yi-Wen , Lin Chu-Yin , Zheng Jun-Ze , Jane Wann-Neng , Ng Chun-Yeung , Lu Mei-Yeh , Lai I-Ling , To Kin-Ying , Li Wen-Hsiung , Ku Maurice S B 
Published: November 2021

Abstract
Chloroplasts are the sites for photosynthesis, and two Golden2-like factors act as transcriptional activators of chloroplast development in rice (Oryza sativa L.) and maize (Zea mays L.). Rice OsGLK1 and OsGLK2 are orthologous to maize ZmGLK1 (ZmG1) and ZmGLK2 (ZmG2), respectively. However, while rice OsGLK1 and OsGLK2 act redundantly to regulate chloroplast development in mesophyll cells, maize ZmG1 and ZmG2 are functionally specialized and expressed in different cell-specific manners. To boost rice chloroplast development and photosynthesis, we generated transgenic rice plants overexpressing ZmG1 and ZmG2, individually or simultaneously, with constitutive promoters (pZmUbi::ZmG1 and p35S::ZmG2) or maize promoters (pZmG1::ZmG1, pZmG2::ZmG2, and pZmG1::ZmG1/pZmG2::ZmG2). Both ZmG1 and ZmG2 genes were highly expressed in transgenic rice leaves. Moreover, ZmG1 and ZmG2 showed coordinated expression in pZmG1::ZmG1/pZmG2::ZmG2 plants. All Golden2-like (GLK) transgenic plants had higher chlorophyll and protein contents, Rubisco activities and photosynthetic rates per unit leaf area in flag leaves. However, the highest grain yields occurred when maize promoters were used; pZmG1::ZmG1, pZmG2::ZmG2, and pZmG1::ZmG1/pZmG2::ZmG2 transgenic plants showed increases in grain yield by 51%, 47%, and 70%, respectively. In contrast, the pZmUbi::ZmG1 plant produced smaller seeds without yield increases. Transcriptome analysis indicated that maize GLKs act as master regulators promoting the expression of both photosynthesis-related and stress-responsive regulatory genes in both rice shoot and root. Thus, by promoting these important functions under the control of their own promoters, maize GLK1 and GLK2 genes together dramatically improved rice photosynthetic performance and productivity. A similar approach can potentially improve the productivity of many other crops.
How to Catch a Falsifier
Authors: Schwanhäuser Silvia , Sakshaug Joseph W , Kosyakova Yuliya 
Published: November 2021

Abstract
Deviant interviewer behavior is a potential hazard of interviewer-administered surveys, with interviewers fabricating entire interviews as the most severe form. Various statistical methods (e.g., cluster analysis) have been proposed to detect falsifiers. These methods often rely on falsification indicators aiming to measure differences between real and falsified data. However, due to a lack of real-world data, empirical evaluations and comparisons of different statistical methods and falsification indicators are scarce. Using a large-scale nationally representative refugee survey in Germany with known fraudulent interviews, this study tests, evaluates, and compares statistical methods for identifying falsified data. We investigate the use of new and existing falsification indicators as well as multivariate detection methods for combining them. Additionally, we introduce a new and easy-to-use multivariate detection method that overcomes practical limitations of previous methods. We find that the vast majority of used falsification indicators successfully measure differences between falsifiers and nonfalsifiers, with the newly proposed falsification indicators outperforming some existing indicators. Furthermore, different multivariate detection methods perform similarly well in detecting the falsifiers.
Degrees of Acceptance
Authors: Dinges Alexander 
Published: November 2021

Abstract
While many authors distinguish belief from acceptance, it seems almost universally agreed that no similar distinction can be drawn between degrees of belief, or credences, and degrees of acceptance. I challenge this assumption in this paper. Acceptance comes in degrees and acknowledging this helps to resolve problems in at least two philosophical domains. Degrees of acceptance play vital roles when we simplify our reasoning, and they ground the common ground of a conversation if we assume context probabilism, i.e., that the common ground must be represented with probability spaces rather than possible worlds.
Assessing predictors of rheumatoid arthritis-associated interstitial lung disease using quantitative lung densitometry
Authors: Alevizos Michail K , Danoff Sonye K , Pappas Dimitrios A , Lederer David J , Johnson Cheilonda , Hoffman Eric A , Bernstein Elana J , Bathon Joan M , Giles Jon T 
Published: November 2021

Abstract

Objective
To assess predictors of subclinical RA-associated interstitial lung disease (RA-ILD) using quantitative lung densitometry (qLD).

Methods
RA patients underwent multi-detector row CT scanning at baseline and after an average of 39 months. Scans were analysed with qLD for the percentage of lung parenchyma with high attenuation areas (%HAA: the percentage of voxels of –600 to –250 Hounsfield units). Additionally, a pulmonary radiologist calculated an expert radiologist scoring (ERS) for RA-ILD features. Generalized linear models were used to identify indicators of baseline %HAA and predictors of %HAA change.

Results
Baseline %HAA was assessed in 193 RA patients and 106 had repeat qLD assessment. %HAA was correlated with ERS (Spearman’s rho = 0.261; P &lt; 0.001). Significant indicators of high baseline %HAA (&gt;10% of lung parenchyma with high attenuation) included female sex, higher pack-years of smoking, higher BMI and anti-CCP ≥200 units, collectively contributing an area under the receiver operator curve of 0.88 (95% CI 0.81, 0.95). Predictors of %HAA increase, occurring in 49% with repeat qLD, included higher baseline %HAA, presence of mucin 5B (MUC5B) minor allele and absence of HLA-DRB1 shared epitope (area under the receiver operator curve = 0.69; 95% CI 0.58, 0.79). The association of the MUC5B minor allele with %HAA change was higher among men and those with higher cumulative smoking. Within the group with increased %HAA, anti-CCP level was significantly associated with a greater increase in %HAA.

Conclusions
%HAA, assessed with qLD, was linked to several known risk factors for RA-ILD and may represent a more quantitative method to identify RA-ILD and track progression than expert radiologist interpretation.
Continuous positive airway pressure and adverse cardiovascular events in obstructive sleep apnea: are participants of randomized trials representative of sleep clinic patients?
Authors: Reynor Ayesha , McArdle Nigel , Shenoy Bindiya , Dhaliwal Satvinder S , Rea Siobhan C , Walsh Jennifer , Eastwood Peter R , Maddison Kathleen , Hillman David R , Ling Ivan , Keenan Brendan T , Maislin Greg , Magalang Ulysses , Pack Allan I , Mazzotti Diego R , Lee Chi-Hang , Singh Bhajan 
Published: November 2021

Abstract

Study Objectives
Randomized controlled trials (RCTs) have shown no reduction in adverse cardiovascular (CV) events in patients randomized to continuous positive airway pressure (CPAP) therapy for obstructive sleep apnea (OSA). This study examined whether randomized study populations were representative of OSA patients attending a sleep clinic.

Methods
Sleep clinic patients were 3,965 consecutive adults diagnosed with OSA by in-laboratory polysomnography from 2006 to 2010 at a tertiary hospital sleep clinic. Characteristics of these patients were compared with participants of five recent RCTs examining the effect of CPAP on adverse CV events in OSA. The percentage of patients with severe (apnea-hypopnea index, [AHI] ≥ 30 events/h) or any OSA (AHI ≥ 5 events/h) who met the eligibility criteria of each RCT was determined, and those criteria that excluded the most patients identified.

Results
Compared to RCT participants, sleep clinic OSA patients were younger, sleepier, more likely to be female and less likely to have established CV disease. The percentage of patients with severe or any OSA who met the RCT eligibility criteria ranged from 1.2% to 20.9% and 0.8% to 21.9%, respectively. The eligibility criteria that excluded most patients were preexisting CV disease, symptoms of excessive sleepiness, nocturnal hypoxemia and co-morbidities.

Conclusions
A minority of sleep clinic patients diagnosed with OSA meet the eligibility criteria of RCTs of CPAP on adverse CV events in OSA. OSA populations in these RCTs differ considerably from typical sleep clinic OSA patients. This suggests that the findings of such OSA treatment-related RCTs are not generalizable to sleep clinic OSA patients.
Randomized Intervention with Continuous Positive Airway Pressure in CAD and OSA (RICCADSA) trial, https://clinicaltrials.gov/ct2/show/NCT00519597, ClinicalTrials.gov number, NCT00519597.
Usefulness of Nasal Continuous Positive Airway Pressure (CPAP) Treatment in Patients with a First Ever Stroke and Sleep Apnea Syndrome, https://clinicaltrials.gov/ct2/show/NCT00202501, ClinicalTrials.gov number, NCT00202501.
Effect of Continuous Positive Airway Pressure (CPAP) on Hypertension and Cardiovascular Morbidity-Mortality in Patients with Sleep Apnea and no Daytime Sleepiness, https://clinicaltrials.gov/ct2/show/NCT00127348, ClinicalTrials.gov number, NCT00127348.
Continuous Positive Airway Pressure (CPAP) in Patients with Acute Coronary Syndrome and Obstructive Sleep Apnea (OSA) (ISAACC), https://clinicaltrials.gov/ct2/show/NCT01335087, ClinicalTrials.gov number, NCT01335087.
Investigating a potential format effect with two-column proofs
Authors: Alarfaj Maryam , Sangwin Chris 
Published: November 2021

Abstract
The current study aims to explore the impact of the two-column format in writing simple mathematical arguments. That is to say, a structured method of presenting a mathematical proof or argument by using a tabular layout with two columns. The underlying goal of the research reported in this paper is to inform understanding of how to effectively assess students’ proof construction, particularly online. In this paper, we report the results of an experiment designed to test the hypothesis that students provide more justifications when using the two-column format in writing mathematical proofs. The participants were 80 first year undergraduate mathematics students at the University of Edinburgh who were enrolled in a calculus course. The findings supported this hypothesis: overall frequency of justification were higher in the two-column condition compared with the traditional condition. This is due to the format structure where students are expected to justify each line in the statements’ column with a corresponding explanation in the justification column. However, as a side effect of increasing the amount of justifications, students in the two-column group generated more non-explanation statements which we classed as paraphrasing. A secondary outcome was our use and further development of the coding scheme.
Impact of COVID-19 Infection on Neonatal Birth Outcomes
Authors: Vizheh Maryam , Allahdadian Maryam , Muhidin Salut , Valiani Mahboubeh , Bagheri Khadijeh , Borandegi Forogh , Ghasimi Golnaz 
Published: November 2021

Abstract

Introduction
There is limited data on newborns born to mothers with COVID-19 infection. This multicenter cohort study aimed to investigate the clinical characteristics and outcomes of neonates born to mothers with and without COVID-19 infection to fill a gap in the literature review.

Methods
The medical records of all neonates in Isfahan, Iran, between October 2020 and March 2021, were retrospectively reviewed.

Results
Among the 600 neonates in this study, 255 (42.5%) were in the infected group and 345 (57.5%) were assigned to the control group as they were born to non-infected mothers. In the infected group, sepsis, fever and pneumothorax were detected in 3 (1.2%), 3 (1.2%) and 4 (1.6%) neonates, respectively, compared with no case in the control group. In the infected group, neonatal respiratory distress (NRDS) (32, 12.5%) was significantly higher than the control group (27, 10.6%). Asphyxia in the infected group was 22(6.4%), compared with 19 (5.5%), in the control group. Preterm labor (PTL) (55, 21.65%), premature rupture of membranes (PROMs) (24, 9.4%) and intra-uterine growth retardation (IUGR) (15, 5.9%) were significantly higher in women with COVID-19 (45, 13.0%, 4, 1.2% and 7, 2.0%, respectively). Low birth weight (LBW) accounted for 42 (16.5%) neonates in the infected group and 25 (7.2%) in the control group (p &lt; 0.05). Of the 255 neonates born to infected mothers, 38 (14.9%) were admitted to the Neonatal Intensive Care Unit (NICU), compared with 31 out of 345 (9.0%) in the control group (p &lt; 0.05). RT-PCR test results were positive in two newborns (0.8%), one of whom died of necrotizing enterocolitis.

Conclusion
As a result of maternal COVID-19 infections, neonates experienced higher rates of sepsis, fever, pneumothorax, asphyxia and NRDS in addition to PTL, PROMs, IUGR, and LBW.
CoVizu: Rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes
Authors: Ferreira Roux-Cil , Wong Emmanuel , Gugan Gopi , Wade Kaitlyn , Liu Molly , Baena Laura Muñoz , Chato Connor , Lu Bonnie , Olabode Abayomi S , Poon Art F Y 
Published: November 2021

Abstract
Phylogenetics has played a pivotal role in the genomic epidemiology of severe acute respiratory syndrome coronavirus 2, such as tracking the emergence and global spread of variants and scientific communication. However, the rapid accumulation of genomic data from around the world—with over two million genomes currently available in the Global Initiative on Sharing All Influenza Data database—is testing the limits of standard phylogenetic methods. Here, we describe a new approach to rapidly analyze and visualize large numbers of SARS-CoV-2 genomes. Using Python, genomes are filtered for problematic sites, incomplete coverage, and excessive divergence from a strict molecular clock. All differences from the reference genome, including indels, are extracted using minimap2 and compactly stored as a set of features for each genome. For each Pango lineage (https://cov-lineages.org), we collapse genomes with identical features into ‘variants’, generate 100 bootstrap samples of the feature set union to generate weights, and compute the symmetric differences between the weighted feature sets for every pair of variants. The resulting distance matrices are used to generate neighbor-joining trees in RapidNJ that are converted into a majority-rule consensus tree for each lineage. Branches with support values below 50 per cent or mean lengths below 0.5 differences are collapsed, and tip labels on affected branches are mapped to internal nodes as directly sampled ancestral variants. Currently, we process about 2 million genomes in approximately 9 h on 52 cores. The resulting trees are visualized using the JavaScript framework D3.js as ‘beadplots’, in which variants are represented by horizontal line segments, annotated with beads representing samples by collection date. Variants are linked by vertical edges to represent branches in the consensus tree. These visualizations are published at https://filogeneti.ca/CoVizu. All source code was released under an MIT license at https://github.com/PoonLab/covizu.
The story of a rock-star: multilocus phylogeny and species delimitation in the starred or roughtail rock agama,Laudakia stellio(Reptilia: Agamidae)
Authors: Karameta Emmanouela , Lymberakis Petros , Grillitsch Heinz , Ilgaz Çetin , Avci Aziz , Kumlutaş Yusuf , Candan Kamil , Wagner Philipp , Sfenthourakis Spyros , Pafilis Panayiotis , Poulakakis Nikos 
Published: November 2021

AbstractSituated at the junction of three continents, Europe, Asia and Africa, the Eastern Mediterranean is an ideal region to study the effects of palaeogeography, ecology and long human presence on animal evolution. Laudakia stellio (Squamata: Agamidae) is found across this region and offers an excellent opportunity for such studies. The high morphological variation across their range suggests that these lizards might represent a species complex. This is the first study exploring their evolutionary history, using molecular markers and individuals from all described subspecies. We employed the latest phylogenetic and species-delimitation methods to identify all distinct evolutionary lineages, their genetic variation and divergence times. The phenotypical diversity of L. stellio matches its genetic differentiation: almost all subspecies correspond to well-supported retrieved subclades and additional distinct lineages representing intermediate morphs have been retrieved. ‘Laudakia stellio’ represents three distinct evolutionary entities that diverged during the Plio-Pleistocene transition, which we propose as distinct species. One includes Greek and Turkish populations, as well as cryptic Anatolian lineages. The second comprises all other Near East populations and the third is endemic to Cyprus. Our results indicate a role of humans in shaping present distribution patterns, and highlight the importance of the Aegean, Anatolia and the Levant as glacial refugia and diversity hotspots.
An Analysis of the Evidence Underpinning the American Academy Orthopaedic Surgery Pediatrics Clinical Practice Guidelines
Authors: Batioja Kelsi L.E. , Nguyen Tiffany , Anderson J. Michael , Detweiler Byron , Checketts Jake , Torgerson Trevor , Hartwell Micah , Vassar Matt 
Published: November 2021

Background:
Randomized control trials (RCTs) serve as evidentiary support for recommendations underpinning clinical practice guidelines (CPGs) with the goal of optimizing patient care. A knowledge gap exists within scientific literature when evaluating the quality of RCTs used as evidence in the American Academy of Orthopaedic Surgery (AAOS) pediatric CPGs. We aim to evaluate the reporting quality and risk of bias in RCTs underlying AAOS Pediatric CPG recommendations.

Methods:
We located all AAOS Pediatric CPGs. We then extracted all RCTs from the CPG reference sections. All included RCTs were evaluated using the Consolidated Standards of Reporting Trials (CONSORT) checklist and Cochrane Collaboration risk of bias assessment tool (RoB 2.0). Descriptive statistics were recorded, and bivariate analysis was used to account for variance in CONSORT scores. A Mann-Whitney U test was completed to compare CONSORT studies published before and after 2010.

Results:
Three CPGs and 23 RCTs met inclusion criteria. Mean CONSORT adherence was 69.8% (21.6/31). The lowest adhered to CONSORT items were 10, 23, and 24, while items 2a, 13a, and 18 displayed the highest adherence. Ten RCTs (43.5%, 10/23) had “low” risk of bias, 5 RCTs (21.7%, 5/23) were of “some concerns,” and 8 RCTs (34.8%, 8/23) received a “high” designation for risk of bias. There were no statistically significant associations in the bivariate regression analysis or Mann-Whitney U test.

Conclusions:
Our results suggest that CONSORT adherence within RCTs used as evidence in AAOS Pediatric CPGs is substandard—relying on evidence that, in some cases, is >20 years old. Many of the RCTs cited as supporting evidence have a “high” risk of bias. Altogether, these CPGs may need to be updated or expanded to include more recent evidence relevant to pediatric orthopaedic surgery.
Identification of Aggravation-Predicting Gene Polymorphisms in Coronavirus Disease 2019 Patients Using a Candidate Gene Approach Associated With Multiple Phase Pathogenesis: A Study in a Japanese City of 1 Million People
Authors: Tanimine Naoki , Takei Daisuke , Tsukiyama Naohumi , Yoshinaka Hisaaki , Takemoto Yuki , Tanaka Yuka , Kobayashi Tsuyoshi , Tanabe Kazuaki , Ishikawa Nobuhisa , Kitahara Yoshihiro , Okimoto Mafumi , Shime Nobuaki , Ohge Hiroki , Sugiyama Aya , Akita Tomoyuki , Tanaka Junko , Ohdan Hideki 
Published: November 2021

IMPORTANCE:
The pathology caused by the coronavirus disease 2019 is mediated by host-mediated lung inflammation, driving severity, and mortality. Polymorphisms in genes encoding host inflammation and immune-related molecules may be associated with the development of serious pathologies, and identifying such gene polymorphisms may lead to the identification of therapeutic targets.

OBJECTIVES:
We attempted to identify aggravation-predicting gene polymorphisms.

DESIGN:
We use a candidate gene approach associated with multiple phase pathogenesis in coronavirus disease 2019 patients among a cohort in Hiroshima, a city with a population of 1 million, in Japan. DNA samples from the study populations were genotyped for 34 functional polymorphisms from 14 distinct candidate genes, which encode proteins related to viral cell entry, regulation of viral replication, innate immune modulators, regulatory cytokines, and effector cytokines.

SETTING AND PARTICIPANTS:
Three core hospitals providing different services for patients with coronavirus disease 2019 under administrative control. A total of 230 patients with coronavirus disease 2019 were recruited from March 1, 2020, to March 31, 2021.

MAIN RESULTS AND MEASUREMENTS:
Among the 14 genes, we found rs1131454 in OAS1 and rs1143627 in IL1B genes as independent genetic factors associated with disease severity (adjusted odds ratio = 7.1 and 4.6 in the dominant model, respectively). Furthermore, we investigated the effect of multiple phase pathogenesis of coronavirus disease 2019 with unbiased multifactor dimensionality reduction analysis and identified a four-gene model with rs1131454 (OAS1), rs1143627 (IL1B), rs2074192 (ACE2), and rs11003125 (MBL). By combining these polygenetic factors with polyclinical factors, including age, sex, higher body mass index, and the presence of diabetes and hypertension, we proposed a composite risk model with a high area under the curve, sensitivity, and probability (0.917, 96.4%, and 74.3%, respectively) in the receiver operating characteristic curve analysis.

CONCLUSIONS AND RELEVANCE:
We successfully identified significant genetic factors in OAS1 and IL1B genes using a candidate gene approach study as valuable information for further mechanistic investigation and predictive model building.